Ruminants are born with an undeveloped, nonfunctional rumen; however, the microbial populations begin to establish shortly after birth [3,15]. Despite misconception, ruminants are not born with a sterile gastrointestinal tract. During parturition, a calf is exposed to microbes from the vaginal canal and perineum, which include microorganisms such as Truperella pyogenes and species from the genera Staphylococcus, Clostridium, Bacteroides, Ureaplasma, and Mannheimia [16,17,18,19]. The calf’s microbiota continues to be colonized by microbes derived from the skin during suckling and the oral cavity during licking [17]. This introduces bacteria commonly found on the skin of the udder, Citrobacter spp. and Leuconostoc spp., which have been detected in the GIT of calves as early as 6 h after birth [20]. In addition to bacterial species being introduced from a calf’s dam, eukaryotic species, protozoa (e.g., Entodinium), and fungi (e.g., Neocallimastix) found in the GIT are introduced through saliva as the mother licks her calf [21,22].

Another major source of bacterial colonization is colostrum which typically contains species from Lactobacillus, Bifidobacterium, Staphylococcus, Escherichia coli, and Streptococcus uberis [23]. Of note, some of these bacterial groups are generally classified as opportunistic pathogens that can take advantage of the uninhabited gastrointestinal tract (GIT) of newborn ruminants. For example, E. coli begins to colonize the rumen as early as 24 h after birth [24]. These pathogens can cause gastrointestinal distress early in calves [25]. Previous research detected many opportunistic pathogenic species, including Escherichia and Salmonella, present in the hindgut of 1-week-old calves, contributing to digestive issues [25].

As a calf’s GIT microbiota matures, there is a change in the composition of the GIT microbiota. The initial pathogenic bacterial species that are generally facultative anaerobes able to utilize oxygen are soon replaced by the more beneficial species that are strict anaerobes [15,26]. With the change in bacteria, the rumen environment becomes anaerobic, with few species, including fungi being able to utilize oxygen. These more beneficial bacterial species (i.e., amylolytic bacteria, lactate utilizers, sulfate-reducing bacteria, and xylan and pectin fermenting bacteria) start out at much lower concentrations but soon dominate the ruminal environment as early as three days of age [3]. The fecal microbiota is dominated by the phyla Bacteroidetes, Firmicutes, and Proteobacteria, with Bifidobacterium, Bacteroides, and Lactobacillus being the most prevalent genera during a calf’s first four weeks of age [27,28,29,30].

As a ruminant’s GIT microbial population continues to establish, diet becomes a key factor contributing to its composition [31,32,33]. When the diet of a ruminant is altered, the GIT microbiota is altered as a result. One of the most dramatic dietary shifts that occurs during the beef production system is the change from a forage-based diet to a concentrate-based feedlot-finishing ration. During this transition, the GIT microbiota becomes unstable resulting in dysbiosis, or an imbalance, allowing GIT distress to occur [34,35]. Many studies have found that the microbial composition of the GIT is altered by age and diet [36,37,38,39]. Previous research revealed that the fecal microbial composition of steers at weaning is different from the microbial composition at yearling and slaughter, which can be attributed to dietary differences [37].

The shift in the microbial composition from a dietary change can affect specific bacterial species with the GIT microbiota. Many bacterial species can be described as either generalists, bacteria able to degrade a wide variety of substrates and thrive in a wide variety of environments, or specialists, bacteria that are only able to degrade a very specific set of substrates that occupy a narrow niche [40]. The abundance of these bacterial species is determined by the nutrients in the diet, which provides a competitive advantage to certain bacteria in the rumen. Earlier in life, when ruminants are fed a predominately forage-based diet, cellulolytic bacteria, including Ruminococcus albus, R. flavefaciens, and Fibrobacter succinogenes, tend to dominate since they are better able to degrade and utilize forages [41,42,43]. The fecal microbial population is made up of mainly the family Ruminococcaceae [37], which has many genes present that can bind cellulose, hemicellulose, and xylan, making this family particularly adapted to degrading plant materials [44,45,46]. Once cattle arrive at the feedlot, the diet shifts to a predominately concentrate-based diet and ruminal fermentation must rapidly change as well. Instead of degrading mainly cellulose and hemicellulose, fermentation must shift to mainly degrading starch and soluble sugars [31,47,48]. After this switch to a high concentrate diet, amylolytic bacteria dominate with Ruminobacter amylophilus, Streptococcus bovis, Succinomonas amylolytica, Butyrivibrio fibrosolvens, Selenomonas ruminantium, and many species from the genus Prevotella being to dominate the ruminal niche [49].

Calves are born with an immature but functional immune system [50]. While in utero, the central organs (e.g., bone marrow and thymus) are fully developed. However, the peripheral organs (e.g., lymph nodes, spleen, and mucosa-associated lymphoid tissues, including the gut-associated mucosal tissue [GALT]), do not fully develop until they are exposed to antigens after birth [51]. The developing GIT microbial population plays a vital role in regulating and activating a calf’s immune system during the early stages of life [17]. Previous research has discovered that the hindgut is crucial for the development of the immune system in monogastric animals [52]. Research is now revealing that the microbial consortium in the hindgut of cattle is equally as important in the development of the calf’s immune system [53], which plays a vital role in the GIT health, feed digestion, and energy production [54].

The epithelial cells in the GIT are joined by an intercellular junction called tight junctions, which are comprised of proteins (e.g., occludin, claudins, zonula occludens) and adhesion molecules. The tight junctions allow the passage of nutrients, ions, and water through the bloodstream while preventing the passage of microbes and their peptides [55,56]. Right after birth, a calf’s tight junctions are not fully formed, and passage into the bloodstream is increased, which improves a calf’s ability to absorb nutrients, immunoglobulins, and leukocytes from the colostrum [57,58]. This permeability begins to decrease around 24 to 36 h after birth and continues to decrease during the calf’s first month [59]. Research has shown that the presence of some bacterial species (e.g., Lactobacillus spp. and Bifodobacterium spp.) and their metabolites can promote the activation of these tight junction proteins [60,61,62]. This can be very important during the first few weeks of life when the intestinal permeability is just starting to decrease. The colostrum calves receive during the early stages of life plays an important role in host immunity by increasing the hindgut abundance of probiotic species such as Bifidobacterium while decreasing the hindgut abundance of opportunistic pathogenic bacteria E. coli and Escherichia-Shigella [63]. Robseburia and Oscillospira have been found to have genes involved in the regulation of host immunity and metabolism, while SCFA receptor genes decrease inflammation and increase intestinal barrier function [14], which is vital during the early stages of development.

Proinflammatory (e.g., interleukin [IL]-8) and anti-inflammatory (e.g., IL-10) cytokines are upregulated during the first week of a calf’s life [64]. These are important because IL-8 works to activate and attract neutrophils into the interstitial space in the body [65], and IL-10 prohibits proinflammatory molecules (e.g., INF-g, TNF-α, IL-6) from activating and prevents the immune system’s ability to recognize antigens [66]. Bacterial species aid the immune system in these functions because Lactobacillus and Bifidobacterium activate IL-10, which helps prevent the immune system from activating a proinflammatory response to beneficial bacteria within the GIT microbiota [67]. Both Lactobacillus and Bifidobacterium are introduced to the GIT through colostrum [23], and both play an important role in the early stages of the establishment of the GIT microbiota, which can contribute to controlling the ruminant’s immune response and preventing any unnecessary inflammatory responses to “self” antigens.

Not only does the GIT microbial population aid in establishing the calf’s immune system in the first few weeks of its life, but it also continues to play a vital role in maintaining and regulating the immune system as cattle mature and grow. As calves are transitioned from a milk-based diet to either a forage- or concentrate-based diet, both the calf’s GIT microbiota and the expression of genes related to intestinal immunity are impacted [68]. The expression of immune genes has been linked to the abundance of luminal bacteria and bacteria correlated with GIT in health in dairy calves [69]. IgA, a secretory immunoglobulin that plays a large role in intestinal immunity, aids the immune system in regulating the relationship between both beneficial and pathogenic bacteria [70]. If this immunoglobulin is removed from the GIT, bacteria can increase uncontrollably in abundance while the immune system upregulates the expression of proinflammatory cytokines [71]. Recovery of IgA will restore intestinal homeostasis by returning commensal bacterial species populations and eliminating inflammation [72].

Another key feature of the gastrointestinal system that helps maintain health and proper functioning is mucus, which provides a barrier to tight junctions and aids in maintaining gut integrity [69,73]. Although beneficial for host health, if the production of mucus becomes abnormal, then the GIT can experience distress and disease [73,74]. The GIT microbial population plays a vital role in the production of intestinal mucus. When comparing germ-free and conventionally raised mice, the mice without functional microbiota had less mucus lining their intestinal epithelial cells [75,76]. Meanwhile, when germ-free mice are exposed to bacterial molecules (e.g., lipopolysaccharides and peptidoglycans), their intestinal mucus production is restabilized [75,77]. These results highlight the importance of the GIT microbiota and its metabolites in promoting and maintaining intestinal mucus production.

Due to the communication between the GIT microbiota and the host’s immune system, any disturbance in the equilibrium of the microbiota or the immune system will affect both. Suppose calves are suddenly switched to a different diet and their GIT microbial population is not given time to acclimate. In that case, the expression of claudin and occludin is downregulated in the mucosal barrier of the intestines resulting in an increase in gut permeability [78]. The decreased GIT integrity can be attributed to an increase in the host’s inflammatory response due to an interaction with pathogenic bacteria and their metabolites, or with pro-inflammatory cytokines [68]. Although the immune’s pro-inflammatory response is a defense mechanism designed to target foreign invaders (e.g., pathogens) and works in conjunction with the GIT microbiota to prevent pathogenic invasion and gastrointestinal dysbiosis, the inflammatory response can become too upregulated and negatively impact host health [79]. Another detrimental interaction between the GIT microbiota and the host’s immune system can occur during the onset of rumen acidosis. This digestive issue is caused when the rumen pH drops and becomes acidic as a result of an abundance of rapidly digestible carbohydrates in the diet producing an abundance of lactic acid (acute acidosis) or volatile fatty acids (subacute acidosis) [54]. As a result, the number of cellulolytic bacteria can decrease, and the number of amylolytic bacteria can increase, resulting in the microbiota experiencing dysbiosis [80]. Additionally, as the pH of the rumen decreases, the rumen epithelial cells become damaged, preventing the absorption of nutrients that can ultimately have negative impacts on the host’s performance and health [54]. This highlights the importance of maintaining balance in the microbial populations in the gut and in the host’s immune system to increase growth and health in the host animal.

Since so much interplay exists between the GIT microbial population and the host’s immune system, GIT microbial therapies can be utilized to improve the overall health of a host. Three main types of therapies are utilized to modulate the GIT microbiota—probiotics, prebiotics, and gut microbial transplants. They range from the introduction of a few key species or fermentable products [81,82,83] to a complete functional microbial population [84,85,86,87,88]. Recently, research has focused on how these therapies can be utilized to stabilize the GIT microbiota to prevent diseases [89]. These therapies mainly work by preventing dysbiosis in the GIT microbial community by preventing an increase in harmful bacteria and a decrease in beneficial bacteria, which is especially valuable when the host is undergoing stress.

One of the most commercially available and widely used GIT microbiota therapies available to promote human and animal health is probiotics, or direct-fed microbials (DFM). Probiotics are living microorganisms found naturally in the GIT that have a direct or indirect impact on host health. They can be mono- or mixed cultures usually comprised of bacteria or fungi [83,90]. Probiotics work by producing metabolites that stimulate the growth of commensal bacteria, inhibiting proliferation and colonization of pathogenic bacteria, regulating gastrointestinal pH, promoting mucus production, and improving the function of intestinal epithelial cells [91]. In livestock production, probiotics are valuable tools utilized to improve GIT health, feed efficiency, and milk quality [92,93]. Additionally, they are crucial to preventing dysbiosis from occurring in the GIT microbiota as a result of stressful events such as transportation [94].

In ruminant animals, probiotics can act as alternatives to antimicrobial feed additives by limiting the colonization of pathogenic species. S. cerevisiae has been found to improve ruminant production by increasing ruminal pH [95], which is beneficial in both beef and dairy production by preventing acidosis when introducing more starch into the diet. S. cerevisiae can aid in nutrient utilization by increasing ruminal fermentation [96]. The introduction of Lactobacillus probiotics to the diet of calves has been shown to increase growth and prevent immunocompetence [97]. Megasphaera elsdenii and Butyrivibiro fibrosolvens have been found to redirect SCFA production from lactate to butyrate, which increases ruminal pH preventing subacute rumen acidosis [98]. Although studies have controversial results on the effects of probiotics in the diet of ruminants, adding probiotics to the diet prior to a stressful event such as weaning or a diet change stabilizes the ruminal ecosystem preventing dysbiosis.

The practice of introducing substrates that bacteria utilize into the GIT instead of the bacterial species themselves is increasing in popularity. These substrates are called prebiotics because they cause the “prebiotic effect,” which is “the selective stimulation of growth and/or activity of one or a limited number of species in the gut microbiota that confer(s) health benefits to the host” [99]. Prebiotics are comprised of non-starch polysaccharides (NSP) or oligosaccharides. Prebiotics are introduced into the diet to be fermented and utilized by beneficial bacteria to improve the health of the GIT [91]. Therefore, to truly be considered a prebiotic, the product must be indigestible by the host, fermentable by commensal GIT microbiota, and increase the growth of beneficial bacteria in the gut [100,101].

Like probiotics, prebiotics can positively impact cattle production and health. They are usually introduced into ruminant diets alongside probiotics to increase substrates that can be utilized by the microorganisms contained in the probiotic to improve its efficacy [81]. Prebiotics can be fed to increase weight gain and feed efficiency and reduce scours and respiratory diseases [102,103,104]. Fructose oligosaccharides (FOS) have previously been shown to lessen enteric issues in calves [105] and decrease colonization of many pathogenic bacteria, including Salmonella and E. coli [106]. Adding Galactosyl-lactose (GL) to milk replacers has previously been shown to increase growth while improving overall health status of dairy calves [102]. Prebiotics, also, work best as a preemptive therapeutic to prevent GIT dysbiosis during a stressful time for the host.

The utilization of sequencing technology has provided many recent advances to people's knowledge of the role of individual microorganisms within the GIT microbiota. However, all the bacteria comprising the GIT microbiota have yet to be elucidated [107]. Currently, people are only able to culture an estimated 23–40% of the microbes within the rumen [107]; therefore, people are limited in our ability to develop gut therapies like probiotics and prebiotics since people still have not identified every microorganism or their function in the GIT. To overcome people's lack of knowledge, gut microbial transplants can be utilized. Within human and small animal medicine, gut microbial transplantation has become a very promising avenue for GIT therapies [84,85,86,87,88]. In terms of cattle production, there can be two types of gut microbial transplants—fecal matter transplants (FMT) and ruminal fluid transplants (RFT).

In ruminant animals, RFT is the most popular form of gut microbial transplants. This introduces rumen fluid from a healthy donor into a recipient experiencing dysbiosis [108]. In sheep experiencing acidosis, an RFT accelerated rumen fermentation, decreased dysbiosis, and repaired damage to the ruminal epithelial cells [109]. An RFT is also a valuable tool prior to weaning in lambs by increasing starch degrading bacteria, thus improving the digestibility of starch-containing diets and increasing propionate production by ruminal microbes [110]. This study also found that an RFT led to faster organ development, especially the hindgut and liver. Although not as commonly used in ruminants, FMT treatment can also be used in cattle. Research has shown an FMT can be an effective treatment for diarrhea [111]. Additionally, this study found that an FMT treatment in a calf’s early life can potentially improve growth performance. Although the idea of inoculation with GIT contents dates back as early as the 1700s [112], research is still needed to fully understand the validity of using an RFT or an FMT as a therapeutic for modulating host health.