Equine Development of Gut Microbiota

A young horse, called a foal. Photo credit: [1]

By Mira Allen

Topic: equine development of gut microbiota

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Introduction

In utero, horses intestinal tracts are close to sterile. Soon after birth, however, microbial colonization skyrockets. Proper colonization lasts about 50 days, and is incredibly important as improper microbial gut content can result in dysbiosis, causing inflammation and metabolic disease [1]. Equine hind-gut microbiota enable nutritional optimization from an otherwise nutrient-poor foraging diet via plant material fermentation [2]. The initial colonization, stabilization, and then weaning period (4-6 months old) as a foal transfers to solid food are important periods in establishing the microbial composition of the colon [1].

Most equine gut bacteria live in the colon, specifically in the caecum [2]. These bacteria degrade otherwise indigestible forage. The equine gut is composed of two main sections [2]:

Upper/fore gut: stomach, jejunum, ileum (Increased microbiota variation and turnover as food is processed here first)
Lower/hind gut: caecum and colon (More stable microbiota, most residing in the colon)

Because the microbiome processes food intake and is responsible for digestion, its disruption can cause inflammation and even result in metabolic disorders [2].

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Gut Colonization: Birth to Maturity

The stages of microbiome colonization in mammals are as follows:
- Initial colonization [1]
- Microbiota stabilization [1]
- Weaning (in foals: 4-6 months) [1]
- Transfer to solid foods (occurs gradually) [1]

While these are generally applicable in mammals, it has been demonstrated that the foal gut microbiome closely resembles their mother's around 60 days of age [1]. This means that their microbiome development occurs more rapidly than most other mammals. A foal’s mother begins to influence its microbiome beginning in utero by circulating microbial metabolites, but the birthing process has a larger impact on colonization [1,3]. Foals have bacteria present in their system immediately after birth. Their microbiome is then diversified and refined via the consumption of mare's milk and manure [1]. The first week of life is a critical time as they are susceptible to infection and disease [3]. Diarrhea is common in this period and is possibly associated with a microbial imbalance [3].

Before 50 days old, gut microbiota composition is transient and dynamic. Research [1] has shown that change in similarity between individual foals and foals and adults occurs in these stages:
Day 0: relatively diverse bacterial colonization likely inherited from the foal's dam (mother) and the environment [3]
Day 1: somewhat decreased microbiota diversity [3]
Day 7: large variation between the microbiota of individual foals
Day 20: more consistent between foals, but different from adults
Day 50: very similar to adult composition

These findings may differ between individuals depending on their housing (ie. stall or turnout), access to adult foods from birth (ie. grain, grass), and geographic location. Domestication and housing type interferes with the sharing of microbiomes between horses. Domesticated horses have lower clostridia phascolarctobacterium, which produces short chain fatty acid propionate [2]. Furthermore, non-domestic horses have higher levels of methanocorpusculum archaea, which are methane producers and may increase the carbohydrate degrading activity of cellulolytic bacteria [2].

Species Composition

The core mature equine microbiome that has so far been documented to include:

- Firmicutes (largest phylum of intestinal bacteria, including clostridia and bacilli) [2]
- Clostridiales: part of the intestinal core microbiome in all mammals [2]
- Produce butyrate: protective of colonocytes [2]
- Lactobacillus mucosae [1]
- Blautia producta [1]
- Streptococcus [1]
- Ruminococcaceae (small percentage, hindgut) [2]
- Fibrobacteraceae (small percentage, hindgut) [2]

Ruminococcaceae and Fibrobacteraceae are involved in plant wall degradation, and seem to be an integral species in gut health [2].

- Proteobacteria (second largest group, driven by environment uptake)(common in upper GIT, most in ileum) may play a role in nitrogen fixation, but overabundance can cause inflammation, sometimes colic [2]
- Enterobacteriales [1][2]
- Pseudomonadales [2]

- Verrucomicrobia (third largest group, present in the caecum, small colon, and rectum)(bacteria is abundant in soil) [2]
- Akkermansia: Mucin degrading, maintains mucin layer integrity, decreases bowel inflammation [2]

Also present in the hindgut [2]:
- Protozoa [2]
- Fungi [2]
- Yeast [2]
- Archaea [2]
- Firmicutes [2]

- Bacteroidetes [2] including:
- Bacteroides uniformis [1]
- Bacteroides fragilis [1]
- Parabacteroides [1]
- Butyricimonas [1]
- Verrucomicrobia [2]
- Methanogenic archaea (metabolize H2 and CO2 to methane; support degradation of cellulolytic bacteria) [2]

The foal gut microbiome has been recorded to contain mostly Firmicutes [2]. Between 2 and 30 days, Verrucomicrobia are the main species [2].

Just after birth (0hrs), the foal microbiome contains mostly Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes groups [3]. Species present include Staphylococcus, Lactobacillus, Bacillus, Streptococcus, Corynebacterium, and Sphingomonas [3]. This is a relatively high diversity of species, which is decreased after the first day [3]. After 24 hours, the gut contains mostly Escherichia/Shigella, Bacteroides, and Firmicutes, with species including Clostridium, streptococcus, enterococcus, and klebsiella [3]. By day 7, the most abundant group is firmicutues, with bacteroides and fusobacteria having increased in abundance decreased proteobacteria [3]. Bacteroides were most abundant genus, present in all foals along with Fusobacterium, Tyzzerella, Streptococcus and Lactobacillus [3].

An Unhappy Microbiome: Effects of Change and Dysbiosis

Changes to the equine microbiome may occur as a result of [2]:
- Exercise
- Transport
- Fasting

An imbalance resulting in a deficiency of one or multiple species can result in the overgrowth of another. It can take up to 25 days to bring the biome back to baseline, but effects can last longer [2]. Foals with a decreased microbiome diversity (specifically decreased lachnospiraceae, ruminococcaceae) have higher likelihoods of developing diarrhea [2].

Septicemia

Sepsis is a disease that occurs when the body improperly reacts to infection. Septic shock causes organ failure due to lack of blood flow and tissue oxygenation. In foals, known causes include failure to transfer immunoglobulins from colostrum [3], issues with gestation or birth, and/or environmental contamination [4]. It can take up to four weeks of intensive care to recover from sepsis, but the recovery rate is still between 50-81% [5].

Colitis

A balanced diet is important for maintaining balanced microbiome. One issue that can occur as a result of imbalance is colitis, which is characterized by acute or long-term inflammation of the gut mucosa in the large bowel (cecum, colon) [2]. Symptoms include a sudden onset of watery diarrhea that causes fluid loss [2]. It can be triggered by [2]:
- Bacterial infections (including Salmonella, Clostridioides Difficile, Clostridium Perfringens, and Neorickettsia Risticii)
- Parasite infections
- Antimicrobial treatment (including Penicillin, Cephalosporins, Fluoroquinolones, and Trimethoprim-sulfadiazine)

Colic

GI issues and stomach pain in horses are collectively known as colic. Colic cases range from mild to severe, but overall are a serious concern for horse-owners as there is only a 63% survival rate [2]. Causes of colic include [2]:
- Sand ingestion
- Stress
- Changes in feeding, which can cause a rapid change in microbiome composition

Laminitis

Laminitis (also known as founder) is a disease in which the supporting tissue connected to the coffin bone (the lowermost bone in a horse's hoof) fails to secure to the hoof wall which can result in the bone twisting or dropping, sometimes completely through the bottom of the hoof. This is incredibly painful, causes severe lameness, and is incurable in severe cases. There are several causes of laminitis, one being sepsis associated [6]. Diseases causing sepsis that have also been associated with laminitis are usually caused by gram negative bacteria [6]. A high starch diet can an increase of bacteria that produce high levels of lactic acid which can cause lactic acidosis, followed by laminitis [2]. Other causes of sepsis related laminitis include retained fetal membranes, colic, and enterocolitis [6]

Anesthesia

Anesthesia is another documented cause of sudden microbiome change, and can further cause enrichment of [2]:
- Anaerostipes
- Ethanoligenens
- Enterococcus (firmicutes)
- Ruminococcus (firmicutes)

References

Authored for BIOL 238 Microbiology, taught by Joan Slonczewski,at Kenyon College,2024