Probiotics as an alternative to antibiotics to reduce resistance in the gut

Article by Kerrie Kavanagh

The leading causes of horse mortality can be attributed to gastrointestinal diseases. Therefore, maintaining the balance of the gut microbiota and avoiding a shift in microbial populations can contribute to improved health status. The gut microbiota, however, can be influenced by countless dynamic events: diet, exercise, stress, illness, helminth infections, aging, environment and notably, antimicrobial therapy (antibiotics). These events can lead to gut dysbiosis—a fluctuation or disturbance in the population of microorganisms of the gut, which can contribute to a wide range of disease. The use of antibiotics in horses is thought to have one of the most notable effects on the gut microbiota (gut dysbiosis), which can lead to diseases such as colitis, colic and laminitis.

Antibiotics, which are antimicrobial agents active against bacteria, are important to equine medicine; and bacterial infections can be resolved quite successfully using antibiotics for antimicrobial therapy, but there are consequences to their use. An antimicrobial agent can be defined as a natural or synthetic substance that kills or inhibits the growth of microorganisms such as bacteria, fungi and algae. One of the consequences of antibiotic use is that of antibiotic-associated diarrhoea, which can contribute to poor performance in the horse and even mortality. In antimicrobial therapy, the target organism is not the only organism affected by the antimicrobial agent but also the commensal microbiota too (the normal flora of the equine gut). Antibiotics can promote fungal infections and resistant organisms and impede or even eliminate the more sensitive organisms; and they can have both short and long-term consequences on the gut microbiota composition and function. 

Research has indicated that antibiotic treatment may adversely affect metabolic function in the gut by decreasing protein expression responsible for biochemical pathways such as glycolysis, iron uptake, glutamate hydrolysis and possibly even more metabolic functions. The use of antimicrobial drugs directly impacts and possibly contributes to the most notable effect on the gut microbiota of the host, leading to gut dysbiosis; and certain antibiotics can have further-reaching consequences on the microbiota than others. The type of antibiotic and mode of action (bacteriostatic versus bactericidal) will differ in their influences on the gut microbiota composition, e.g., clindamycin operates a bacteriostatic mode of action by inhibiting protein synthesis and exerts a larger impact on the gut microbiota compared to other antimicrobials. These influential consequences that are imparted by the antimicrobial agent are relatively yet to be elucidated and may result in the manifestation of illness or conditions later in life. For example, the development of asthma in humans has been linked to antibiotic treatment in early childhood as a result of bacterial infections. It may yield interesting results if researchers were to examine the gut microbiome of horses suffering from chronic obstructive pulmonary disease (COPD) and other chronic respiratory illnesses and to establish if there is indeed a link with antibiotic therapy used in horses from an early age. 

In comparison to the vast wealth of human studies conducted so far, the volume of equine studies falls disappointingly far behind, but that is changing as researchers focus their interest on developing and filling this gap of knowledge. One such study which examined the effect of antibiotic use on the equine gastrointestinal tract, demonstrated a significant reduction in culturable cellulolytic bacteria (>99%) from equine faeces during the administration period of trimethoprim sulfadiazine and ceftiofur in a study comparing responses to antibiotic challenge. That reduction was still evident at the end of the withdrawal period when compared to the control group. In other words, there was a significant reduction in the ‘normal’ bacteria of the gut. The ability of antibiotics to modulate the gut microbiota was evidenced by the proliferation of pathogenic Salmonella and Clostridia difficile (commonly associated with diarrhoea in horses) in the antibiotic challenged horses. This trend of reduction in cellulolytic bacteria associated with antibiotic use was also mirrored in a relatively recent study conducted in 2019, where a short-term reduction in culturable cellulolytic bacteria was combined with a progressive increase in amylolytic bacteria. The heavy reliance on cellulolytic bacteria in the role of equine digestion (without these types of bacteria the horse cannot break down their food) may, therefore, adversely affect the dietary energy available from forage during antimicrobial therapy and may therefore impact performance.

Another study that compared the effect of penicillin, ceftiofur and trimethoprim sulfadiazine (TMS) on the gut microbiota in horses using next-generation sequencing showed that TMS had the most profound impact on the microbiota, in particular the phylum Verrucomicrobia. This same study also reported a significant decrease in bacterial richness and diversity of the faecal microbiota. A reduction in bacterial diversity is certainly a trend that is commonly seen in gastrointestinal disease in horses. The restoration of the normal gut microbiota after completion of antibiotic treatment can take up to 40 days, but the organisational structure of the bacterial populations can take many years to re-establish the original structure map that was laid out in the gut pre-antibiotic treatment. 

The equine studies certainly show similarities to the human studies, indicating the consequences of antibiotics that can be seen across more than one species. Human studies have reported long-term consequences of antibiotic treatment on the human microbiota. One such human study investigated a 7-day clindamycin treatment and monitored the patients for two years. The impact on the human microbiota remained evident two years post-treatment, where a reduction in bacterial diversity and detection of high-resistance to clindamycin were detected. 

Interestingly, no resistant clones were detected in the control group over the two-year sampling period. Another study focusing on the effects of antibiotic treatment for Helicobacter pylori showed findings mirrored in similar studies of that field. The findings demonstrated the rapidly reducing bacterial diversity (one week) after antibiotic treatment and found that disturbances in the microbiota and high levels of macrolide resistance were evident four years post-treatment. Human studies may predict that equine studies will find similar trends with equine antimicrobial therapy. These studies highlight the impact of antibiotic use and the long-term persistence of antibiotic resistance remaining in the intestinal microbiome, which is a concern for both humans and animals. 

Antibiotics can lead to the selectivity and proliferation of resistant bacteria, which is evidenced by the long-term effects observed on the gut microbiota harbouring drug-resistant encoded genes. Horizontal gene transfer (HGT) commonly occurs in the gut (can be up to 25 times more likely to occur in the gut than in other environments). HGT can be attributed to the close proximity of the microbiota in the gut, allowing the transfer of genetic material via routes such as plasmids and conjugation; in other words, the bacteria in the gut have developed a pathway to transfer antibiotic resistant genes from one generation to another. Resistance to antibiotics is now a global issue for the treatment of many diseases. 

With the unfavourable association tied to Clostridium difficile infections (CDI) and the onset of colitis particularly in mature horses treated with β-lactam antibiotics (commonly used for equine infections), the incidences in which antimicrobial therapy is considered should be minimised and only used if entirely necessary. The use of broad-spectrum antibiotics in recurrent presentations of symptoms of disease such as urinary tract infections in humans or diarrhoea as a result of CDI in both humans and horses is promoting drug resistance.

The antibiotics, by disrupting the gut microbiota (which act as a defence against the establishment and proliferation of such pathogenic bacteria) are allowing the opportunity of growth for these multi-resistant microorganisms such as C. difficile, vancomycin-resistant enterococci (VRE), and multi-resistant Staphylococcus aureus (MRSA). The organism C. difficile and its antibiotic resistance has been demonstrated in the treatment of CDI for both humans and animals. The introduction of vancomycin (a glycopeptide antibiotic) in 1959 for the control of CDI remained effective until the 1990s when a more virulent form of C. difficile emerged. This new form of C. difficile with reported broad-spectrum antibiotic resistance resulted in chronic conditions and increased human mortality. C. difficile is most noted with human hospital-acquired infections. C. difficile BI/NAP1/027 has been shown to have resistance to fluoroquinolone antibiotics, moxifloxacin and gatifloxacin, which was not seen in historical genotypes. As C. difficile infections are found to cause gastrointestinal disease in horses as well as humans, this is certainly of concern.

Alternative therapies to antibiotic therapy to restore or modulate the gut microbiome after a gut dysbiosis event could be considered in certain circumstances where antibiotics are no longer effective (e.g., CDI), nor may they not be the best course (presence of Extended-spectrum -β-lactamase producing (ESBL) organisms) nor essential for example, when the diagnosis of the bacterial cause is uncertain. The rationale to using probiotic treatment along with antimicrobial treatment is that the antibiotic will target the pathogenic bacteria (e.g., C. difficile) and also the commensal microbiota of the gut, but the probiotic bacteria will help to re-establish the intestinal microbiota and in-turn prevent the re-growth of the pathogenic bacteria in the case or residual spores of C. difficile surviving the antibiotic treatment. Alternative therapies such as faecal microbiome transplant (FMT) or probiotic solutions can reduce the risk of proliferation of antibiotic-resistant bacteria and also have fewer implications on the gut microbiome as evidenced by antibiotic use. 

Probiotics have been defined by the Food and Agricultural Organisation (FAO) and the World Health Organisation (WHO) as “live non-pathogenic microorganisms that, when administered in adequate amounts, confer a health benefit on the host”. The word ‘probiotic’ is Greek in origin, meaning, ‘for life’; and the term was coined by Ferdinand Vergin in 1954. While the mechanisms of action of probiotics are complex and require a deeper knowledge of the modulations of the gastrointestinal microbiota, and the health benefits due to their use are the subject of some debate, there is no doubt that probiotics are considered by many as a vital resource to human and animal health.   

The use of probiotics in animal production, particularly in intensive swine and poultry production, has increased in recent years, primarily as an alternative to the use of antimicrobials in the prevention of disease. The problem of antibiotic-resistance and antimicrobial residues in food-producing animals (the horse is considered a food-producing animal), as a result of historical antibiotic use with the corresponding reduction in antibiotic efficacy in humans, leads to having to look at more sustainable options such as probiotic use to combat disease. Probiotics in horses are predominantly used as a treatment modality in the gastrointestinal microbial populations to combat illnesses such as diarrhoea—to prevent diarrhoea (particularly in foals) or help improve digestibility.  Shifts or fluctuations in the microbial populations of the equine gastrointestinal tract have been associated with diseases such as laminitis and colic.  

Gut dysbiosis, as mentioned previously is, a fluctuation or disturbance in the population of microorganisms of the gut is now being recognised as a cause of a wide range of gastrointestinal diseases; and in horses, it is one of the leading causes of mortality. The ability of probiotics in conferring health benefits to the host can occur via several different mechanisms: 1) inhibiting pathogen colonisation in the gut by producing antimicrobial metabolites or by competitive exclusion by adhering to the intestinal mucosa preventing pathogenic bacteria attachment by improving the function and structure; 2) protecting or restabilising the commensal gut microbiota; 3) protecting the intestinal epithelial barrier; 4) by inducing an immune response.

It is known that there is a wealth of factors that will adversely affect the gut microbiome, antibiotics, disease, diet, stress, age and environment are some of these compounding contributors. To mirror one researcher’s words echoing from an era where antibiotics were used as growth promoters in the animal industry, “The use of probiotic supplements seeks to repair these deficiencies. It is, therefore, not creating anything that would not be present under natural conditions, but it is merely restoring the flora to its full protective capacity”. In the case of using concurrent antibiotic and probiotic treatment, this strategic tweaking of the microbiota could be used as a tool to prevent further disease consequence and perhaps help improve performance in the horse.

The benefits of probiotic use in horses have not been investigated extensively but as mentioned previously, they are now being focused upon by researchers in the equine field. The most common bacterial strains used in equine probiotic products are Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, Bacillus and yeast strains of Saccharomyces. Lactobacillus, Bifidobacterium and Enterococcus strains typically account for less than 1% of the microbiota large gastrointestinal populations.

Regulation is lacking regarding labelling of probiotic products, often not displaying content with clarification and quality control (such as confirmed viability of strain[s]) not excised with over-the-counter probiotic products. There is evidence to suggest that host-adapted strains of bacteria and fungi enjoy a fitness advantage in the gut of humans and animals.  Therefore, there may be an advantage in using the individual animal’s own bacteria as potential probiotics. Probiotics and antibiotics used concurrently could be the way to minimise the introduction of antibiotic-resistant bacterial strains in the gut, and in turn, protect future antibiotic efficacy. 

Probiotics – The key to a well-balanced equine gut

By Kerrie Kavanagh

It is no surprise that the health maintenance of the racehorse is a top priority for trainers. And probiotics can be used as a treatment modality to manipulate the gut microbiome to improve or maintain health. Equine studies to date have shown that probiotic strains can offer an advantageous approach to minimising disturbances in the gut microbial populations, repair these deficiencies—should they occur—and re-establish the protective role of the healthy gut microbiome. Other probiotic-associated health benefits include reducing diet-related diseases such as colic and laminitis, preventing diarrhoea, conferring host resistance to helminth infection, improving stress-related behavioural traits (e.g., locomotion) and even promote the development of an effective gut-brain communication pathway. 

Probiotics have been used by humans for more than 5,000 years with their development closely linked to that of dairy products and fermented foods. Today, probiotics are seen as an excellent non-pharmaceutical way to improve the health of both humans and animals, and there are a plethora of products to choose from. But what exactly is a probiotic, and how do they work? Why would your horse need one? What types of probiotics are available for horses? These are all questions that horse trainers ask frequently, which we will attempt to answer here. 

The Equine Gut Microbiome

Probiotics and the equine microbiome can benefit from a valuable symbiotic relationship; probiotics are seen as a restorative treatment modality for the gut, to re-establish the bacterial populations there and also to re-establish the protective role that the health gut microbiome confers to the host. But when we discuss the equine microbiome, what are we really talking about? 

The gut microbiota/microbiome can be categorised by anatomical location such as the oral microbiota/microbiome in the mouth and the intestinal microbiota/microbiome in the intestines, etc. Therefore, the gut microbiome pertains to the microbiota in the gastrointestinal tract. This population of microorganisms (bacteria, fungi, viruses, protozoa) is referred to as the ‘microbiota’ of the gut, while the term ‘gut microbiome’ refers to the genetic material associated with these microorganisms. The microbiome can be defined as the sum of the microbes and their genomic elements in a particular environment. If we look at the definition of the microbiome having the propensity to an equation, then any equation must be balanced; to maintain that balance is key. If the microbial community exists in an environment in a balanced state, then any upset or disturbance to the microbial populations will cause the balance to shift (known as dysbiosis). To maintain the balance, we need to firstly understand the way the microorganisms exist within their community (i.e. their microorganism-to-microorganism interactions and also microorganism-to-environment interactions) and secondly, their functioning role. If we can understand their (microorganism) position and role, then we can maintain the balance or re-establish the balance if a shift occurs.  

Fig. 1 Factors that can lead to gut Dysbiosis

The human intestinal microbiome is now recognised as an organ and likewise, the equine intestinal microbiome is deemed an ‘organ’ of the body and is vital for the breakdown of complex food and subsequent release of energy, protection against the pathogenic bacterial colonisation and in regulating the immune system and metabolic functions. There has been much debate regarding the content of the healthy equine microbiome, and even to deduce what ‘healthy’ or ‘normal’ is requires a level of understanding of the microbiota associated with healthy horses. This question has been posed by many researchers and frankly has yet to be answered with certainty. There are many reasons why the ‘normal’ microbiota keeps eluding us; and this can be attributed to the many reasons as to why the gut microbiota (of a healthy horse) can be affected (see Figure 1). It is thought that the diversity of the human gut microbiota and the general assembly of microbial communities within the gut (with the dominant phyla being classed as belonging to Firmicutes and Bacteroidetes) is a shared hypothesis across most species (i.e., humans and animals share a similar gut microbiome structure). Firmicutes and Bacteroidetes have been shown to constitute the main dominant phyla in equine, bovine, canine and feline gut microbiome studies indicating the cruciality of the role they play in the maintenance of a healthy microbial ecology in the gastrointestinal tract. Several studies do agree that dominant phyla of the equine gut microbiota are obligate anaerobes: the gram-positive Firmicutes and the gram-negative Bacteroidetes; other phyla are identified as Proteobacteria, Verrucomicrobia, Actinobacteria, Euryarchaeota, Fibrobacteres and Spirochaetes. Ninety-five percent of the  Firmicutes phyla contains the Clostridia genus in addition to genera related to gut health such as Lachnospiraceae, Faecalibacterium and Ruminococcaceae. The other main dominant phyla, Bacteroidetes, on the other hand contains a large variety of the genus. 

Role of the Equine Gut Microbiota

The role of the gut intestinal microbiota serves to protect and prevent disease. The gut microbiota has several purposes: prevention of pathogen colonisation by competing for nutrients, enrichment and maintenance of the intestinal barrier—their ability to renew gut epithelial cells and repair damage to the mucosal barrier, the breakdown of food and releasing energy and nutrients, such as synthesising vitamins D and K and also conserving and restoration of the immune system by the formation of antimicrobial metabolites and blocking access to the binding sites of the mucosal wall. The gut microbiota is also thought to play some role of influencing the neuro-active pathways that affect behaviour. It is not surprising to see that gut disorders and gastrointestinal diseases can arise when gut dysbiosis occurs. The role of the gut microbiota may have even more importance than is realised and may have a role to play with developing illness or disease later in life.

The microbial colonisation of the intestinal tract begins at birth. The foal begins its colonisation through contact with the microbiota of the mare’s vaginal and skin surfaces plus the surrounding environments to which the foal is exposed and reaches a relatively stable population by approximately 60 days in age. It is perhaps a fight for dominance to achieve establishment in the gut among the bacterial populations that sees the foal’s microbiota as being more diverse and quick to change when compared to that of the older horse. The subsequent colonisation of the intestinal tract will reflect the foal’s diet, changing environment, introduction to other animals, ageing and health.

What exactly is a probiotic?

Beneficial bacteria can be isolated and harvested to prepare a bespoke probiotc

The word ‘probiotic’ is of Greek origin meaning ‘for life’ and the WHO/FAO have defined probiotics as ‘live microorganisms which when administered in adequate amounts confer a health benefit on the host’.  People have long believed that exposure to non-pathogenic microorganisms can benefit the health of humans and animals. The thinking behind this is that daily consumption of sufficient numbers of ‘good’ microorganisms (either bacteria or fungi) can maintain a healthy population of microorganisms in the gut and benefit overall health.  

Probiotics are used to manipulate the bacterial populations of the gut in order to re-establish the delicate microbial balance there which, in turn, confers health benefits on the host. As the benefits associated with some of the ‘good’ bacteria within the gut became known, these were referred to as probiotic bacteria. 

How do probiotics work?

There are 4 main mechanisms by which probiotics are thought to exert their effects.

1. By inhibiting pathogen colonisation in the gut through the production of antimicrobial metabolites or by competitive exclusion; in other words, they prevent the ‘bad’ bacteria from growing in the gut.

2. By protecting or re-stabilising the commensal gut microbiota, probiotics can be a means to re-establish the balance of the gut microbial populations.

3. By protecting the intestinal epithelial barrier, they maintain the health of the intestinal wall.

4. By inducing an immune response, probiotics can boost the immune response and help prevent disease.

If we consider the definition of a probiotic as ‘live non-pathogenic microorganisms that, when administered in adequate amounts, confer a health benefit on the host’, then this reference to ‘adequate amounts’ must be emphasised, and the dose administered is critical to ensure that the probiotic has the desired effect. For horses, we must consider the route through the digestive tract that the probiotic strains must travel to arrive at their destination is a distance over 15 metres long. It is a race for survival! The gastrointestinal system has many obstacles along the passage such as the acidic stomach environment and the dangers of exposure to bile and digestive enzymes, in which they must survive. The initial dose of ‘live’ probiotic strains is therefore crucial to ensure survival in the gut. Prebiotics are ingredients such as carbohydrates and fibre, which promote the growth of these probiotic bacterial/yeast strains in the gut. Prebiotics are essentially the food for the probiotic strains and can help form a symbiotic relationship with the probiotic to improve the overall health status of the horse. 

Why would you need to give your horse a probiotic?

Gut dysbiosis is a fluctuation or disturbance in the population of microorganisms of the gut, which may be linked to a wide range of diseases in horses. Gut dysbiosis can be caused by many factors ranging from dietary changes, antibiotics, disease, intense exercise and training, age, worms, environment, travel, or even minor stress events—resulting in major consequences such as colic. Dysbiosis is generally associated with a reduction in microbial species diversity. 

Diet is one of the major factors contributing to gut dysbiosis. Unlike the ruminant cattle and sheep that use foregut fermentation, horses are hindgut fermenters. The large intestine is the main area where fermentation occurs. The horse utilises the microbial enzymes of the hindgut microbial population in the colon and caecum to break down the plant fibres (cellulose fermentation) sourced mainly from grasses and hay. The horse itself does not possess the hydrolytic enzymes that are required to break the bonds of the complex structures of the plant carbohydrates (in the form of celluloses, hemicelluloses, pectins) and starch; so therefore, it strongly relies on the microbiota present to provide those critical enzymes required for digestion. The main phyla Firmicutes and Bacteroidetes possess enzymes capable of breaking down the complex carbohydrates (such as starch and cellulose). Research has shown that forage-based diets (grasses and hay) promote the most stable gut microbiomes, but ultimately the equine athlete requires far more energy than a forage-based diet can supply. Supplementing the diet with concentrates containing starch such as grain, corn, barley and oats can affect the number and type of bacteria in the gut. Optimising diet composition is so important as carbohydrate overload—as seen with high-starch diets (>1g/kg body weight per meal)—can change the populations of bacteria in the gut, alter pH, upset digestion and the gut environment, and ultimately result in diseases such as colitis, colic and laminitis. The correct diet is essential for maintaining the delicate balance of bacterial populations. Probiotics can be used to either replace the bacteria missing in the gut and/or can help maintain the delicate microbial balance even in the face of adversity such as abrupt dietary changes, antibiotic treatment and stress.

What types of probiotics are available for horses?

There are several probiotic products on the market, and most are in powder or liquid form. There are two main categories of probiotics: generic and autogenous. Generic probiotics are off-the-shelf products that contain specific strains of bacterial or yeast, singularly or in combination. The Lactobacillus and Bifidobacterium families, Enterococci and yeasts such as Saccharomyces cerevisae and boulardii are the most common equine probiotic strains. Advantages of generic probiotics are that they are widely available, easy to administer, and they may be beneficial to horse health (if the strains are alive in sufficient numbers). Autogenous probiotics are specifically formulated using bacteria obtained from the horse’s own faecal sample and, as such, are uniquely adapted to that individual animal. These host-adapted bacteria are more likely to survive in the gut than non-adapted generic strains and can quickly replenish absent or low levels of bacteria unique to the individual horse, thus maintaining health.