Most of the research efforts involving the bovine gastrointestinal microbiota have focused on cattle’s forestomach, particularly the rumen, so information concerning the bovine fecal microbiota is more scarce, especially in young beef cattle. The present study was performed to evaluate the ruminal and fecal microbiotas of beef calves as they reached the end of their nursing phase. A total of 18 Angus cow/calf pairs were selected and assigned to one of two treatment groups for the last 92 days of the calves’ nursing period, as follows: 1) calves were supplemented with concentrate in a creep feeding system; or 2) control group with no supplementation of calves. After 92 days, ruminal and fecal samples were individually obtained from calves in both groups, and their microbiotas were evaluated using 16S rRNA gene sequencing. Ruminal samples were predominated by Prevotella (18 to 23% of the total bacterial abundance), regardless if calves received supplementation or not; however, in the feces, Prevotella was only the seventh most abundant genus (0.6 to 2.1% of total bacterial abundance). Both the rumen (P = 0.01) and the feces (P = 0.05) of calves that received supplementation had greater abundance of Firmicutes. In addition, calves that were supplemented had lower abundance of Fibrobacteres (P = 0.03) in their rumens. Regardless if the calves were supplemented or not, Faith’s Phylogenetic Diversity index (P ≤ 0.007) and total concentration of short chain fatty acids (P < 0.001) were both greater in the rumen than in the feces of calves. In summary, the ruminal and fecal microbiotas of weanling beef calves were considerably distinct. Additionally, supplementation with creep feed caused some significant changes in the composition of the gastrointestinal microbiota of the calves, especially in the rumen, where supplementation caused an increase in Firmicutes and a decrease in abundance of Fibrobacteres.

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.

Concerns over animal welfare continue to be a critical component of law and policies associated with commercial food animal production. Social and market pressures are the driving forces behind the legislation and result in the change of poultry production management systems. As a result, the movement toward cage-free and aviary-based egg production systems has become standard practices. Cage-based systems being replaced by alternative methods that offer a suitable housing environment to meet or exceed poultry welfare needs and require different management, including the ban of antibiotics in poultry diets. For broiler production, pasture- raised and free-range management systems have become more popular. However, challenges remain from exposure to disease-causing organisms and foodborne pathogens in these environments. Consequently, probiotics can be supplemented in poultry diets as commercial feed additives. The present review discusses the impacts of these probiotics on the performance of alternative poultry production systems for improving food safety and poultry health by mitigating pathogenic organisms and improving egg and meat quality and production.

Due to consumer demand and changing welfare standards on health, ecology, equity, and safety concepts, poultry production has changed markedly over the past 20 y. One of the greatest changes to poultry production standards is now offering poultry limited access to the outdoors in alternative and organic poultry production operations. Although operations allowing access to the outdoors are still only a small portion of commercial poultry production, it may impact the gastrointestinal (GIT) health of the bird in different ways than birds raised under conventional management systems. The present review describes current research results in alternative systems by identifying how different poultry production operations (diet, environmental disruptive factors, diseases) impact the ecology and health of the GIT. Various research efforts will be discussed that illustrate the nutritional value of free-range forages and how forages could be beneficial to animal health and production of both meat and eggs. The review also highlights the need for potential interventions to limit diseases without using antibiotics. These alternatives could enhance both economics and sustainability in organic and free-range poultry production.

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.

The objective of this study was to explore the relationships between ruminal microbial populations from Angus steers that were divergent in carcass traits related to adipose accumulation. Twenty-four feedlot-finished Angus steers (age: 538 ± 21 d; body weight following lairage: 593.9 ± 43.7 kg) were slaughtered, and ruminal contents and carcass data were collected. Ruminal microbial deoxyribonucleic acid (DNA) extraction and 16S ribosomal ribonucleic acid (rRNA) gene sequencing were performed to determine microbial relative abundances, to estimate microbial diversity, and to predict microbial metabolic pathways. A variety of correlation analyses and one-way ANOVA were performed to investigate the relationships between the rumen microbiome and carcass traits. Marbling score (P = 0.001) and longissimus lipid content (P = 0.009) were positively correlated to Chao1 Richness Index, suggesting that increased intramuscular fat was associated with increased numbers of ruminal microbial species. The phyla Tenericutes and TM7 were negatively correlated (P ≤ 0.05) to marbling score and longissimus lipid content, indicating that lower abundances of these phyla may be associated with improvements in intramuscular fat content. Greater abundance of the bacterial family S24-7 was positively correlated (P = 0.002) to marbling score. Analysis by marbling classification revealed further linkages to microbial richness (P ≤ 0.063), diversity (P = 0.044), and S24-7 (P < 0.001) populations. Computational prediction of the microbial metabolic pathways revealed no differences (P ≥ 0.05) in metabolic pathway expression in rumen microbes between steers in the high- and low-marbling classes. Several phyla, families, and genera were positively correlated (P ≤ 0.05) to both rib fat thickness and yield grade. Collectively, our results suggest that microbial composition is associated to differing performance in carcass adipose traits. Overall, most of the bacterial taxa correlated to the intramuscular and subcutaneous fat depots did not overlap, suggesting the microbial population end products likely impacted adipose accumulation largely via separate adipogenic pathways of the host animal.