Effects of early feeding on the host rumen transcriptome and bacterial diversity in lambs

Periparturient Mineral Metabolism: Implications to Health and Productivity

Mineral metabolism, in particular Ca, and to a lesser extent phosphorus (P) and magnesium (Mg), is altered with the onset of lactation because of extensive irreversible loss to synthesize colostrum and milk. The transient reduction in the concentration of Ca in blood, particularly when it lasts days, increases the risk of mineral-related disorders such as hypocalcemia and, to a lesser extent, hypophosphatemia. Although the incidence of clinical hypocalcemia can be reduced by prepartum dietary interventions, subclinical hypocalcemia remains prevalent, affecting up to 60% of the dairy cows in the first 3 d postpartum. More importantly, strong associations exist between hypocalcemia and increased susceptibility to other peripartum diseases and impaired reproductive performance. Mechanistic experiments have demonstrated the role of Ca on innate immune response in dairy cows, which presumably predisposes them to other diseases. Hypocalcemia is not related to inadequate Ca intake as prepartum diets marginal to deficient in Ca reduce the risk of the disease. Therefore, the understanding of how Ca homeostasis is regulated, in particular how calciotropic hormones such as parathyroid hormone and 1,25-dihydroxyvitamin D3, affect blood Ca concentrations, gastrointestinal Ca absorption, bone remodeling, and renal excretion of Ca become critical to develop novel strategies to prevent mineral imbalances either by nutritional or pharmacological interventions. A common method to reduce the risk of hypocalcemia is the manipulation of the prepartum dietary cation-anion difference. Feeding acidogenic diets not only improves Ca homeostasis and reduces hypocalcemia, but also reduces the risk of uterine diseases and improves productive performance. Feeding diets that induce a negative Ca balance in the last weeks of gestation also reduce the risk of clinical hypocalcemia, and recent work shows that the incorporation of mineral sequestering agents, presumably by reducing the absorption of P and Ca prepartum, increases blood Ca at calving, although benefits to production and health remain to be shown. Alternative strategies to minimize subclinical hypocalcemia with the use of vitamin D metabolites either fed prepartum or as a pharmacological agent administered immediately after calving have shown promising results in reducing hypocalcemia and altering immune cell function, which might prove efficacious to prevent diseases in early lactation. This review summarizes the current understanding of Ca homeostasis around parturition, the limited knowledge of the exact mechanisms for gastrointestinal Ca absorption in bovine, the implications of hypocalcemia on the health of dairy cows, and discusses the methods to minimize the risk of hypocalcemia and their impacts on productive performance and health in dairy cows.

Effects of Bacillus subtilis on in vitro ruminal fermentation and methane production

The objective of this study was to evaluate the effect of a proprietary strain of a Bacillus subtilis on in vitro ruminal fermentation and methane production in batch culture serum bottles. One hundred forty-nine batch culture bottles were used in a complete randomized block design. The arrangement of treatments was a 3 × 3 × 4 factorial to evaluate the effects of inoculum, time, diet, and their respective interactions. There were three experimental runs total, where the run was used as block. Inoculum treatments were 1.85 mg/mL of microcrystalline cellulose (CON); 10 billion B. subtilis plus microcrystalline cellulose (A1); and 60 billion B. subtilis plus microcrystalline cellulose (A2). Diet treatments were 0.50 g of early lactation diet (E, 30% starch), mid-lactation diet (M, 25% starch), or dry cow diet (D, 18% starch). The combination resulted in total of nine treatments. Each treatment had five replicates, two of which were used to determine nutrient degradability at 24 and 48 h after inoculation, and three were used to determine pH, ammonia nitrogen (NH3-N), volatile fatty acids, lactate, total gas, and methane production at 3, 6, 24, and 48 h after inoculation. Fixed effects of inoculum, diet, and their interaction were tested using the GLIMMIX procedure of SAS. Significance was declared at P ≤ 0.05. We observed that, compared to control, the supplementation of B. subtilis, decreased the production of acetate and propionate, while increasing the production of butyrate, iso-butyrate, valerate, iso-valerate, and caproate within each respective diet. Additionally, the total methane production exhibited mixed responses depending on the diet type. Overall, the inclusion of B. subtilis under in vitro conditions shows the potential to reduce ruminal methane production when supplemented with a mid-lactation diet, constituting a possible methane mitigation additive for dairy cattle diets.

Breastfeeding is associated with enhanced intestinal gluconeogenesis in infants

BACKGROUND

Breastfeeding (BF) confers metabolic benefits to infants, including reducing risks of metabolic syndrome such as obesity and diabetes later in life. However, the underlying mechanism is not yet fully understood. Hence, we aim to investigate the impacts of BF on the metabolic organs of infants.

METHODS

Previous literatures directly studying the influences of BF on offspring's metabolic organs in both animal models and humans were comprehensively reviewed. A microarray dataset of intestinal gene expression comparing infants fed on breastmilk versus formula milk was analyzed.

RESULTS

Reanalysis of microarray data showed that BF is associated with enhanced intestinal gluconeogenesis in infants. This resembles observations in other mammalian species showing that BF was also linked to increased gluconeogenesis.

CONCLUSIONS

BF is associated with enhanced intestinal gluconeogenesis in infants, which may underpin its metabolic advantages through finetuning metabolic homeostasis. This observation seems to be conserved across species, hinting its biological significance.

Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review

Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.

The impact of lactating Hu sheep's dietary protein levels on lactation performance, progeny growth and rumen development

This study aimed to investigate whether lactating Hu sheep's dietary protein levels could generate dynamic effects on the performance of their offspring. Twelve ewes with similar parity were fed iso-energy diets which contained different protein levels (P1: 9.82%, P2: 10.99%) (n = 6), and the corresponding offspring were divided into SP1 and SP2 (n = 12). At 60 days, half of the lambs were harvested for further study: the carcass weight (p = 0.043) and dressing percentage (p = 0.004) in the SP2 group were significantly higher than SP1. The acetic acid (p = 0.007), propionic acid (p = 0.003), butyric acid (p < 0.001) and volatile fatty acids (p < 0.001) in rumen fluid of SP2 were significantly lower than SP1. The expression of MCT2 (p = 0.024), ACSS1 (p = 0.039) and NHE3 (p = 0.006) in the rumen of SP2 was lower than SP1, while the HMGCS1 (p = 0.026), HMGCR (p = 0.024) and Na+/K+-ATPase (p = 0.020) was higher than SP1. The three dominant phyla in the rumen are Bacteroidetes, Proteobacteria and Firmicutes. The membrane transport, amino acid metabolism and carbohydrate metabolism of SP1 were relatively enhanced, the replication and repair function of SP2 was relatively enhanced. To sum up, the increase of dietary protein level significantly increased the carcass weight and dressing percentage of offspring and had significant effects on rumen volatile fatty acids, acetic acid activation and cholesterol synthesis related genes. HIGHLIGHTSIn the early feeding period, the difference in ADG of lambs was mainly caused by the sucking effect.The increase in dietary protein level of ewes significantly increased the carcass weight and dressing percentage of offspring.The dietary protein level of ewes significantly affected the volatile fatty acids (VFAs) and genes related to acetic acid activation and cholesterol synthesis in the rumen of their offspring.The membrane transport, amino acid metabolism and carbohydrate metabolism of the offspring of ewes fed with a low protein diet were relatively enhanced.The replication and repair function of the offspring of ewes fed with a high protein diet was relatively strengthened.

Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

Transcriptome profiling in rumen, reticulum, omasum, and abomasum tissues during the developmental transition of pre-ruminant to the ruminant in yaks

The development of the four stomachs of yak is closely related to its health and performance, however the underlying molecular mechanisms are largely unknown. Here, we systematically analyzed mRNAs of four stomachs in five growth time points [0 day, 20 days, 60 days, 15 months and 3 years (adult)] of yaks. Overall, the expression patterns of DEmRNAs were unique at 0 d, similar at 20 d and 60 d, and similar at 15 m and adult in four stomachs. The expression pattern in abomasum was markedly different from that in rumen, reticulum and omasum. Short Time-series Expression Miner (STEM) analysis demonstrated that multi-model spectra are drastically enriched over time in four stomachs. All the identified mRNAs in rumen, reticulum, omasum and abomasum were classified into 6, 4, 7, and 5 cluster profiles, respectively. Modules 9, 38, and 41 were the most significant three colored modules. By weighted gene co-expression network analysis (WGCNA), a total of 5,486 genes were categorized into 10 modules. CCKBR, KCNQ1, FER1L6, and A4GNT were the hub genes of the turquoise module, and PAK6, TRIM29, ADGRF4, TGM1, and TMEM79 were the hub genes of the blue module. Furthermore, functional KEGG enrichment analysis suggested that the turquoise module was involved in gastric acid secretion, sphingolipid metabolism, ether lipid metabolism, etc., and the blue module was enriched in pancreatic secretion, pantothenate and CoA biosynthesis, and starch and sucrose metabolism, etc. Our study aims to lay a molecular basis for the study of the physiological functions of rumen, reticulum, omasum and abomasum in yaks. It can further elucidate the important roles of these mRNAs in regulation of growth, development and metabolism in yaks, and to provide a theoretical basis for age-appropriate weaning and supplementary feeding in yaks.

Effects of graded levels of dietary protein supplementation on milk yield, body weight gain, blood biochemical parameters, and gut microbiota in lactating ewes

Diet-associated characteristics such as dietary protein levels can modulate the composition and diversity of the gut microbiota, leading to effects on the productive performance and overall health of animals. The objective of this study was to see how changes in dietary protein levels affect milk yield, body weight gain, blood biochemical parameters, and gut microbiota in lactating ewes. In a completely randomized design, eighteen ewes were randomly assigned to three groups (n = 6 ewes/group), and each group was assigned to one of three dietary treatments with different protein contents. The ewes' groups were fed on 8.38% (S-I), 10.42% (S-m), and 13.93% (S-h) dietary protein levels on a dry basis. The body weight gain and milk yield were greater (p < 0.05) in ewes fed the S-h dietary treatment than in those fed the S-m and S-1 diets, respectively. However, milk protein contents were similar (p > 0.05) across the treatments. The blood glucose, total protein, cholesterol, triglycerides, high-density lipoprotein, low-density lipoprotein, lactate, creatinine, and C-reactive protein contents of lactating ewes were not influenced (p > 0.05) by different dietary protein levels. The alanine transaminase, aminotransferase, and lactate dehydrogenase activities were also not changed (p > 0.05) across the groups. However, blood urea nitrogen and albumin contents of lactating ewes were changed (p < 0.05) with increasing levels of dietary protein, and these metabolite concentrations were higher (p < 0.05) for S-h than the rest of the treatments. In the different treatment groups, Firmicutes and Bacteroidetes were found to be the most dominant phyla. However, the abundance of Lachnospiraceae species decreased as dietary protein levels increased. Within the Bacteroidetes phylum, Rikenellaceae were more abundant, followed by Prevotellaceae, in ewes fed the S-m diet compared to those fed the other diets. Based on the results, feeding at an optimal protein level improved milk yield and body weight gain through modifying the digestive tract's beneficial bacterial communities. The results of blood metabolites suggested that feeding higher-protein diets has no negative impact on health.

Effects of a High-Concentrate Diet on the Blood Parameters and Liver Transcriptome of Goats

The objective of this study was to determine the effect of high-concentrate diets on the blood parameters and liver transcriptome of goats. Eighteen goats were allocated into three dietary treatments: the high level of concentrate (HC) group, the medium level of concentrate (MC) group, and the low level of concentrate (LC) group. The blood parameters and pathological damage of the gastrointestinal tract and liver tissues were measured. In hepatic portal vein blood, HC showed higher LPS, VFAs, and LA; in jugular vein blood, no significant differences in LPS, VFAs, and LA were recorded among groups (p > 0.05). Compared to the LC and MC groups, the HC group showed significantly increased interleukin (IL)-1β, IL-10, TNF-α, and diamine oxidase in jugular vein blood (p < 0.05). Liver transcriptome analysis discovered a total of 1269 differentially expressed genes (DEGs) among the three groups and most of them came from the HC vs. LC group. There were 333 DEGs up-regulated and 608 down-regulated in the HC group compared to the LC group. The gene ontology enrichment analysis showed that these DEGs were mainly focused on the regulation of triacylglycerol catabolism, lipoprotein particle remodeling, and cholesterol transport. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the liver of the HC group enhanced the metabolism of nutrients such as VFAs through the activation of AMPK and other signaling pathways and enhanced the clearance and detoxification of LPS by activating the toll-like receptor signaling pathway. A high-concentrate diet (HCD) can significantly promote the digestion of nutrients; the liver enhances the adaptability of goats to an HCD by regulating the expression of genes involved in nutrient metabolism and toxin clearance.

Early Solid Diet Supplementation Influences the Proteomics of Rumen Epithelium in Goat Kids

It is well known that solid diet supplementation in early life can significantly promote rumen development and metabolic function in young ruminants. However, the changes in the expressed proteome and related metabolism in rumen epithelium in response to a supplemented solid diet remain unclear. In this study, rumen epithelial tissue from goats in three diet regimes including milk replacer only (MRO), milk replacer supplemented concentrate (MRC), and milk replacer supplemented concentrate plus alfalfa pellets (MCA) were collected for measurement of the expression of epithelial proteins using proteomic technology (six per group). The results showed that solid diet significantly improved the growth performance of goats, enhanced the ability of rumen fermentation, and promoted the development of epithelial papilla (p < 0.05). Proteome analysis revealed the distinct difference in the expressed protein in the MRC and MCA group compared with the MRO group (42 upregulated proteins and 79 downregulated proteins in MRC; 38 upregulated proteins and 73 downregulated proteins in MCA). Functional analysis showed that solid diet supplementation activated a variety of molecular functions in the epithelium, including protein binding, ATP binding, structural constituent of muscle, etc., in the MRC and MCA groups. Meanwhile, the expression of proteins related to fatty acid metabolism, the PPAR signaling pathway, valine, leucine, and isoleucine degradation, and butanoate metabolism were upregulated, being stimulated by solid feed. In contrast, the proteins associated with carbohydrate digestion and absorption and glycosaminoglycan degradation were downregulated. In addition, the protein expression of enzymes involved in ketone body synthesis in the rumen was generally activated, which was caused by solid feed. In summary, solid feed promoted the development of rumen epithelium by changing the expression of proteins related to fatty acid metabolism, energy synthesis, and signal transduction. The ketone body synthesis pathway might be the most important activated pathway, and provides energy for rumen development.

Effects of inoculation with active microorganisms derived from adult goats on growth performance, gut microbiota and serum metabolome in newborn lambs

This study evaluated the effects of inoculation with adult goat ruminal fluid on growth, health, gut microbiota and serum metabolism in lambs during the first 15 days of life. Twenty four Youzhou dark newborn lambs were selected and randomly distributed across 3 treatments (n = 8/group): autoclaved goat milk inoculated with 20 mL sterilized normal saline (CON), autoclaved goat milk inoculated with 20 mL fresh ruminal fluid (RF) and autoclaved goat milk inoculated with 20 mL autoclaved ruminal fluid (ARF). Results showed that RF inoculation was more effective at promoting recovery of body weight. Compared with CON, greater serum concentrations of ALP, CHOL, HDL and LAC in the RF group suggested a better health status in lambs. The relative abundance of Akkermansia and Escherichia-Shigella in gut was lower in the RF group, whereas the relative abundance of Rikenellaceae_RC9_gut_group tended to increase. Metabolomics analysis shown that RF stimulated the metabolism of bile acids, small peptides, fatty acids and Trimethylamine-N-Oxide, which were found the correlation relationship with gut microorganisms. Overall, our study demonstrated that ruminal fluid inoculation with active microorganisms had a beneficial impact on growth, health and overall metabolism partly through modulating the gut microbial community.

Effects of milk replacer feeding level on growth performance, rumen development and the ruminal bacterial community in lambs

Feeding with a suitable level of milk replacer (MR) can improve the survival rate and stimulate the growth potential of early lambs. However, feeding excessive MR might be detrimental to rumen development and microbial colonization. Herein, we investigated the effects of feeding different levels of MR on rumen digestive function and ruminal microorganisms. Fourteen healthy male Hu lambs with similar birth weights and detailed pedigree records were divided into two groups to receive low (2% of average body weight per day) and high (4% of average body weight per day) levels of MR. We analyzed the effects of the MR feeding level on growth performance, fiber degradation rates, rumen fermentation parameters, enzyme activities and rumen histomorphology. We found that feeding with a high level of MR improved the average daily gain of early lambs, but decreased the starter intake, rumen weight and papillae length. We also analyzed the effects of the MR feeding level on the rumen microbiota using 16S-rRNA amplicon sequencing data. The results showed that high a MR feeding level increased the rumen microbial diversity but decreased the abundance of many carbohydrate degrading bacteria. Several bacterial genera with significant differences correlated positively with rumen cellulase activity and the acid detergent fiber degradation rate. Our results suggested that a high level of MR could improve the growth performance of early lambs in the short term; however, in the long term, it would be detrimental to rumen development and have adverse effects on the adaptation process of the microbiota to solid feed.

Effects of oat (Avena sativa L.) hay diet supplementation on the intestinal microbiome and metabolome of Small-tail Han sheep

Supplementation of the sheep diet with oats (Avena sativa L.) improves animal growth and meat quality, however effects on intestinal microbes and their metabolites was not clear. This study aimed to establish the effect of dietary oat supplementation on rumen and colonic microbial abundance and explore the relationship with subsequent changes in digesta metabolites. Twenty Small-tail Han sheep were randomly assigned to a diet containing 30 g/100 g of maize straw (Control) or oat hay (Oat). After 90-days on experimental diets, rumen and colon digesta were collected and microbial diversity was determined by 16S rRNA gene Illumina NovaSeq sequencing and metabolomics was conducted using Ultra-high performance liquid chromatography Q-Exactive mass spectrometry (UHPLC-QE-MS). Compared to Control group, oat hay increased the abundance of Bacteroidetes and Fibrobacteres as well as known short-chain fatty acid (SCFA) producers Prevotellaceae, Ruminococcaceae and Fibrobacteraceae in rumen (p < 0.05). In rumen digesta, the Oat group showed had higher levels of (3Z,6Z)-3,6-nonadienal, Limonene-1,2-epoxide, P-tolualdehyde, and Salicylaldehyde compared to Control (p < 0.05) and these metabolites were positively correlated with the abundance of cecal Prevotellaceae NK3B31. In conclusion, supplementation of the sheep diet with oat hay improved desirable microbes and metabolites in the rumen, providing insight into mechanisms whereby meat quality can be improved by oat hay supplementation.

Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep

Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.

Alleviation effects of niacin supplementation on beef cattle subjected to heat stress: A metagenomic insight

The objective of this study was to investigate the alleviation effects of niacin supplementation on beef cattle subjected to heat stress and to provide a theoretical basis for exploring the alleviation methods of heat stress environmental factors on the rumen of beef cattle. In the experiment, 36 Jinjiang bull cattle with a body weight of about 400 ± 20.0 kg were randomly divided into three treatments, each treatment contains four replicates, with three cattle in each replicate. Treatments included thermoneutral treatment (TN; temperature: 24–25°C, humidity: 45–55%), heat stress treatment, exposure to environmental temperature (HS; average THI: 82.74), and heat stress supplemented with niacin treatment (HN; high temperature + 800 mg/kg NA). Measured indicators were body temperature, respiratory rate, production performances, rumen fermentations, and microbial diversity. Results showed that adding niacin reduced the body temperature and respiratory rate (P &lt; 0.05) but had no significant effect on the production performances compared with heat-stressed beef cattle. HS treatment significantly increased body temperature and respiratory rate (P &lt; 0.01), while decreasing the content of acetic acid, butyric acid, and total volatile fatty acids (P &lt; 0.05) compared with the TN treatment. Supplement of niacin did not affect ruminal fermentation parameters (P &gt; 0.05) but had a decreased tendency on A/P (P &lt; 0.1). Microbial diversity results showed that, at the phylum level, the relative abundance of Desulfobacterota in the HS treatment was increased compared with TN and HN treatment (P &lt; 0.05). At the genus level, the relative abundance of Succiniclasticum and Family_XIII_AD3011 group in the HN treatment significantly proliferated compared with the HS treatment (P &lt; 0.05). In conclusion, niacin supplementation may alleviate heat stress by proliferating those bacteria belonging to the phylum Succiniclasticum, which may further contribute to the digestion of cellulose and the improvement of the metabolic function of Jinjiang cattle under heat-stress conditions.

Mixed silage with Chinese cabbage waste enhances antioxidant ability by increasing ascorbate and aldarate metabolism through rumen Prevotellaceae UCG-004 in Hu sheep

Silage is rich in nutrients, which can make up for the lack of seasonal roughage, and has a certain promotion effect on the intensive feeding of ruminants. In addition, silage can maintain the rumen function of ruminants to a certain extent and reduce the risk of rumen acidosis and abomasum translocation. The purpose of this study was to investigate the effects of the mixed silage of Chinese cabbage waste and rice straw (mixed silage) on antioxidant performance, rumen microbial population, and fermentation metabolism of Hu sheep. The 16 healthy Hu sheep (eight rams and eight ewes, 39.11 ± 1.16 kg, 5.5 months) were randomly divided into two groups (the control group and the mixed silage group) with eight animals (four rams and four ewes) in each group. The control group was fed with farm roughage (peanut seedlings, corn husk, and high grain shell) as forage, and the mixed silage group was fed with the mixed silage as forage. The results showed that the mixed silage had no effect on the growth performance of Hu sheep (p &gt; 0.05). Ruminal butyric acid, total volatile fatty acids (TVFA), and ammonia nitrogen (NH3-N) concentration in the mixed silage group were increased, whereas the pH was decreased (p &lt; 0.05). The blood and rumen total antioxidants capacity (T-AOC) concentration in the mixed silage group was higher, and the malondialdehyde (MDA) content in rumen, serum, liver, and kidney was lower than that in the control group (p &lt; 0.05). PCoA and ANOSIM results of Illumina sequencing indicated that the mixed silage affected the bacterial composition of the rumen microbes. The mixed silage increased the proportion of Prevotellaceae UCG-004 which was in a positive correlation with Vitamin C (Vc). In addition, PICRUSt functional prediction analysis showed that ascorbate and aldarate metabolism were up-regulated in the mixed silage group (p &lt; 0.05). In conclusion, higher contents of VC and acid detergent fiber (ADF) in the mixed silage were beneficial to the growth and reproduction of Prevotellaceae UCG-004, resulting in increased production of the butyric acid significantly upregulated the metabolism of ascorbate and aldarate metabolism, thereby improving the antioxidant properties of Hu sheep.

Early feeding strategies in lambs affect rumen development and growth performance, with advantages persisting for two weeks after the transition to fattening diets

This study aimed to explore the effects of early feeding strategies on the growth and rumen development of lambs from pre-weaning to the transition to fattening diets. Ninety-six newborn, male lambs with similar body weights were randomly assigned to three treatments: fed starter at 42 days old + weaned at 56 days old (Ctrl, n = 36), fed starter at 7 days old + weaned at 56 days old (ES, n = 36), and fed starter at 7 days old + weaned at 28 days old (ES + EW, n = 24). The fattening diets of all lambs were gradually replaced from 60 to 70 days of age. Six randomly selected lambs from each treatment were slaughtered at 14, 28, 42, 56, 70, and 84 days of age. The results showed that the richness and diversity of rumen microbiota of lambs in the Ctrl group were distinct from those of lambs in the other groups at 42 days of age. Moreover, transcriptome analysis revealed 407, 219, and 1,211 unique differentially expressed genes (DEGs) in the rumen tissue of ES vs. Ctrl, ES vs. ES + EW, and ES + EW vs. Ctrl groups, respectively, at 42 days of age. Different early feeding strategies resulted in differences in ruminal anatomy, morphology, and fermentation in lambs from 42 to 84 days of age (P < 0.05). Lambs in the ES + EW group had a higher average starter diet intake than those in the other groups (P < 0.05) from 28 to 56 days of age, which affected their growth performance. After 42 days of age, the body and carcass weights of lambs in the ES and ES + EW groups were higher than those in the Ctrl group (P < 0.05). These findings demonstrate that feeding lambs with a starter diet at 7 days of age and weaning them at 28 days of age can promote rumen development and improve growth performance, and this advantage persists for up to 2 weeks after transition to the fattening diet.

Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions

In mammals, the introduction of solid food is pivotal for the establishment of the gut microbiota. However, the effects of the first food consumed on long-term microbiota trajectory and host response are still largely unknown. This study aimed to investigate the influences of (i) the timing of first solid food ingestion and (ii) the consumption of plant polysaccharides on bacterial community dynamics and host physiology using a rabbit model. To modulate the first exposure to solid nutrients, solid food was provided to suckling rabbits from two different time points (3 or 15 days of age). In parallel, food type was modulated with the provision of diets differing in carbohydrate content throughout life: the food either was formulated with a high proportion of rapidly fermentable fibers (RFF) or was starch-enriched. We found that access to solid food as of 3 days of age accelerated the gut microbiota maturation. Our data revealed differential effects according to the digestive segment: precocious solid food ingestion influenced to a greater extent the development of bacterial communities of the appendix vermiformis, whereas life course polysaccharides ingestion had marked effects on the cecal microbiota. Greater ingestion of RFF was assumed to promote pectin degradation as revealed by metabolomics analysis. However, transcriptomic and phenotypic host responses remained moderately affected by experimental treatments, suggesting little outcomes of the observed microbiome modulations on healthy subjects. In conclusion, our work highlighted the timing of solid food introduction and plant polysaccharides ingestion as two different tools to modulate microbiota implantation and functionality.

IMPORTANCE Our study was designed to gain a better understanding of how different feeding patterns affect the dynamics of gut microbiomes and microbe–host interactions. This research showed that the timing of solid food introduction is a key component of the gut microbiota shaping in early developmental stages, though with lower impact on settled gut microbiota profiles in older individuals. This study also provided in-depth analysis of dietary polysaccharide effects on intestinal microbiota. The type of plant polysaccharides reaching the gut through the lifetime was described as an important modulator of the cecal microbiome and its activity. These findings will contribute to better define the interventions that can be employed for modulating the ecological succession of young mammal gut microbiota.

Impact of dietary supplementation of β-hydroxybutyric acid on performance, nutrient digestibility, organ development and serum stress indicators in early-weaned goat kids

The objective of this study was to determine the effect of dietary supplementation of β-hydroxybutyric acid (BHBA) on performance, nutrient digestibility, organ development, and serum composition in early-weaned goat kids. Sixty-four goat kids at 30 d of age were assigned to 4 treatments in a completely randomized design: 1) control (basal diet); 2) low (basal diet with 3 g/d per animal BHBA); 3) medium (basal diet with 6 g/d per animal BHBA; and 4) high (basal diet with 9 g/d per animal BHBA). Subsequently, 48 (6 kids per treatment) goat kids were randomly selected and slaughtered at 60 and 90 d of age. Compared with the control group, BHBA at low and high doses increased body weight (P < 0.05), average daily gain (P < 0.01), and average daily starter intake (P < 0.01). The BHBA improved organ development, especially at the lowest dose (P < 0.01). The digestibility of dry matter and crude protein increased with age (P < 0.05). However, BHBA did not affect nutrient digestibility. Compared with the control group, serum ceruloplasmin increased (P < 0.05) with high BHBA level at 90 d of age. However, the serum creatinine (P < 0.05) increased over time but was not affected by BHBA. The serum total antioxidant capacity and superoxide dismutase decreased with the high dose of BHBA at 90 d of age (P < 0.01). In contrast, the serum glutathione peroxidase and malondialdehyde increased with the high doses of BHBA (P < 0.01). Overall, low doses of BHBA were positive for growth performance, organ development, and health status against weaning stress. Whereas high doses of BHBA in the long term could negatively affect antioxidant status.

Transcriptomic Profiling of Circular RNAs in the Goat Rumen During Fetal and Prepubertal Period

Circular RNAs (circRNAs) are key regulatory factors with vital functions in various biological activities. However, little has been reported concerning the genetic regulation of circRNAs during rumen development in goats. The aim of this study was to identify the genome-wide expression profiles of circRNAs in the rumen of goats during fetal development and before and after weaning. Histological morphology showed that from the fetal period (days 60 and 135 of gestation) to the prepuberal period (days 60 and 150 of age) the rumen papilla developed gradually, and the thickness of the rumen muscular layer increased. A total of 11,149 circRNAs were identified in the four development stages by RNA-sequencing. From this, 1,518 were differentially expressed circRNAs (DECs). Fifty-eight DECs were up-regulated from 60 to 135 days of gestation, and 93 from day 135 of pregnancy to 30 days after birth. A large proportion (598) of DECs were down-regulated from day 135 of gestation to 30 days after birth. The expression levels of six randomly selected circRNAs were validated by qPCR, and their back-splicing junction (BSJ) sites were also confirmed. Ontology and pathway analyses revealed that the parental genes of DECs were mainly involved in the signaling pathways related to cell proliferation and apoptosis. The interaction network of circRNAs with their target miRNAs showed its involvement in cell proliferation and apoptosis signaling pathways. In conclusion, we identified the genome-wide expression profiles of circRNAs in the rumen of goats during fetal development and before and after weaning. These results provide a basis for further study on the regulatory effect of circRNAs on the development of rumen tissues.

Integration of Long Non-Coding RNA and mRNA Profiling Reveals the Mechanisms of Different Dietary NFC/NDF Ratios Induced Rumen Development in Calves

The aim of the present study was to explore the effects of dietary non-fibrous carbohydrate to neutral detergent fiber (NFC/NDF) ratios on rumen development of calves, and to investigate the mechanisms by integrating of lncRNA and mRNA profiling. Forty-five weaned Charolais hybrid calves [body weight = 94.38 ± 2.50 kg; age = 70 ± 2.69 d] were randomly assigned to 1 of 3 treatment groups with different dietary NFC/NDF ratios: 1.10 (H group), 0.94 (M group) and 0.60 (L group), respectively. The ventral sac of the rumen was sampled for morphological observation and transcriptional sequencing. The average daily gain of calves in the high NFC/NDF ratio group was significantly higher than that in other groups (p < 0.05). Papillae width was largest in high NFC/NDF ratio group calves (p < 0.05). Identified differentially expressed genes that were significantly enriched in pathways closely related to rumen epithelial development included focal adhesion, Wingless-int signaling pathway, thyroid hormone signaling pathway, regulation of actin cytoskeleton and cGMP-PKG signaling pathway. The lncRNA-mRNA network included XLOC_068691 and MOAB, XLOC_023657 and DKK2, XLOC_064331 and PPP1R12A which we interpret to mean they have important regulatory roles in calve rumen development. These findings will serve as a theoretical basis for further analysis of the molecular genetic mechanism of dietary factors affecting rumen development in calves.

Effects of Phragmites australis Shoot Remainder Silage on Growth Performance, Blood Biochemical Parameters, and Rumen Microbiota of Beef Cattle

The objective of the present study was to assess the effects of replacing corn silage with Phragmites australis shoot remainder (PSR) silage on intake, growth performance, serum biochemical parameters, and rumen microbial diversity of growing-finishing beef. Fifteen Angus beef cattle with an average body weight of 253 ± 2.94 kg were randomly divided into three groups (five replicas vs. each group vs. Angus beef cattle). The three treatments were group A fed 60% PSR silage + 40% concentrate, group B fed 30% PSR silage + 30% corn silage + 40% concentrate, and group C fed 60% corn silage + 40% concentrate. The adaptation period was 15 days, and the trial period lasted for 45 days. Results showed that the ADG was significantly higher, and FCR was significantly lower both in groups A and B compared with group C. The results of serum biochemical parameters showed that the concentration of GLU was significantly lower in group B than both groups A and C. Microbial diversity results showed that the OTUs, Shannon, Chao1, and ACE indices were significantly lower in group A compared with groups B and C. At the phyla level, the relative abundances of Tenericutes and Melainabacteria had significant differences among the three groups, and the relative abundances of Papillibacter, Anaeroplasma, and Anaerovorax had significant differences among the three groups at the genus level. Additionally, Rikenellaceae was the unique biomarker among the three groups. Furthermore, the results of function prediction showed that the gene families associated with metabolism of cofactors and vitamins, cellular processes and signaling, metabolism, biosynthesis of other secondary metabolites, infectious diseases, signaling molecules and interaction, nervous system, and digestive system were significantly decreased, while lipid metabolism was dramatically increased from groups A to C at KEGG level 2. At KEGG level 3, 11 metabolic pathways were significantly influenced among the three groups. In summary, these findings indicated that PSR silage substituted the corn silage totally or partially improved the growth performance, and altered the rumen microbial composition and diversity and the corresponding change in prediction function of rumen bacteria in Angus beef cattle.

Proteomic identification of ruminal epithelial protein expression profiles in response to starter feed supplementation in pre-weaned lambs

The present study aimed to comparatively characterize the ruminal epithelial protein expression profiles in lambs fed ewe milk or milk plus starter diet using proteome analysis. Twenty new-born lambs were randomly divided into a group receiving ewe milk (M, n = 10) and a group receiving milk plus starter diet (M + S, n = 10). From 10 d old, M group lambs remained with the ewe and suckled ewe milk without receiving the starter diet. The lambs in the M + S group were separated from the ewe and received starter feed. All lambs were slaughtered at 56 d old. Eight rumen epithelia samples (4 per group) were collected to characterize their protein expression profiles using proteomic technology. Proteome analysis showed that 31 upregulated proteins and 40 downregulated proteins were identified in the rumen epithelium of lambs in response to starter diet supplementation. The results showed that starter feeding regulates a variety of biological processes in the epithelium, especially blood vessel development and extracellular matrix protein expression. Meanwhile, the expression of proteins associated with synthesis and degradation of ketone bodies, butanoate metabolism, and citrate cycle signaling transduction pathway were upregulated in the group with starter diet supplementation, including 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGCS2, fold change [FC] = 1.93), 3-hydroxybutyrate dehydrogenase 1 (BDH1, FC = 1.91), and isocitrate dehydrogenase 1 (IDH1, FC = 8.12). The metabolic processes associated with ammonia detoxification and antioxidant stress were also affected by starter diet supplementation, with proteins, microsomal glutathione S-transferase 3 (MGST3, FC = 2.37) and IDH1, linked to the biosynthesis of glutamate and glutathione metabolism pathway being upregulated in the group with starter diet supplementation. In addition, starter feeding decreased the expression of Ras-related protein rap-1A (RAP1A, FC = 0.48) enriched in Rap1 signaling pathway, Ras signaling pathway, cyclic adenosine monophosphate (cAMP) signaling pathway, and mitogen-activated protein kinase (MAPK) signaling pathway. In summary, starter feed supplementation changed the expression of proteins related to energy production, ammonia detoxification, antioxidant stress, and signaling pathways related to proliferation and apoptosis, which facilitates the rumen epithelia development in lambs. The results provide new insights into the molecular adaptation of rumen epithelia in response to starter diet supplementation at the protein level in lambs.

Transcriptome profiling reveals differential gene expression in the rumen of Hu lambs at different developmental stages

The development of the rumen is a critical physiological challenge in newborn ruminants. However, the molecular mechanism underlying different stages of rumen development in sheep remains poorly understood. Here, RNA sequencing and bioinformatics analysis were performed to compare the transcription profiles of rumen development at 7, 28 and 56 days of birth (D7, D28 and D56). We identified 1246, 2257 and 627 differentially expressed genes (DEGs) between D7 and D28, between D7 and D56, between D28 and D56, respectively. Also, 70 DGEs were co-expressed at these three time points. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated most DEGs mainly related to transporter activity, channel activity and metabolism pathways. Noteworthy, the expression levels of most genes (CA4, CA9, CA12 and CA14) in nitrogen metabolic pathways were negatively correlated with the papilla length and width, but the papilla length and width were positively correlated with the expression of genes (PLA2G3, SLC26A9, SLC34A3) in ion transport pathway, suggesting that these genes may be involved in nitrogen metabolic and ion transport pathway and thus affect rumen development. These results provide new insight into the changes in RNA expression at different time points of rumen development in Hu sheep.

Transcriptional Reprogramming in Rumen Epithelium during the Developmental Transition of Pre-Ruminant to the Ruminant in Cattle

Simple Summary

The rumen is the critical organ mediating nutrient uptake and use in cattle. Health development is essential to ensure animal feed efficiency. In this report, we present an analysis of gene expression dynamic in rumen epithelium during the transition from pre-ruminant to ruminant in cattle fed with hay or concentrated diets at weaning. The global shifts in gene expression and correlated transcription factors activities indicate transcriptional reprogramming during weaning. Transcriptional reprogramming in rumen epithelial tissue reflects critical nutrient-gene interactions occurring during the developmental progression. The results unveiled that nutrient-gene interactions compel transcriptional reprogramming. Our findings also suggest that this transcriptional reprogramming is the molecular basis of the transitional development of pre-ruminant to the ruminant in cattle.

Abstract

We present an analysis of transcriptomic dynamics in rumen epithelium of 18 Holstein calves during the transition from pre-rumination to rumination in cattle-fed hay or concentrated diets at weaning. Three calves each were euthanized at 14 and 42 d of age to exemplify preweaning, and six calves each were provided diets of either milk replacer and grass hay or calf starter to introduce weaning. The two distinct phases of rumen development and function in cattle are tightly regulated by a series of signaling events and clusters of effectors on critical pathways. The dietary shift from liquid to solid feeds prompted the shifting of gene activity. The number of differentially expressed genes increased significantly after weaning. Bioinformatic analysis revealed gene activity shifts underline the functional transitions in the ruminal epithelium and signify the transcriptomic reprogramming. Gene ontogeny (GO) term enrichment shows extensively activated biological functions of differentially expressed genes in the ruminal epithelium after weaning were predominant metabolic functions. The transcriptomic reprogramming signifies a correlation between gene activity and changes in metabolism and energy production in the rumen epithelium, which occur at weaning when transitioning from glucose use to VFA use by epithelium during the weaning.

Effects of Dietary Energy Levels on Rumen Fermentation, Gastrointestinal Tract Histology, and Bacterial Community Diversity in Fattening Male Hu Lambs

This study investigated rumen fermentation and histological and microbial diversity in male Hu lamb fed diets with different metabolizable energy (ME) levels (MEA, 9.17 MJ/kg, MEB, 10.00 MJ/kg, and MEC, 10.82 MJ/kg). Thirty-six male Hu lambs were randomly allotted to three treatments, and the feeding trial lasted for 67 days. Rumen fermentation results suggest that the iso-valerate had a significant effect on dietary energy level. The papillary height (PH) of rumen was the highest in the MEB group, the crypt depth (CD) was significantly increased in the duodenum and jejunum, and the villus height (VH)-to-CD ratio (VH/CD) was significantly decreased in the duodenum by increasing dietary energy levels; the VH, villus width (VW), and VH/CD also had significant differences in the ileum. 16S rRNA sequencing results showed that the operational taxonomic units (OTUs) number, the ACE, and Chao1 indices were linearly decreased by increasing dietary energy level; 24 phyla including 124 genera were identified, and the relative abundance of Papillibacter and Quinella linearly decreased by increasing the dietary energy level. Compared to MEA and MEB groups, the relative abundance of unidentified_Veillonellaceae and Anaerovibrio was significantly increased in the MEC group at the genus level. The relative abundance of the carbohydrate metabolism pathway predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was linearly increased by increasing the dietary energy levels. Three metabolic pathways identified in Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 were significantly influenced as the dietary energy level increased. In summary, these results demonstrated that the dietary energy levels affected the rumen fermentation parameters, morphological structures of the gastrointestinal tract (GIT), and the composition and function of rumen microflora in male Hu sheep.

Microbiome and fermentation parameters in the rumen of dairy buffalo in response to ingestion associated with a diet supplemented with cysteamine and hemp seed oil

In this study, high-throughput gene amplicon sequencing was used to investigate the effects of 6 treatments [2 levels of hemp seed oil (HSO) × 3 levels of cysteamine (CS)] on bacterial and fungal communities in the rumen of 30 crossbred dairy buffalo. Our results indicate that the total numbers of bacterial and fungal taxa were unaffected regardless of diet (p > 0.05), while the total number of archaea was affected (p < 0.05) by the interaction of HSO and CS. Compared with control treatment, microbial composition of archaea was strongly influenced by CS (p < 0.05), while the addition of HSO, CS or both had a weak effect on fungus and bacteria. In addition, there was a significant increase in the lactic acid content with the addition of HSO, and the addition of CS to the feed caused a significant decrease in the ratio of acetic acid to propionic acid, compared with control treatment (p < 0.05). Correlation analysis showed that Acetobacter was significantly positively correlated with the genera Pichia, Klebsiella and Acinetobacter. pH was found to have a significant effect on the methanogens, and total volatile fatty acids (VFA) had a strong correlation with Butyrivibrio. The strong influence of CS on some methanogens shows that it may have potential in the development of methane reduction interventions.

Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.)

In a previous study, we found that the growth performance of the new strain of Huanghe carp is related to gene expression and bacterial community in the gut. In order to better understand the relationship between the gene expression level and bacterial abundance in the gut, we studied the growth performance, gut bacterial structure, and transcriptome profile in the 4th generation of the new carp strain (selection group) at harvesting time, and compared them with the control line (traditional Huanghe carp). Body weight, depth, width, and length increased 14.58, 7.14, 5.04, and 5.07%, respectively. The gut microbiome of the selection group also exhibited significantly higher species diversity parameters (Shannon, Simpson, and chao1). Both PCA and phylogenetic analyses divided all gut samples into two parts: control and selection group. Aeromonas was the dominant taxon in the control group, followed by Firmicutes and Roseomonas; in the selection group, Roseomonas was the dominant taxon, followed by Firmicutes and then Aeromonas. Among the 249 significantly differentially expressed genes, 194 were downregulated and 55 were upregulated. Functional GO annotation produced 13 terms in the biological process, 8 in the cellular component, and 7 in the molecular function categories. KEGG annotation indicated that most of these genes were associated with the immune-related pathways. A total of 2,892 pairs of genes (245) and baceterial genera (256) were analyzed using Pearson's correlation analysis. Most of the identified associations were mapped to the immune system, bacterial community, and cell differentiation categories. The top-10 bacterial genera identified by these analyses were Methylocystis, Ohtaekwangia, Roseomonas, Shewanella, Lutispora, GpVI, Desulfovibrio, Candidatus_Berkiella, Bordetella, and Azorhizobium. Genes paired with bacteria flora were divided into four functional categories: immune, growth, adipocyte differentiation, and nerve regulation. These genes may be related to the comparatively fast growth and high muscle polyunsaturated fatty acid content of the Huanghe carp new strain. Meanwhile, nerve regulation-related genes may be a reflection of the microbiota-gut-brain axis. These results illustrate that gut bacterial community structure is associated with the growth performance and gene expression in the Huanghe carp new strain.

Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats

Background

Preweaned rumen development is vital for animal health and efficient fermentation. In this study, we integrated ruminal transcriptomic and metagenomic data to explore the dynamics of rumen functions, microbial colonization, and their functional interactions during the first 8 weeks of life in goats.

Results

The dynamic rumen transcriptomic and microbial profiles both exhibited two distinct phases during early rumen development. The differentially expressed genes of the rumen transcriptome between the two phases showed that the immune-related response was enriched in the first phase and nutrient-related metabolism was enriched in the second phase, whereas the differentially expressed genes of the rumen microbiome were enriched in bacteriocin biosynthesis and glycolysis/gluconeogenesis activities. The developmental shift in the rumen transcriptome (at d 21) was earlier than the feed stimulus (at d 25) and the shift in the rumen microbiome (at d 42). Additionally, 15 temporal dynamic rumen gene modules and 20 microbial modules were revealed by coexpression network analysis. Functional correlations between the rumen and its microbiome were primarily involved in rumen pH homeostasis, nitrogen metabolism and the immune response. Rumen gene modules associated with the microbial alpha diversity index were also enriched in the immune response process.

Conclusions

The present study touched the critical developmental process of rumen functions, microbial colonization and their functional interactions during preweaned development. Taken together, these results demonstrated that rumen development at the first phase is more likely a programmed process rather than stimulation from feed and the microbiome, while the shift of rumen metagenomes was likely regulated by both the diet and host. The intensive functional correlations between rumen genes and the microbiome demonstrated that synergistic processes occurred between them during early rumen development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07595-1.

Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning

Background

The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen sampling procedures but the oral cavity of ruminants is expected to harbour rumen microbes due to regurgitation activity. The present study used buccal swab samples to define the rumen core microbiome and characterize the shifts in rumen and oral microbial communities occurring as result of calf’s age as well as time of weaning.

Results

Buccal swab samples of 59 calves were collected along the first 140 days of life and compared to stomach tubing sample of the rumen at day 140. Animals were randomly divided into two weaning groups. Microbiota of saliva and rumen content was analysed by 16S rRNA gene amplicon sequencing. Our study showed that most rumen-specific bacterial taxa were equally observed in rumen samples as well as in the buccal swabs, though relative abundance varied. The occurrence of rumen-specific OTUs in buccal swab samples increased approximately 1.7 times from day 70 to day 140, indicating the gradual development of rumen as calf aged. The rumen-specific bacterial taxa diversity increased, and inter-animal variations decreased with age. Early weaning (7 weeks of age) rapidly increased the rumen microbial diversity from pre- to post-weaned state. Rumen microbiota of early-weaned calves seemed to have a suppressed growth of starch- and carbohydrate-utilizing bacteria and increased fibre degraders. Whereas, in late-weaned calves (17 weeks of age) no impact of dietary modifications on rumen microbiota composition was observed after weaning. Oral-specific bacterial community composition was significantly affected by calf’s age and time of weaning.

Conclusions

The present study showed the significant impact of calf’s age and weaning on the establishment of rumen- and oral-specific bacterial communities utilizing buccal swab samples. The results emphasize the possibility of using buccal swab samples as a replacement of complex stomach tube method for large-scale predictive studies on ruminants. For in-depth rumen microbiome studies, the time of sampling should be carefully considered using an active phase of regurgitation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00095-3.

Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia

Reduced reproductive efficiency results in economic losses to the Australian sheep industry. Reproductive success, particularly after artificial insemination, is dependent on a number of contributing factors on both ewe and ram sides. Despite considerable emphasis placed on characterising ewe side contributions, little emphasis has been placed on characterising ram side contributions to conception success. Over 14,000 transcripts are in spermatozoa of other species, which are transferred to the ova on fertilisation. These transcripts conceivably influence early embryonic development and whether conception is successful. Semen was collected (n = 45) across three breeds; Merino, Dohne, and Poll Dorset. Following collection, each ejaculate was split in two; an aliquot was assessed utilising Computer Assisted Semen Analysis (CASA) and the remaining was utilised for RNA extraction and subsequent next-generation sequencing. Overall, 754 differentially expressed genes were identified in breed contrasts and contrast between ejaculates of different quality. Downstream analysis indicated that these genes could play significant roles in a broad range of physiological functions, including maintenance of spermatogenesis, fertilisation, conception, embryonic development, and offspring production performance. Overall results provide evidence that the spermatozoal transcriptome could be a crucial contributing factor in improving reproductive performance as well as in the overall productivity and profitability of sheep industries.

Dynamic progression of the calf's microbiome and its influence on host health

The first year of a calf's life is a critical phase as its digestive system and immunity are underdeveloped. A high level of stress caused by separation from mothers, transportation, antibiotic treatments, dietary shifts, and weaning can have long-lasting health effects, which can reduce future production parameters, such as milk yield and reproduction, or even increase the mortality of calves. The early succession of microbes throughout the gastrointestinal tract of neonatal calves follows a sequential pattern of colonisation and is greatly influenced by their physiological state, age, diet, and environmental factors; this leads to the establishment of region- and site-specific microbial communities. This review summarises the current information on the various potential factors that may affect the early life microbial colonisation pattern in the gastrointestinal tract of calves. The possible role of host-microbe interactions in the development and maturation of host gut, immune system, and health are described. Additionally, the possibility of improving the health of calves through gut microbiome modulation and using antimicrobial alternatives is discussed. Finally, the trends, challenges, and limitations of the current research are summarised and prospective directions for future studies are highlighted.

Characterization of the rumen microbiota and its relationship with residual feed intake in sheep

Feed efficiency is a highly important economic trait in sheep production and has a significant impact on the economic benefits of sheep farming. Microbial fermentation of the rumen has a vital role in the host's nutrition; the rumen microbiota might affect host feed efficiency. However, the relationship between the rumen microbiota and feed efficiency in sheep is unclear. In the present study, the microbiota of 195 Hu sheep was investigated and their residual feed intake (RFI), a commonly used measure of feed efficiency, was determined. From birth, all sheep were subjected to the same management practices. At slaughter, samples of liquid rumen contents were collected and subjected to amplicon sequencing for the 16S rDNA gene on the IonS5™XL platform. To identify the bacterial taxa differentially represented at the genus or higher taxonomy levels, we used linear discriminant analysis coupled with effect size and curve fitting. In the sheep rumen, the four most abundant phyla were Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria; and the dominant genera were unidentified Prevotellaceae, Fibrobacter, unidentified Lachnospiraceae, Saccharofermentans, and Succinivibrio. Pathway analysis of the 16S rDNA sequencing data from the rumen microbiota identified that carbohydrate metabolism was enriched. Using α-diversity analysis, we further identified that Observed species, ACE, Good's coverage, and Chao1 are more abundant (P < 0.01) in the low-RFI (L-RFI) group compared to the high-RFI (H-RFI) group. High-RFI sheep had a higher abundance of three bacterial taxa (Prevotellaceae, Negativicutes, and Selenomonadales), and one taxa was overrepresented in the L-RFI sheep (Succinivibrio), respectively. Furthermore, model fitting showed that Veillonellaceae, Sphaerochaeta, Negativibacillus, Saccharofermentans, and members of the Tenericutes, Kiritimatiellaeota, Deltaproteobacteria, and Campylobacterales were correlated with the sheep RFI classification and thus were indicative of a role in animal efficiency. Tax4Fun analysis revealed that metabolic pathways such as "energy metabolism," "metabolism of cofactors and vitamins," "poorly characterized," and "replication recombination and repair proteins" were enriched in the rumen from H-RFI sheep, and "genetic information processing" and "lipopolysaccharide biosynthesis" were overrepresented in L-RFI sheep rumen. In addition, six Kyoto Encyclopedia of Genes and Genomes orthology pathways were identified as different between H-RFI and L-RFI groups. In conclusion, the low RFI phenotype (efficient animals) consistently (or characteristically) exhibited a more abundant and diverse microbiome in sheep.

Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai-Tibetan Plateau

In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P < 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P < 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 < P < 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

BACKGROUND

Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level.

RESULTS

The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks.

CONCLUSIONS

Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

Effects of dietary energy levels on rumen fermentation, microbiota, and gastrointestinal morphology in growing ewes

This study investigated whether dietary metabolizable energy (ME) could generate dynamical effects on rumen fermentation, gastrointestinal tract (GIT) morphology, and microbial composition of growing ewes. A total of twenty-eight female Hu lambs were randomly allotted to two treatments with different dietary ME levels: 9.17 (FEA) and 10.41 MJ/kg (FEB). These lambs were further made ready for a 67-day feeding trial. Results showed that the molar proportions of butyrate (p = .020), iso-valerate (p = .028), and valerate (p = .005) were significantly higher in the FEB group than those in the FEA group. The results of the GIT morphologic properties showed that the villus height (VH) (p = .005) was significantly higher and crypt depth was significantly deeper (CD) (p = .005) in the duodenum and that the rumen papillary height (PH) was significantly higher (p = .020) in FEB group compared with the FEA group. High-throughput sequencing results showed that 1826 operational taxonomic units (OTUs) were obtained and that the OTU number (p = .039), the ACE (p = .035), and Chao1 indices (p = .005) were lower in the FEB group. Moreover, 76 genera belonging to 21 phyla were detected in all samples; the relative abundance of Papillibacter (p = .036) and Flexilinea (p = .046) was significantly lower in the high energy group, whereas the relative abundance of unidentified Lachnospiraceae (p = .019), Acetitomaculum (p = .029), unidentified Veillonellaceae (p = .017), Anaerovibrio (p = .005), and Succinivibrio (p = .035) was significantly higher in the FEB group at the genus level. Furthermore, the relative abundance of genes and metabolic pathways were predicted by PICRUSt. The relative abundance of gene families related to carbohydrate metabolism was particularly higher (p = .027) in the FEB group. In summary, these results reveal that the dietary energy levels altered the composition and function of rumen microbiota and GIT morphology in growing female Hu sheep and provide a reference for optimizing diet formula and 10.41MJ/kg of ME level has been recommended in the growing period.

Chopping Roughage Length Improved Rumen Development of Weaned Calves as Revealed by Rumen Fermentation and Bacterial Community

Roughage particle size can influence rumen development, which is also determined by rumen microorganisms and their metabolic end-products. Therefore, the aim of this study was to evaluate the comprehensive effects of roughage length and rumen bacterial community on the rumen development of weaned calves. A total of thirty-six weaned Angus female calves (125 ± 3 d; 161.2 ± 13.0 kg) were randomly assigned to three diets differing in roughage particle size: 4 cm (short length); 24 cm (medium length); and 44 cm (long length). Results showed that chopping roughage increased dry matter intake and organic matter apparent digestibility; altered rumen fermentation indicated by the increased rumen butyrate and valerate concentrations; and increased plasma glucose, cholesterol, and total protein. Chopping roughage affected rumen bacterial community, as indicated by altering the diversity indices; by increasing ruminal bacteria Papillibacter and Eubacterium_hallii_group, which are involved in butyrate production; and by increasing Synergistetes and Mogibacterium, which are involved in bacterial colonization. In conclusion, chopping roughage at 4 cm was shown to improve the rumen bacterial community, alter rumen fermentation, eventually promote the development of rumen.

Milk Replacer Supplementation Ameliorates Growth Performance and Rumen Microbiota of Early-Weaning Yimeng Black Goats

Increasing evidence has indicated the ameliorative effect of milk replacer supplementation in ruminants for regulating their early growth and rumen development. However, it is still unclear whether milk replacer supplementation has a beneficial role in the growth performance and rumen microbiota of Yimeng black goats (YBGs). Therefore, this study was performed to investigate the effects of milk replacer on growth performance and rumen microbiota of YBGs. Our results revealed that milk replacer supplementation could significantly improve the growth performance of YBGs. Additionally, the results of alpha and beta diversities indicated that there was no significant difference in richness and diversity between the control and milk replacer-treated YBGs. At the phylum level, Bacteroidetes, Firmicutes, and Proteobacteria were the most dominant phyla in all the samples at different stages. Moreover, the YBGs treated with milk replacer possessed a higher abundance of Verrucomicrobia than that in the control YBGs, while the level of Actinobacteria was obviously decreased. It is noteworthy that the abundance of Proteobacteria in the control YBGs was higher than that in the YBGs supplemented with milk replacer throughout the experiment. At the level of genus, the differences in the richness between control and milk replacer supplement YBGs were gradually observed. Compared with the control YBGs, the proportion of Akkermansia, Veillonella, Anaerovibrio, Ruminococcaceae_NK4A214_group, Ruminococcus_1, and Ruminococcus_2 was increased in the YBGs treated with milk replacer, whereas Turicibacter was decreased. In conclusion, milk replacer supplementation may serve as a good applicant for ameliorating early YBGs development and rumen microbiota.

Dihydropyridine Enhances the Antioxidant Capacities of Lactating Dairy Cows under Heat Stress Condition

Simple Summary

Additives contribute to improving the health of dairy cows, enhancing antioxidative capacities, and/or increasing milk production, etc. To alleviate the harmful effects of heat stress on dairy cows, a few feed additives studies have been conducted. Dihydropyridine has been used as a feed additive in dairy cow diets. However, the underlying mechanisms of its beneficial effects still remain unclear. In the present study, dairy cows were randomly divided into a control group and a dihydropyridine treatment group under heat stress in summer. The rumen and blood samples of dairy cows were collected to determine the changes in their antioxidative capacities. Meanwhile, the effects of dihydropyridine on ruminal microbial communities were also analyzed. Our data demonstrated that dihydropyridine enhanced the antioxidative capacities of dairy cows under heat stress conditions.

Abstract

Heat stress (HS), a nonspecific response to environmental heat, can seriously affect dairy cow health. Feed additives may alleviate HS in dairy cows by improving rumen fermentation efficacy, stimulating feed consumption, enhancing vasodilation, and/or improving antioxidant capacity. The temperature–humidity index (THI) indicates that spring is a non-HS season, and summer is an HS season. HS results in the decrease in dairy cow antioxidant capacities. Our results indicated the decrease in superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT), and total antioxidation (T-AOC) levels and the increase in malondialdehyde (MDA) level during HS season. Meanwhile, antioxidant indexes (SOD, GSH-Px, and T-AOC) were positively correlated with milk yield (p < 0.01), whereas MDA exhibited a significant negative correlation with milk yield (p < 0.05). In addition, the effects of dihydropyridine (DHP) on antioxidant capacity and ruminal microbial communities in dairy cows under HS were investigated. During summer, dairy cows were randomly assigned into two groups under HS, including a standard diet (S-ND) group and standard diet with 3 g/day/cow DHP (S-D) group. DHP treatment significantly restored SOD and GSH-Px levels under HS. Denaturing gradient gel electrophoresis results indicated that the DHP altered ruminal bacterial community mainly composed Proteobacteria and Firmicutes in dairy cows under HS. Our results suggest that DHP can enhance the antioxidant abilities of dairy cows with favorable effects on ruminal microbial communities under HS, further alleviating HS on dairy cows.

The functional development of the rumen is influenced by weaning and associated with ruminal microbiota in lambs

Rumen development is critical for the development of early lambs. This work aims to evaluate the effects of abrupt weaning at day 21 on rumen fermentation, histomorphological traits and the ruminal microbiota compared with continuous suckling. Twelve pairs of artificially reared full-sib neonatal male Hu lambs were allocated to two groups, one of which was weaned at day 21 (EW group) and the other which was not weaned (CON group). At day 26 and day 49, six lambs from each group were randomly selected and sacrificed to collect ruminal contents and rumen tissue samples. Results showed that weaning influenced the fermentation parameters in the rumen, and altered the microbial community composition on day 49 (p < 0.05). Several genera were associated with rumen fermentation parameters (p < 0.05). Volatile fatty acid (VFA) concentration is the key parameter impacting microbiota composition. Weaning influenced the expression of genes associated with VFA metabolism and regulation of cell proliferation (p < 0.05). In conclusion, weaning significantly influenced the morphological and functional development of the rumen, and bacterial community composition. The microbial community composition was strongly associated with rumen weight and fermentation profiles, but not with morphological development.

Shrub coverage alters the rumen bacterial community of yaks (Bos grunniens) grazing in alpine meadows

Proliferation of shrubs at the expense of native forage in pastures has been associated with large changes in dry-matter intake and dietary components for grazing ruminants. These changes can also affect the animals’ physiology and metabolism. However, little information is available concerning the effect of pastoral-shrub grazing on the rumen bacterial community. To explore rumen bacteria composition in grazing yaks and the response of rumen bacteria to increasing shrub coverage in alpine meadows, 48 yak steers were randomly assigned to four pastures with shrub coverage of 0%, 5.4%, 11.3%, and 20.1% (referred as control, low, middle, and high, respectively), and ruminal fluid was collected from four yaks from each pasture group after 85 days. Rumen fermentation products were measured and microbiota composition determined using Ion S5^TM XL sequencing of the 16S rRNA gene. Principal coordinates analysis (PCoA) and similarity analysis indicated that the degree of shrub coverage correlated with altered rumen bacterial composition of yaks grazing in alpine shrub meadows. At the phyla level, the relative abundance of Firmicutes in rumen increased with increasing shrub coverage, whereas the proportions of Bacteroidetes, Cyanobacteria and Verrucomicrobia decreased. Yaks grazing in the high shrub-coverage pasture had decreased species of the genus Prevotellaceae UCG-001, Lachnospiraceae XPB1014 group, Lachnospiraceae AC2044 group, Lachnospiraceae FCS020 group and Fretibacterium, but increased species of Christensenellaceae R-7 group, Ruminococcaceae NK4A214 group, Ruminococcus 1, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005 and Lachnospiraceae UCG-008. These variations can enhance the animals’ utilization efficiencies of cellulose and hemicellulose from native forage. Meanwhile, yaks grazed in the high shrub-coverage pasture had increased concentrations of ammonia nitrogen (NH₃-N) and branched-chain volatile fatty acids (isobutyrate and isovalerate) in rumen compared with yaks grazing in the pasture without shrubs. These results indicate that yaks grazing in a high shrub-coverage pasture may have improved dietary energy utilization and enhanced resistance to cold stress during the winter. Our findings provide evidence for the influence of shrub coverage on the rumen bacterial community of yaks grazing in alpine meadows as well as insights into the sustainable production of grazing yaks on lands with increasing shrub coverage on the Qinghai-Tibet Plateau.

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves

Mulberry leaves, which have high nutritional value, have not been fully utilized. Few research systems have indicated whether mulberry leaves can replace traditional feed ingredients in goats. In this study, we investigated the effects of feeding white cashmere goats ensiled (Group E) or sun-dried mulberry leaves (Group S) on changes in ruminal microbial communities, rumen fermentation parameters and serum biochemical indices. The control group (Group C) received a typical total mixed ration (TMR). 16S rRNA gene sequencing revealed 209 genera belonging to 19 bacterial phyla dominated by Firmicutes and Bacteroidetes. Only the relative abundances of Erysipelotrichaceae_UCG-009 were significantly different among the three groups (p < 0.05). Physiological and biochemical findings revealed that only the serum leptin concentrations were significantly decreased when mulberry leaves were added to the diets (p < 0.05). Correlation analysis revealed that Ruminococcus_2 were significantly positively correlated with the butyrate concentration. These findings suggested that supplementation with mulberry leaves only induced minor changes in the abovementioned indicators, implying that the rumen fermentation status was still stable after adding mulberry leaves to the diets.

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs

Early supplementary feeding of lambs before weaning is important to meet their nutritional needs, promote the development of rumen and improve performance. To study the effect of early supplementary feeding on rumen development and the microbiota of lambs, 22 Hu lambs were randomly divided into two groups: one group was fed with milk replacer (group C), and the other group was fed with milk replacer and starter (group S). At 28 days, six lambs in each group were slaughtered, and the rumen content and tissue samples were collected for detection and analysis. The starter significantly promoted the length of rumen papilla (P = 0.03), the concentration of acetate, propionate, butyrate and total volatile fatty acids (TVFA) (P < 0.01), which were higher in group S compared with group C. Group C had a higher rumen microbial diversity than group S. The dominant bacteria in the two groups were the same (Bacteroidetes, Firmicutes and Proteobacteria); however, they differed notably at the genus level. The microbial abundance of the two groups was significantly different for 22 species. In group C, the first three dominant bacteria were Bacteroides, Porphyromonas, and Campylobacter, while in group S they were Succinivibrio, unidentified_Prevotellaceae, and unidentified_Lachnospiraceae. Spearman correlation analysis showed that some ruminal bacteria were closely related to internal environmental factors, e.g., the relative abundances of unidentified_Bacteria, Euryarchaeota, Fusobacteria, and Gracilibacteria correlated negatively with acetate, propionate, butyrate, and TVFA (P < 0.05), while the relative abundances of Firmicutes correlated positively with acetate, propionate, butyrate and TVFA (P < 0.05). Bacteroidetes correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Synergistetes correlated negatively with acetate, propionate, and butyrate (P < 0.05); Deinococcus-Thermus correlated negatively with propionate, butyrate, and TVFA (P < 0.05); Spirochaetes correlated negatively with propionate and TVFA (P < 0.05); and Elusimicrobia correlated negatively with propionate and butyrate (P < 0.05). Actinobacteria and Verrucomicrobia correlated positively correlated with NH₃-N. In conclusion, supplementary feeding of lambs before weaning promoted the development of rumen tissue morphology and rumen microorganisms.

Co-modulation of Liver Genes and Intestinal Microbiome of Largemouth Bass Larvae (Micropterus salmoides) During Weaning

In recent years, largemouth bass have become one of the most commonly aquacultured species in China, however, its low survival rate during larval weaning has always been a bottleneck that has restricted industrial development. Understanding the changes in liver metabolism and intestinal microflora during the weaning of largemouth bass larvae can help to design better weaning strategies and improve survival. In this study, liver mRNA and intestinal microflora 16S rRNA genes were analyzed using high-throughput sequencing at the pre, mid, and post weaning stages [15, 30, 45 days post hatching; total length (cm) were 2.21 ± 0.12, 3.45 ± 0.21, 5.29 ± 0.33, respectively]. The transcriptome results revealed that the genes with increased expression were related to amino acid metabolism in the pre-weaning stage, but they were related to fatty acid metabolism in the post-weaning stage. A similar phenomenon was observed in the intestinal microflora where the dominant microbe Proteobacteria (relative abundance 56.32%) in the pre-weaning stage was gradually replaced by Firmicutes (relative abundance 62.81%) by the post-weaning stage. In addition, the three most important digestive enzymes (trypsin, lipase, and amylase) in the intestine were significantly decreased during the mid-weaning stage (P < 0.05), which was also true for some genes crucial to immune pathways in the liver. Overall, these findings showed that weaning in largemouth bass can cause changes in liver metabolism and intestinal microbial communities, which has improved our understanding of fish adaptation to changes in food sources during weaning.

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep

The tolerance of ruminants to gossypol, a natural phenolic compound derived from the cotton plant, is greater than that of monogastric animals, partially because of the gossypol-degrading bacteria in the rumen of the ruminants. In this study, we aimed to examine the effect of gossypol supplementation on fermentation characteristics, bacterial α-diversity and community structure in the rumen fluid of sheep to analyse the change of bacterial in response to gossypol. 8 sheep with permanent fistula were randomly divided into 2 groups, a control and gossypol acetate supplementation groups. Sheep in the latter group were supplemented with gossypol acetate at the levels of 600 mg and 1,200 mg/animal per day during the first (S1, days 1 to 27) and subsequent (S2, days 28 to 47) stages. Gossypol supplementation significantly increased the molar proportion of acetate, and decreased the molar proportion of isobutyric acid, butyric acid, and isovaleric acid in the rumen fluid. Gossypol supplementation have no significant effect on bacterial diversity in the rumen fluid. At the phylum level, gossypol had no effect on bacterial community. At the genus level, gossypol supplementation significantly increased the relative abundance of Treponema_2. However, there were no significant differences in the relative abundance of dominant bacterial genera. In conclusion, gossypol supplementation had an effect on molar proportion of acetate, isobutyric acid, butyric acid, and isovaleric acid, but had no significant effect on the bacterial diversity and relative abundance of dominant bacteria in rumen fluid of sheep.

Effect of Alfalfa Hay and Starter Feeding Intervention on Gastrointestinal Microbial Community, Growth and Immune Performance of Yak Calves

The present study aims to evaluate the effects of different early weaning paradigms, which supplied with extra alfalfa hay, or starter feeding, or both alfalfa hay and starter feeding, along with the milk replacer, on the gastrointestinal microbial community, growth, and immune performance of yak calves. Twenty 30-day-old male yak calves were randomly assigned to four groups, including the control (CON), alfalfa hay (A), starter feeding (S), and starter plus alfalfa hay (SA) groups. The gastrointestinal microbial colonization, the gastrointestinal development and function, and the growth and immune performance of all the yak calves were separately measured. Supplementation with alfalfa and starter feeding during the pre-weaning period significantly increased body weight, body height, body length, and chest girth. The significantly improved rumen fermentation and promoted intestinal digestion-absorption function in alfalfa and starter feeding groups, including the identified significantly increased concentrations of ruminal total volatile fatty acid (VFA); the significantly increased concentrations and proportions of acetate, butyrate, and isovalerate; the increased α-amylase activities in the duodenum, jejunum, and ileum; the increased papillae length and width of rumen epithelium and rumen wall thickness; and the increased villus height and crypt depth of the duodenum, jejunum, and ileum, could all contribute to promote the growth of calves. These significant improvements on rumen fermentation and intestinal digestion-absorption function could be further attributed to the increased proliferation of starch-decomposing, and cellulose- or hemicellulose-decomposing bacteria identified in the rumen, jejunum, and ileum. Furthermore, based on the expression of intestinal inflammatory cytokines and the rumen epithelial RNA sequencing results, alfalfa supplementation reduced the occurrence of ruminal and intestinal inflammation, whereas starter feeding supplementation was mainly beneficial to the differentiation of immune cells and the improved immune function. Meanwhile, the significantly altered relative abundances of genera in the SA group, including increased relative abundance of Limnobacter, Escherichia/Shigella, and Aquabacterium in the rumen and increased relative abundance of Coprococcus, Pseudobutyrivibrio, Flavonifractor, Synergistes, and Sutterella in jejunum, were able to reduce gastrointestinal inflammation and enhance the immune function, which enhanced the immune function of the yak calves fed with alfalfa and starter feeding. Overall, milk replacer supplemented with alfalfa and starter feeding during the pre-weaning period could alter gastrointestinal microbiota and then benefit the gastrointestinal development, digestion-absorption function, growth, and immune performance of the yak calves.

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians

BACKGROUND

African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia.

RESULTS

We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids.

CONCLUSIONS

These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.

Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

Maternal versus artificial rearing shapes the rumen microbiome having minor long-term physiological implications

Increasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak.