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Crnčević, N.; Hukić, M.; Deumić, S.; Selimagić, A.; Dozić, A.; Gavrankapetanović, I.; Klepo, D.; Avdić, M. Impact of Antibiotic Resistance on Gastrointestinal Tract Environment. Encyclopedia. Available online: https://encyclopedia.pub/entry/25806 (accessed on 14 July 2025).
Crnčević N, Hukić M, Deumić S, Selimagić A, Dozić A, Gavrankapetanović I, et al. Impact of Antibiotic Resistance on Gastrointestinal Tract Environment. Encyclopedia. Available at: https://encyclopedia.pub/entry/25806. Accessed July 14, 2025.
Crnčević, Neira, Mirsada Hukić, Sara Deumić, Amir Selimagić, Ada Dozić, Ismet Gavrankapetanović, Dženana Klepo, Monia Avdić. "Impact of Antibiotic Resistance on Gastrointestinal Tract Environment" Encyclopedia, https://encyclopedia.pub/entry/25806 (accessed July 14, 2025).
Crnčević, N., Hukić, M., Deumić, S., Selimagić, A., Dozić, A., Gavrankapetanović, I., Klepo, D., & Avdić, M. (2022, August 03). Impact of Antibiotic Resistance on Gastrointestinal Tract Environment. In Encyclopedia. https://encyclopedia.pub/entry/25806
Crnčević, Neira, et al. "Impact of Antibiotic Resistance on Gastrointestinal Tract Environment." Encyclopedia. Web. 03 August, 2022.
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The spread of antibiotic resistance represents one of the major global health care concerns. Antibiotics severely affect the diversity of the gastrointestinal microbiome. This can lead to the loss of essential taxa and changes in the host’s metabolism.
antibiotic resistance
gastrointestinal tract environment
gastrointestinal tract microbiota
1. Introduction
The dynamic small bowel environment is not very suitable for microbial colonies due to digestive enzymes and bile, short transit time, and food ingestion. Because of this, its microbial life is less diverse and needs to adjust and respond quickly to different luminal conditions. The bacteria present in this environment have lower biomass, and the number of bacterial colonies changes in various locations in the small bowel. The bacterial population in the duodenum is approximately 104–105 CFU/mL. From the duodenum, this number increases gradually to 107–108 CFU/mL in the ileum. Moreover, the bacteria present also changes from the proximal-distal segments of the small bowel and the colon. There is an increase in the proportion of Gram-positive to Gram-negative bacteria. Moreover, the balance of strict anaerobic and facultative anaerobic bacteria increases in this direction. The genera usually found in the small bowel include Staphylococcus, Lactobacillus, Bacteroides, Clostridium, and Streptococcus, and their presence is affected by aging and diet [1]. Due to aging, the conditions such as diabetes, pancreatic disease, and cancer have potential adverse effects on the formation and function of the small bowel. The aging enteric nervous system may cause selective neurodegeneration contributing to the GI symptoms such as dysphagia, GI reflux, and constipation [2]. The bacterial composition and content of the gastrointestinal (GI) tract is seen in Table 1.
Table 1. GI tract bacterial count and composition in humans.
| GI Tract | Bacterial Count | Bacterial Composition |
|---|---|---|
| Stomach | 103–104/mL content | Streptococcus Staphylococcus Enterococcus Lactobacillus |
| Duodenum/jejunum | 103–104/mL content | Corynebacterium |
| Ileum | 108/mL content | Escherichia coli Klebsiella Enterobacter Bacteroides Eubacterium Clostridium Ruminococcus |
| Colon | 1011/mL content | Bifidobacterium |
The importance of microbial life in the small bowel can be seen in its involvement in folate, vitamin K, and amino acid metabolism. This phenomenon was examined in an experiment in which the metabolism of germ-free and healthy mice was compared [3][4]. It was found that germ-free mice need supplementation with vitamin B, more specifically B12, folate, biotin, and vitamin K. These two vitamins are produced by bacterial genera including Eubacterium, and Fusobacterium, Bacteroides, and Propionibacterium. Moreover, another function of the resident small bowel bacteria represents the protection of the intestinal mucosa from invading pathogens, production of bacteriocins, and biofilm formation. This is achieved by preventing the pathogens from entering epithelial cells and is also known as the barrier effect [5].
The host diet plays a vital role in the small intestine environment. The primary biochemical process that occurs is the fermentation of carbohydrates. Compared to the fecal metagenome, the small intestinal metagenome has significantly more genes involved in the metabolism of carbohydrates. The main processes include lactate fermentation, the pentose phosphate pathway, and the sugar phosphotransferase systems. Studying the small intestine can be very challenging due to its inaccessibility. In experiments involving the human small intestine microbiota, specific invasive methods have to be used. The most common methods for studying the small intestine include nasoduodenal catheters and esophagoduodenogastroscopy. Because of this, it is difficult to find individuals who would participate in this kind of study [1].
Recently, molecular diagnostic techniques have started to become more popular. The microbial composition in the GI tract can also be determined by analyzing the 16s ribosomal RNA gene in bacteria. The findings from molecular diagnostic techniques suggest that there are approximately 200 bacterial strains. Bacteroidetes and Firmicutes are predominantly found in vertebrates. They represent more than 90% of all bacteria in the GI tract. Factors that affect gut microbiota diversity include genetics, diet, gender, and environment [6].
Many external factors affect the small intestine environment, including alcohol, tobacco, antibiotics, chemotherapeutics, cytostatics, and other ingested materials. This can result in various diseases and conditions such as gastric cancer, idiopathic inflammatory disorders, post-infectious syndromes, and squamous cell esophageal cancer. On the other hand, external factors such as food antigens can cause different diseases to develop, such as food allergies, eosinophilic esophagitis, and celiac disease [7].
Studying the small intestine environment possesses many difficulties because of its inaccessibility. Hence, most studies use samples obtained from sudden death victims, colonoscopies, and small intestine transplantations. The accuracy of this method is compromised since there is a risk of contamination from the colon. There is not enough clinical data about this topic that could help doctors find the optimal treatment for each patient. Recent diagnostic methods such as double-balloon enteroscopy and wireless capsule endoscopy represent a beginning of a new diagnostic era for minor intestine abnormalities with good precision and accuracy. Since the dynamic environment of the small intestine is involved in the functioning of the entire body, more research in this field will provide people with answers about the overall homeostasis of the host and the development of associated diseases [8].
2. Impact of Antibiotic Resistance on Gastrointestinal Tract Environment
The spread of antibiotic resistance represents one of the major global health care concerns. The post-antibiotic era crisis is becoming more severe every day due to the overuse of antibiotics. The severity of this problem is seen as an increased rate of mortality among patients with bacterial infections [9]. Antibiotics severely affect the diversity of the gastrointestinal microbiome. This can lead to the loss of essential taxa and changes in the host’s metabolism. If this occurs, the antibiotic resistance in the remaining taxa is further stimulated [10].
Since antibiotic-susceptible bacteria are eradicated, the remaining antibiotic-resistant bacteria grow and multiply to take their place. Although the microbiome’s diversity is reduced, the overall amount of bacteria in the gastrointestinal tract can increase after the use of antibiotics. A study was conducted on patients to test the effect of broad-spectrum antibiotics on the overall microbial load. The results revealed that treatments with β-lactams for seven days resulted in an increased microbial load. This was concluded after the analysis of the patient’s fecal samples. Their microbial load was two-fold higher when compared to their negative controls. Furthermore, the ratio of Bacteroidetes to Firmicutes was also increased [11].
In addition, the overuse of antibiotics also affects the host’s immune system. In a study conducted to examine the effect of antibiotics on mice, it was shown that the overuse of antibiotics results in changes in gene expression and immune system regulation. The mice were given antibiotic treatments from birth. The incidence of type 1 diabetes was increased after using pulsed dosing in susceptible mice. Moreover, these mice were shown to have a lower relative level of anti-inflammatory T cells [12].
References
- Kastl, A.J.; Terry, N.A.; Wu, G.D.; Albenberg, L.G. The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions. Cell. Mol. Gastroenterol. Hepatol. 2020, 9, 33–45.
- Saffrey, M.J. Ageing of the Enteric Nervous System. Mech. Ageing Dev. 2004, 125, 899–906.
- Bentley, R.; Meganathan, R. Biosynthesis of Vitamin K (Menaquinone) in Bacteria. Microbiol. Rev. 1982, 46, 241–280.
- Wostmann, B.S. The Germfree Animal in Nutritional Studies. Annu. Rev. Nutr. 1981, 1, 257–279.
- Canny, G.O.; McCormick, B.A. Bacteria in the Intestine, Helpful Residents or Enemies from Within? Infect. Immun. 2008, 76, 3360–3373.
- Haag, L.-M.; Siegmund, B. Intestinal Microbiota and the Innate Immune System—A Crosstalk in Crohn’s Disease Pathogenesis. Front. Immunol. 2015, 6, 489.
- Hall, E.H.; Crowe, S.E. Environmental and Lifestyle Influences on Disorders of the Large and Small Intestine: Implications for Treatment. Dig. Dis. 2011, 29, 249–254.
- Tang, Q.; Jin, G.; Wang, G.; Liu, T.; Liu, X.; Wang, B.; Cao, H. Current Sampling Methods for Gut Microbiota: A Call for More Precise Devices. Front. Cell. Infect. Microbiol. 2020, 10, 151.
- Llor, C.; Bjerrum, L. Antimicrobial Resistance: Risk Associated with Antibiotic Overuse and Initiatives to Reduce the Problem. Ther. Adv. Drug Saf. 2014, 5, 229–241.
- Lange, K.; Buerger, M.; Stallmach, A.; Bruns, T. Effects of Antibiotics on Gut Microbiota. Dig. Dis. 2016, 34, 260–268.
- Panda, S.; El Khader, I.; Casellas, F.; López Vivancos, J.; García Cors, M.; Santiago, A.; Cuenca, S.; Guarner, F.; Manichanh, C. Short-Term Effect of Antibiotics on Human Gut Microbiota. PLoS ONE 2014, 9, e95476.
- Willing, B.P.; Russell, S.L.; Finlay, B.B. Shifting the Balance: Antibiotic Effects on Host—Microbiota Mutualism. Nat. Rev. Microbiol. 2011, 9, 233–243.
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