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The rumen is the largest of the four chambers of the “stomach” in ruminant animals, which harbors an incredibly dense, diverse, and dynamic microbial community crucial for feedstuff degradation, animal health, and production. The primary objective of this article is to enhance knowledge and comprehension of rumen microbiology by providing an introductory-level overview of the field of rumen microbiology. Ruminants possess a distinctive digestive system optimized for the microbial breakdown of complex plant materials. The ruminant ”stomach” consists of four chambers (e.g., reticulum, rumen, omasum, and abomasum), which is home to a microbial population that degrades feedstuffs consumed by ruminant animals. Dr. Robert Hungate and Dr. Marvin Bryant’s groundbreaking research in the 1960s laid the foundation for understanding the function of the ruminal microbial ecosystem. Recent advancements (e.g., next-generation sequencing) have provided the field with deeper insight into populations, boosting our understanding of how the microbial population of the rumen functions in a variety of conditions. The ruminal microbial ecosystem is comprised of bacteria, along with archaea, protozoa, bacteriophage, and fungi, each contributing to the symbiotic relationship between the microbial ecosystem and the host animal that is essential for optimal animal health and efficient animal production. Traditional anaerobic growth techniques have facilitated the study of individual anaerobic bacteria but have been limited by dependence on growth in laboratory conditions. The development of 16S rRNA sequencing allows the identification of microbial populations that cannot be grown and allows an unbiased view of microbial diversity. Diet shapes the rumen microbial population composition, influencing animal production metrics such as feed efficiency, methane emissions, and immunological functions. Feed additives (e.g., essential oils, eubiotics) hold promise by manipulating and unraveling the microbial biochemical potential for improving animal health, feed efficiency, environmental impacts, and overall production sustainability. Future research impacts include the development of probiotics, prebiotics, and genetic strategies for optimizing the rumen microbiome’s multifaceted impacts.

A 21-d experiment was conducted to study the effect of xylanase, protease, and xylo-oligosaccharides on growth performance, nutrient utilization, gene expression of nutrient transporters, cecal short-chain fatty acids (SCFA), and cecal microbiota profile of broilers challenged with mixed Eimeria spp. The study utilized 392 zero-d-old male broiler chicks allocated to 8 treatments in a 4 × 2 factorial arrangement, as follows: corn-soybean meal diet with no enzyme (Con); Con plus xylanase alone (XYL); Con plus xylanase combined with protease (XYL + PRO); or Con plus xylo-oligosaccharides (XOS); with or without Eimeria challenge. Diets were based on a high-fiber (100 g/kg soluble fibers and 14 g/kg insoluble fibers) basal diet. At d 15, birds in challenged treatment were gavaged with a solution containing Eimeria maxima, Eimeria acervulina, and Eimeria tenella oocysts. At d 21, birds were sampled. Eimeria depressed (P

Abstract Impaired gut homeostasis is associated with stroke often presenting with leaky gut syndrome and increased gut, brain, and systemic inflammation that further exacerbates brain damage. We previously reported that intracisternal administration of Tanshinone IIA-loaded nanoparticles (Tan IIA-NPs) and transplantation of induced pluripotent stem cell-derived neural stem cells (iNSCs) led to enhanced neuroprotective and regenerative activity and improved recovery in a pig stroke model. We hypothesized that Tan IIA-NP + iNSC combination therapy-mediated stroke recovery may also have an impact on gut inflammation and integrity in the stroke pigs. Ischemic stroke was induced, and male Yucatan pigs received PBS + PBS (Control, n = 6) or Tan IIA-NP + iNSC (Treatment, n = 6) treatment. The Tan IIA-NP + iNSC treatment reduced expression of jejunal TNF-α, TNF-α receptor1, and phosphorylated IkBα while increasing the expression of jejunal occludin, claudin1, and ZO-1 at 12 weeks post-treatment (PT). Treated pigs had higher fecal short-chain fatty acid (SCFAs) levels than their counterparts throughout the study period, and fecal SCFAs levels were negatively correlated with jejunal inflammation. Interestingly, fecal SCFAs levels were also negatively correlated with brain lesion volume and midline shift at 12 weeks PT. Collectively, the anti-inflammatory and neuroregenerative treatment resulted in increased SCFAs levels, tight junction protein expression, and decreased inflammation in the gut.

Pediatric traumatic brain injury (TBI) is a leading cause of death and disability in children. Due to bidirectional communication between the brain and gut microbial population, introduction of key gut bacteria may mitigate critical TBI-induced secondary injury cascades, thus lessening neural damage and improving functional outcomes. The objective of this study was to determine the efficacy of a daily fecal microbial transplant (FMT) to alleviate neural injury severity, prevent gut dysbiosis, and improve functional recovery post TBI in a translational pediatric piglet model. Male piglets at 4-weeks of age were randomly assigned to Sham + saline, TBI + saline, or TBI + FMT treatment groups. A moderate/severe TBI was induced by controlled cortical impact and Sham pigs underwent craniectomy surgery only. FMT or saline were administered by oral gavage daily for 7 days. MRI was performed 1 day (1D) and 7 days (7D) post TBI. Fecal and cecal samples were collected for 16S rRNA gene sequencing. Ipsilateral brain and ileum tissue samples were collected for histological assessment. Gait and behavior testing were conducted at multiple timepoints. MRI showed that FMT treated animals demonstrated decreased lesion volume and hemorrhage volume at 7D post TBI as compared to 1D post TBI. Histological analysis revealed improved neuron and oligodendrocyte survival and restored ileum tissue morphology at 7D post TBI in FMT treated animals. Microbiome analysis indicated decreased dysbiosis in FMT treated animals with an increase in multiple probiotic Lactobacilli species, associated with anti-inflammatory therapeutic effects, in the cecum of the FMT treated animals, while non-treated TBI animals showed an increase in pathogenic bacteria, associated with inflammation and disease such in feces. FMT mediated enhanced cellular and tissue recovery resulted in improved motor function including stride and step length and voluntary motor activity in FMT treated animals. Here we report for the first time in a highly translatable pediatric piglet TBI model, the potential of FMT treatment to significantly limit cellular and tissue damage leading to improved functional outcomes following a TBI.

In recent years, there has been an exponential increase in the number of papers that have investigated the microbiome of animals and humans [...]

The catabolic activity of the ruminal microbial community of cattle enables the conversion of low-quality feedstuffs into meat and milk. The rate at which this conversion occurs is termed feed efficiency, which is of crucial importance given that feed expenses account for up to 70% of the cost of animal production. The present study assessed the relationship between cattle feed efficiency and the composition of their ruminal microbial communities during the feedlot finishing period. Angus steers (n = 65) were fed a feedlot finishing diet for 82 days and their growth performance metrics were evaluated. These included the dry matter intake (DMI), average daily gain (ADG), and residual feed intake (RFI). Steers were rank-ordered based upon their RFI, and the five lowest RFI (most efficient) and five highest RFI (least efficient) steers were selected for evaluations. Ruminal fluid samples were collected on days 0 and 82 of the finishing period. Volatile fatty acids (VFA) were quantified, and microbial DNA was extracted and the 16S rRNA gene was sequenced. The results showed that the ADG was not different (p = 0.82) between efficiency groups during the 82-day feedlot period; however, the efficient steers had lower (p = 0.03) DMI and RFI (p = 0.003). Less-efficient (high RFI) steers developed higher (p = 0.01) ruminal Methanobrevibacter relative abundances (p = 0.01) and tended (p = 0.09) to have more Methanosphaera. In high-efficiency steers (low RFI), the relative abundances of Ruminococcaceae increased (p = 0.04) over the 82-day period. The molar proportions of VFA were not different between the two efficiency groups, but some changes in the concentration of specific VFA were observed over time. The results indicated that the ruminal microbial populations of the less-efficient steers contained a greater relative abundance of methanogens compared to the high-efficiency steers during the feedlot phase, likely resulting in more energetic waste in the form or methane and less dietary energy being harvested by the less-efficient animals.

ABSTRACT: A total of 392 Cobb 500 off-sex male broiler chicks were used in a 21-day experiment to study the effect of protease, xylanase, and xylo-oligosaccharides (XOS) on improving growth performance, nutrient utilization (ileal digestibility and total tract retention), gene expression of nutrient transporters, cecal short-chain fatty acids (SCFAs), and microbiota profile of broilers challenged with Eimeria spp. Chicks at 0-day old were allocated to 8 treatments in a 4 × 2 factorial arrangement: 1) corn-soybean meal diet with no enzyme (Con); 2) Con plus 0.2 g/kg protease alone (PRO); 3) Con plus 0.2 g/kg protease combined with 0.1 g/kg xylanase (PRO + XYL); or 4) Con plus 0.5 g/kg xylo-oligosaccharides (XOS); with or without Eimeria challenge. The 4 diets were formulated to be marginally low in crude protein (183 g/kg). Challenged groups were inoculated with a solution containing E. maxima, E. acervulina, and E. tenella oocysts on d 15. Eimeria depressed (P < 0.01) growth performance and nutrient utilization. Supplemental protease improved (P < 0.05) body weight gain and feed intake in the prechallenge phase (d 0–15) but had no effect during the infection period (d 15–21). There was no interaction between infection and feed supplementation for nutrient utilization. The supplementations of either PRO or XOS alone increased (P < 0.01) total tract retention of Ca and tended (P < 0.1) to improve total tract retention of N, P, AME, and AMEn. Eimeria decreased (P < 0.05) expressions of GLUT2, GLUT5, PepT1, ATP2B1, CaSR, Calbidin D28K, NPT2, and ZnT1 but increased (P < 0.01) expression of GLUT1. XOS supplementation increased (P < 0.05) ATP2B1 expression. Protease decreased (P < 0.05) isobutyrate concentration in unchallenged treatments but not in challenged treatments. Eimeria decreased (P < 0.01) cecal saccharolytic SCFAs acetate and propionate but increased (P < 0.01) branched-chain fatty acid isovalerate. The supplementation of PRO + XYL or XOS increased (P < 0.05) cecal butyrate or decreased cecal isobutyrate concentrations, respectively. PRO + XYL and XOS decreased cecal protein levels in unchallenged birds but not challenged ones. Eimeria challenge significantly (P < 0.05) decreased the microbial richness (Observed features) and diversity (Shannon index and phylogenetic diversity) and changed the microbial composition by reducing the abundance of certain bacteria, such as Ruminococcus torques, and increasing the abundance of others, such as Anaerostipes. In contrast, none of the additives had any significant effect on the cecal microbial composition. In conclusion, PRO or XOS supplementation individually improved nutrient utilization. All the additives decreased the cecal content of branched-chain fatty acids, consistent with decreased cecal N concentration, although the effects were more pronounced in unchallenged birds. In addition, none of the feed additives impacted the Eimeria-induced microbial perturbation.

Abstract Bovine fescue toxicosis (FT) is caused by grazing ergot alkaloid-producing endophyte (Epichloë coenophiala)-infected tall fescue. Endophyte’s effects on the animal’s microbiota and metabolism were investigated recently, but its effects in planta or on the plant–animal interactions have not been considered. We examined multi-compartment microbiota–metabolome perturbations using multi-‘omics (16S and ITS2 sequencing, plus untargeted metabolomics) in Angus steers grazing non-toxic (Max-Q) or toxic (E+) tall fescue for 28 days and in E+ plants. E+ altered the plant/animal microbiota, decreasing most ruminal fungi, with mixed effects on rumen bacteria and fecal microbiota. Metabolic perturbations occurred in all matrices, with some plant-animal overlap (e.g., Vitamin B6 metabolism). Integrative interactomics revealed unique E+ network constituents. Only E+ had ruminal solids OTUs within the network and fecal fungal OTUs in E+ had unique taxa (e.g., Anaeromyces). Three E+-unique urinary metabolites that could be potential biomarkers of FT and targeted therapeutically were identified.

The objective of this study was to determine the impact of varying dietary manganese and selenium concentrations, antioxidant cofactors, on the growth performance and fecal microbial populations of nursery pigs. The piglets (N = 120) were blocked by weight (5.22 ± 0.7 kg) and sex. The pens (n = 5/treatment) within a block were randomly assigned to diets in a 2 × 3 factorial design to examine the effects of Se (0.1 and 0.3 mg/kg added Se) and Mn (0, 12, and 24 mg/kg added Mn) and were fed in three phases (P1 = d 1–7, P2 = d 8–21, P3 = d 22–35). The pigs and orts were weighed weekly. Fecal samples were collected d 0 and 35 for 16S rRNA bacterial gene sequencing and VFA analysis. The data were analyzed as factorial via GLM in SAS. There was a linear response (p < 0.05) in overall ADG across dietary Mn. Supplementing 24 mg/kg Mn tended to decrease (p < 0.10) the relative abundance of many bacteria possessing pathogenic traits relative to Mn controls. Meanwhile, increasing Mn concentration tended to foster the growth of bacteria correlated with gut health and improved growth (p < 0.10). The data from this study provide preliminary evidence on the positive effects of manganese on growth and gut health of nursery pigs.

This study was conducted to investigate the effects of different dosages of tannic acid (TA) on growth performance, nutrient digestibility, gut health, immune system, oxidative status, microbial composition, volatile fatty acids (VFA), bone mineral density, and fat digestion and accumulation in broilers and to find optimal dosages of TA for efficient growth and gut health in broilers. A total of 320 male Cobb500 broilers were randomly distributed to 4 treatments with 8 replicates including 1) tannic acid 0 (TA0): basal diet without TA; 2) tannic acid 0.5 (TA0.5): basal diet with 0.5 g/kg TA; 3) tannic acid 1.5 (TA1.5); and 4) tannic acid 2.5 (TA2.5). Supplemental TA at levels greater than 972 mg/kg tended to reduce BW on D 21 (p = 0.05). The TA2.5 had significantly lower apparent ileal digestibility (AID) of crude protein compared to the TA0 group. The AID of ether extract tended to be reduced by TA at levels greater than 525 mg/kg (p = 0.08). The jejunal lipase activities tended to be reduced by TA at levels less than 595.3 mg/kg (p = 0.09). TA linearly decreased goblet cell density in the crypts of the jejunum (p < 0.05) and reduced mRNA expression of mucin two at levels less than 784.9 mg/kg and zonula occludens two at levels less than 892.6 mg/kg (p < 0.05). The TA0.5 group had higher activities of liver superoxide dismutase compared to the TA0 group (p < 0.05). Bone mineral density and contents tended to be linearly decreased by TA (p = 0.05), and the ratio of lean to fat was linearly decreased (p < 0.01). Total cecal VFA production tended to be linearly reduced by TA at levels greater than 850.9 mg/kg (p = 0.07). Supplemental TA tended to increase the relative abundance of the phylum Bacteroidetes (p = 0.1) and decrease the relative abundance of the phylum Proteobacteria (p = 0.1). The relative abundance of the family Rikenellaceae was the lowest at 500 mg/kg TA, and the relative abundance of the family Bacillaceae was the highest at 1,045 mg/kg TA. Collectively, these results indicate that the optimum level of supplemental TA would range between 500 and 900 mg/kg; this range of TA supplementation would improve gut health without negatively affecting growth performance in broilers under antibiotic-free conditions.

Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.

Fescue toxicosis is caused by grazing ergot alkaloid-producing endophyte (Epichloë coenophiala)-infected tall fescue (E+). Summer grazing of E+ leads to decreased productivity, associated impaired thermoregulation, and altered behavior. The goal of this study was to determine the role of E+ grazing-climate interaction on animal behavior and thermoregulation during late fall. Eighteen Angus steers were placed on nontoxic (NT), toxic (E+) and endophyte-free (E−) fescue pastures for 28 days. Physiological parameters, such as rectal temperature (RT), respiration rate (RR), ear and ankle surface temperature (ET, AT), and body weights, were measured. Skin surface temperature (SST) and animal activity were recorded continuously with temperature and behavioral activity sensors, respectively. Environmental conditions were collected using paddocks-placed data loggers. Across the trial, steers on E+ gained about 60% less weight than the other two groups. E+ steers also had higher RT than E− and NT, and lower SST than NT post-pasture placement. Importantly, animals grazing E+ spent more time lying, less time standing, and took more steps. These data suggest that late fall E+ grazing impairs core and surface temperature regulation and increases non-productive lying time, which may be partly responsible for the observed decreased weight gains.

Numerous studies have examined the link between the presence of specific gastrointestinal bacteria and the feed efficiency of cattle. However, cattle undergo dietary changes during their productive life which can cause fluctuations in their microbial consortium. The objective of the present study was to assess changes in the fecal microbiome of beef steers genetically selected to be divergent in feedlot feed efficiency, to determine whether differences in their fecal microbiomes could be detected as early as weaning, and continued throughout the rearing process regardless of dietary changes. Fecal samples were collected at weaning, yearling age, and slaughter for a group of 63 steers. Based on their feedlot-finishing performance, the steers were selected and divided into two groups according to their residual feed intake (RFI): efficient steers (low-RFI; n = 7) and inefficient steers (high-RFI; n = 8). To ascertain the fecal microbial consortium and volatile fatty acid (VFA) content, 16S rRNA gene sequencing and VFA analysis were performed. Overall, bacterial evenness and diversity were greater at weaning compared to yearling and slaughter for both efficiency groups (P < 0.001). Feedlot RFI linearly decreased as both Shannon diversity and Ruminococcaceae abundance increased (R2 = 65.6 and 60.7%, respectively). Abundances of Ruminococcaceae, Rikenellaceae, and Christensenellaceae were higher at weaning vs. yearling age and slaughter (P < 0.001); moreover, these families were consistently more abundant in the feces of the low-RFI steers (for most of the timepoints evaluated; P ≤ 0.05), compared to the high-RFI steers. Conversely, abundances of Bifidobacteriaceae were numerically higher in the feces of the high-RFI steers throughout their lifespan. Total VFA concentrations increased at slaughter compared to weaning and yearling for both efficiency groups (P < 0.001). The acetate:propionate ratio decreased linearly (P < 0.001) throughout the life of the steers regardless of their efficiency, reflective of dietary changes. Our results indicate that despite fluctuations due to animal age and dietary changes, specific bacterial families may be correlated with feed efficiency of steers. Furthermore, such differences may be identifiable at earlier stages of the production cycle, potentially as early as weaning.

This study investigated the use of carbadox in the diet of nursery pigs. Ten pens of weanling piglets were assigned to 2 treatments: one containing carbadox and another without it. From days 21 to 35 of age, the first group of piglets was fed carbadox at 55 mg/kg of diet; followed by 27.5 mg/kg from days 36 to 49; and 0 mg/kg from days 50 to 63. The second group of pigs was fed a control diet without carbadox from days 21 to 63 of age. On days 35, 49, and 63, fecal samples were collected directly from the rectum of 2 piglets in each pen, and the samples were subjected to microbial DNA sequencing and metagenomic functional analysis using the 16S rRNA gene. Feed conversion from days 21 to 63 was improved (P = 0.04) in the group of piglets fed carbadox. Faith's phylogenetic diversity was similar (P = 0.89) for both groups of piglets on day 35, but it was diminished (P = 0.01) in the carbadox-fed group on day 49; however, following the complete removal of carbadox from their diets, this microbial diversity index was once again found to be similar (P = 0.27) in both groups on day 63. Likewise, abundances of Slackia, Peptococcus, Catenibacterium, Coprococcus, and Blautia were all similar between the two groups (P ≥ 0.40) on day 35, but were smaller in the carbadox group (P ≤ 0.05) on day 49; however, on day 63, abundances of all these genera were once again similar (P ≥ 0.29). Metabolic pathways involved in cellular growth, death, and genetic information processing (translation) were found to be similarly expressed in the microbiota of piglets from both groups on day 35 (P ≥ 0.52), but decreased in the carbadox group on day 49 (P ≤ 0.05), and were similar again in both groups on day 63 (P ≥ 0.51). These results revealed that feeding carbadox to piglets during the first 4 weeks after weaning significantly affected their fecal microbiotas; however, 2 weeks after the removal of carbadox, those changes tended to disappear, indicating that the shifts were carbadox-dependent.

Dynamic changes in the oral microbiome have gained attention due to their potential diagnostic role in neurological diseases such as Alzheimer’s disease and Parkinson’s disease. Traumatic brain injury (TBI) is a leading cause of death and disability in the United States, but no studies have examined the changes in oral microbiome during the acute stage of TBI using a clinically translational pig model. Crossbred piglets (4–5 weeks old, male) underwent either a controlled cortical impact (TBI, n = 6) or sham surgery (sham, n = 6). The oral microbiome parameters were quantified from the upper and lower gingiva, both buccal mucosa, and floor of the mouth pre-surgery and 1, 3, and 7 days post-surgery (PS) using the 16S rRNA gene. Faith’s phylogenetic diversity was significantly lower in the TBI piglets at 7 days PS compared to those of sham, and beta diversity at 1, 3, and 7 days PS was significantly different between TBI and sham piglets. However, no significant changes in the taxonomic composition of the oral microbiome were observed following TBI compared to sham. Further studies are needed to investigate the potential diagnostic role of the oral microbiome during the chronic stage of TBI with a larger number of subjects.

The microorganisms inhabiting the gastrointestinal tract (GIT) of ruminants have a mutualistic relationship with the host that influences the efficiency and health of the ruminants. The GIT microbiota interacts with the host immune system to influence not only the GIT, but other organs in the body as well. The objective of this review is to highlight the importance of the role the gastrointestinal microbiota plays in modulating the health of a host through communication with different organs in the body through the microbiome-gut-organ axes. Among other things, the GIT microbiota produces metabolites for the host and prevents the colonization of pathogens. In order to prevent dysbiosis of the GIT microbiota, gut microbial therapies can be utilized to re-introduce beneficial bacteria and regain homeostasis within the rumen environment and promote gastrointestinal health. Additionally, controlling GIT dysbiosis can aid the immune system in preventing disfunction in other organ systems in the body through the microbiome-gut-brain axis, the microbiome-gut-lung axis, the microbiome-gut-mammary axis, and the microbiome-gut-reproductive axis.

The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (n = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were selected for evaluation. Fecal samples were collected on 0-d and 82-d of the finishing period and microbial DNA was extracted and evaluated by 16S rRNA gene sequencing. During the feedlot trial, inefficient steers had decreased (p = 0.02) Ruminococcaceae populations and increased (p = 0.01) Clostridiaceae populations. Conversely, efficient steers had increased Peptostreptococcaceae (p = 0.03) and Turicibacteraceae (p = 0.01), and a trend for decreased Proteobacteria abundance (p = 0.096). Efficient steers had increased microbial richness and diversity during the feedlot period, which likely resulted in increased fiber-degrading enzymes in their hindgut, allowing them to extract more energy from the feed. Results suggest that cattle with better feed efficiency have greater diversity of hindgut microorganisms, resulting in more enzymes available for digestion, and improving energy harvest in the gut of efficient cattle.

The ruminal microbiota of Angus cows and steers were characterized using 16s rRNA gene sequencing, and the expression of their metabolic pathways was predicted. Samples were collected on weaning day from the steers and the cows, and subsequently on three other occasions from the steers. Results showed that microbial richness, evenness, and diversity decreased (p < 0.001) in the rumen of the steers as they were weaned and transitioned to a high-concentrate feedlot diet. However, on the day of weaning, microbial evenness was similar to that observed in the rumen of cows (p = 0.12). The abundance of archaea was similar (p = 0.59) between the cows and steers at weaning, but it decreased (p = 0.04) in the rumen of steers after weaning, and remained stable (p ≥ 0.44) for the remainder of their lives. Likewise, no difference (p = 0.51) in the abundance of Bacteroidetes was detected between the cows and the calves on the day they were weaned, but the abundance of this phylum increased (p = 0.001) and remained stable after that. These results suggest that cows may have a strong influence on the composition, and help modulate the ruminal microbiota of young calves; however, following weaning, their ruminal microbiotas tend to differentiate from that state observed at earlier ages.

The purpose of the study was to investigate effects of different inoculation dosages of E. tenella on growth performance, gastrointestinal permeability, oocyst shedding, intestinal morphology, fecal consistency, ileal apparent digestibility, antioxidant capacity, and cecal VFA profile in broiler chickens. Five different dosages (T0: 0, T1: 6250, T2: 12,500, T3: 25,000, and T4: 50,000) of E. tenella oocysts were inoculated via oral gavage to fourteen-day-old broilers. Inoculation of E. tenella linearly increased FCR (p < 0.05), and feed intake was quadratically increased on 6 days post-infection (dpi; p = 0.08) and 7 dpi (p = 0.09). Cecal lesion score of each treatment was T0: 0; T1: 0.39 ± 0.14; T2: 0.93 ± 0.21; T3: 1.25 ± 0.16; and T4: 1.58 ± 0.2. Cecal total VFA production was linearly reduced due to E. tenella infection on 6 dpi (p < 0.01). E. tenella infection deepened cecal crypts depth on 6 dpi (CD; p < 0.05). Gastrointestinal permeability tended to be linearly increased (p = 0.07). E. tenella infection tended to linearly reduce duodenal VH (p = 0.1) and jejunal VH on 9 dpi (p = 0.09). Different dosages of E. tenella modulated the tendency of fecal moisture content and oocyst shedding. Therefore, E. tenella infection impaired feed efficiency and small intestinal health mainly by reducing cecal VFA production and deepening cecal CD in broilers.

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche.

The succession of bacterial species as birds mature can impact their growth efficiency, health, and food safety due to the ability of a mature gastrointestinal microbial population to exclude opportunistic pathogenic bacteria from colonization. There has been an increase in the number of chickens fed a soy-free diet compared to the standard soybean-containing rations in pastured poultry. Therefore, the present study was designed to describe the impacts of feeding a soy-containing (SOY) or a soy-free diet (SF) on the bacterial succession in the gut of pasture-raised chickens. In order to compare microbiome compositions as birds aged, 16s rRNA gene sequencing was performed on the gastrointestinal tract of 1-day-old birds, on fecal material obtained at different ages, and on the cecal contents collected at slaughter from broilers fed each of the 2 diets. Results showed that at the phylum level, regardless of diet and birds' stage of life, there was a predominance of the phylum Firmicutes, which ranged from 50 to 90% of all OTUs in all samples. Moreover, the number of observed OTUs significantly increased (P < 0.001) as birds in the SF diet grew older; however, no significant variations (P = 0.11) in this trait were observed as birds in the SOY diet aged. Shannon Diversity indices calculated for birds in both diets had greater values (P < 0.001) in the cecal contents of adult birds collected at slaughter, compared to samples obtained at earlier ages. Also in spite of which diet was offered, the abundance of Oscillospira, Faecalibacterium, Ruminococcus, and 2 unidentified genera from the orders Clostridiales and RF39 all increased as birds aged, while abundance of Lactobacillus decreased. The predicted metabolic functions using microbiome data showed no differences (P ≥ 0.26) in metabolism of amino acids, carbohydrates, lipids, and energy for both diets. These findings demonstrate that, under these experimental conditions, while diet modulates some microbial changes in the gut of pasture-raised chicken, overall, a similar successional pattern is observed for both diets. Moreover, the resulting metabolic functions are very similar between diets regardless of age.

A study was conducted to examine the effects of supplementing beef calves during their suckling phase (popularly known as creep feeding) with supplements that contained or did not contain the enzyme xylanase. Forty-two cow-calf pairs were divided into three groups and assigned to one of three treatments for a period of 105 days, as follows: (1) No supplemental feed for calves (control; CON); (2) Corn and soybean meal-based supplement feed for calves (positive control; PCON); and (3) Same feed regimen as PCON with xylanase added to the supplement (enzyme; ENZ). After 105 days, out of the 42 calves participating in the study, 25 male calves were randomly selected (8 from CON, 9 from PCON, and 8 from ENZ) and samples of their forestomach were collected by esophageal tubing. Immediately after this procedure, all calves were weaned, commingled, and placed in a common post-weaning diet for 4 weeks. At the end of this period, ruminal fluid was once again collected from the same 25 calves. All samples were subjected to DNA extraction and 16S rRNA gene sequencing. At weaning, most of the alpha diversity indexes were greater in CON; however, no differences (P ≥ 0.23) in alpha diversity were observed in samples collected 4 weeks after weaning. Regardless of treatment, 2 phyla – Bacteroidetes and Firmicutes – comprised approximately 80% of the total bacterial abundance of samples collected on both days. At the genus level, an effect of diet (P = 0.02) was observed for Prevotella in the samples collected at weaning; however, no differences were detected in the samples collected 4 weeks after weaning. Calf average daily gain (ADG) during the 105-day creep feeding trial tended (P = 0.09) to be greater in the groups that received supplementation, with the greatest numerical value observed in ENZ. Moreover, there was a positive correlation (ρ = 0.43; P = 0.03) between ADG and abundance of Prevotella, indicating the importance of this bacterial group for ruminants. In summary, most of the significant differences found in this study were detected at weaning, and the majority of them disappeared 4 weeks after the calves were weaned and commingled.

One-day-old chicks were assigned one of four dietary treatments in a 2 × 2 factorial design in which the main effects were diet (adequate vs. low protein) and the addition of protease (0 vs. 200 g/1000 kg of feed). Chick performance (days 0–14) was recorded and their excreta were analyzed for short chain fatty acids, ammonia, and composition of the microbiota using 16S rRNA gene sequencing. Birds fed the low protein diet had lower body weight gain and poorer overall feed conversion ratio (FCR) (p ≤ 0.04); however, these parameters were not affected by the inclusion of protease (p ≥ 0.27). Protease inclusion did not affect any particular bacterial genus in the excreta, but it increased the total number of observed OTUs (p = 0.04) and Faith’s phylogenetic diversity (p = 0.05). Abundance of Proteus and Acinetobacter were lower in the excreta of chicks fed the low protein diet (p = 0.01). Abundance of Bacteroides was associated with poorer FCR, while Proteus was associated with improved FCR (p ≤ 0.009). Although diet had a stronger impact than protease on chick performance, both diet and protease yielded some changes in the intestinal microbiotas of the birds.