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Ali, A.; Alhussaini, K.I. Hidden World of Gut Microbiota. Encyclopedia. Available online: (accessed on 16 April 2024).
Ali A, Alhussaini KI. Hidden World of Gut Microbiota. Encyclopedia. Available at: Accessed April 16, 2024.
Ali, Asghar, Khalid I. Alhussaini. "Hidden World of Gut Microbiota" Encyclopedia, (accessed April 16, 2024).
Ali, A., & Alhussaini, K.I. (2024, March 12). Hidden World of Gut Microbiota. In Encyclopedia.
Ali, Asghar and Khalid I. Alhussaini. "Hidden World of Gut Microbiota." Encyclopedia. Web. 12 March, 2024.
Hidden World of Gut Microbiota

Metabolites generated from the gut microbiota play an essential role in the host’s health by regulating metabolic homeostasis. A disruption in this equilibrium can lead to the emergence of numerous illnesses and their etiology. Pesticides have been shown in a few recent studies to harm the host’s gut microbiome.

persistent organic pollutants dysbiosis metabolic homeostasis

1. Introduction

Food consumption has grown exponentially as the world population is rising. Pesticides of various varieties are now extensively employed worldwide to improve agricultural product quality and enhance crop yields, resulting in major economic benefits. Pesticides enter the soil, water, air, and non-target creatures such as people [1]. Various medical problems concerning pesticide hazards to animals have risen dramatically [2]. A growing number of studies have linked pesticides to a variety of pathologies, including, immune system dysregulation, neurotoxicity metabolic diseases (such as obesity and type 2 diabetes), endocrine alterations, reproductive disorders, and even tumors, whereas the gastrointestinal microbiota plays a critical role in a variety of host metabolic and immune functions [3]. In most circumstances, the gut can come into direct contact with dietary pollutants, and pesticides are likely to be absorbed by the human gastrointestinal tract and gut flora. Consider an in vitro study that found that exposing bacterial colonies directly to the herbicide glyphosate might modify the constitution of the bacterium [4]. Many authors have specifically proven that different types of environmental contaminants, including certain pesticides, may impact and modify gut microbiota (GM), hence the function of the gut microbiota in pesticide-induced toxicity in non-target species is receiving interest [5].

2. Gut Microbiome

Gut microbiota are microbes that dwell in the gastrointestinal (GI) tract and constitute the gut microbiome when coupled with their bioactivity and genetic material. The human gastrointestinal (GI) tract contains billions of diversified microorganisms, including viruses, bacteria, fungi, and protozoa. The human gut is dominated by mainly four phyla: Proteobacteria, Firmicutes (Clostridium, Lactobacillus, Eubacteria, and Peptoniphilus), Actinobacteria (Bifidobacterium), and Bacteroidetes (Prevotella, Bacteroides). The Firmicutes and Bacteroidetes phyla account for around 90% of all microorganisms, each having a distinct role [6]. Methanosphaera stadtmanae and Methanobrevibacter smithii are examples of Archaea, whereas yeast predominates the Eukarya in the gut [7]. However, various individual differences and underlying variables such as food, pregnancy, hormonal changes, age, illness, gender, and medication (e.g., antibiotics and proton pump inhibitors) result in variations in the composition and concentration of gut microbes [8]. Gut microbes play a significant role in regulating metabolism (e.g., bile acids) and body homeostasis by controlling immune, digestive, and neurological processes with the help of the gut–brain axis (GBA–a network of highly interrelated complicated physiological pathways). In response, the human host provides a nutrient-rich environment [9]. Other functions of gut microbes in children are the strengthening of immunity of the gut mucosa (e.g., induction of secretory regulatory T cells and secretory IgA) and structural gastrointestinal development (e.g., payer’s patches–gut-associated lymphoid tissues, epithelium) [10]. Many proteins which are not present in the human body are encoded by the gut microbes, e.g., enzymes required for the breakdown of hemicellulose and indigestible dietary fibers [9]. Gut bacteria synthesize short-chain fatty acids and monosaccharides by fermenting nutritional fibers. SCFAs (short-chain fatty acids) like acetate and butyrate are necessary energy providers [11].

2.1. Function of Gut Microbe Metabolites

The human host and the gut microbiota interact as a “metabolic organ” which carries out a variety of vital tasks to safeguard human health [12]. The human host can make use of various energy sources due to the gut bacteria’s metabolic activities. Studies on the metabolic profiles of humans and animals have shown that the microbiota can particularly influence how dietary lipids are absorbed, stored, and used. Understanding the functions of these gut microbiome metabolites is crucial for unravelling their impact on host health. The gut microbiota produces organic fatty acids called SCFAs (short-chain fatty acids) through the anaerobic fermentation of non-digestible proteins and fibers, mostly from acetate, propionate, and butyrate [13]. SCFAs play a crucial role in energy metabolism, immune modulation, and maintaining gut barrier integrity. Recent studies have highlighted their potential therapeutic applications in conditions such as inflammatory bowel disease and metabolic disorders [14]. The production of SCFAs is a crucial “microbiota function”. Intestinal epithelial cell proliferation and differentiation are positively influenced by SCFAs, particularly acetate, propionate, and butyrate, which also have diverse metabolic properties [15]. Actually, under normal circumstances, SCFAs supply 5–10% of the usual energy requirements. Key microbial species involved in this process, such as Bacteroides and Firmicutes, contribute to the enzymatic breakdown of complex carbohydrates, yielding SCFAs [16]. The colonic defense barrier can be strengthened by butyrate by increasing mucin production, trefoil factors, and antimicrobial peptides. SCFAs influence host energy metabolism by serving as substrates for mitochondrial beta-oxidation. Additionally, they enhance gut barrier integrity through the upregulation of tight junction proteins, such as ZO-1 and occludin [17]. Butyrate is employed as an energy source for colonocytes. Additionally, butyrate has several impacts on a range of cell types, including immunological regulation, cell cycle inhibition, the induction of programmed cell death, and cellular differentiation [18]. Gut microbiome metabolites also include bile acids, which are produced through the metabolism of host-derived bile. The gut microbiome influences bile acid composition, impacting host metabolism and signaling pathways [19]. The GM modulates bile acid homeostasis. By modulating the expression of bile acid-production enzymes, the microbiome participates in the synthesis of principal bile acids, cholic acid and chenodeoxycholic acid. Other bile acid metabolism processes affected by the GM include conjugation in the liver, reabsorption in the terminal ileum, and deconjugation in the small intestine [20][21]. Figure 1 summarizes the role of metabolites.
Figure 1. The function of metabolites synthesized by gut microbes. SCFA: short-chain fatty acids; BA: bile Acids; TMA: trimethylamine.

2.2. Dysbiosis

Gut dysbiosis refers to disbalance in the function and composition of gut bacteria, alteration in the distribution of gut bacteria, or changes in bacterial metabolic activities. Gut dysbiosis can result from many factors, including antibiotic use, dietary choices, lifestyle, and genetic predispositions [22]. Though antibiotics effectively target pathogens, they can unintentionally disrupt the equilibrium of beneficial microbes, resulting in dysbiosis. Additionally, consuming diets rich in processed foods and deficient in fiber fosters an environment that promotes dysbiosis. Lifestyle factors, such as stress and lack of physical activity, further contribute to microbial imbalance [23]. Studies have revealed that dysbiosis is often characterized by a reduction in beneficial bacteria, such as Bifidobacterium and Lactobacillus, coupled with an overgrowth of potentially harmful microbes, including certain species of Clostridium and Enterobacteriaceae [24]. This shift in microbial composition can profoundly affect the host’s health, influencing immune function, nutrient absorption, and overall gut homeostasis. The disruption of microbial balance leads to alterations in immune function, increased intestinal permeability, and systemic inflammation [25]. Dysbiosis comprises three types: (i) Decline in diversity of gut microbes. (ii) Reduction in valuable organisms. (iii) Proliferative growth of possibly hazardous microbes [26]. Two primary variables might contribute to dysbiosis: host-related factors and environmental factors [27]. Symptoms might initially point to dysbiosis in a person before a particular health issue is detected. Vaginal or rectal itching, foul breath (halitosis), diarrhea, constipation, bloating, nausea, and chest discomfort are typical dysbiosis symptoms. Dysbiosis can also cause malnutrition due to a disturbed digestive system. Depression, reduced concentration level, and anxiety are also possible cognitive weakening symptoms of dysbiosis [28]. Considering the vital role of the gut microbiota in maintaining the homeostasis of the host, its influence spans across all the organ systems of the human body, expanding to various extraintestinal sites. Such bidirectional influences are extended via the gut–brain axis, the gut–heart axis, the gut–liver axis, the gut–lung axis, the gut–skin axis, and the gut–reproductive axis, among others. It has been proved that dysbiosis is one of the leading causes of many chronic diseases like obesity, type 1 and 2 diabetes, gastrointestinal cancer, inflammatory bowel disease, non–alcoholic fatty liver disease (NAFLD), chronic kidney disease (CKD), cardiovascular diseases such as acute ischemic stroke (AIS), and it was even suggested to play a role in the development and progression of neurological disorders such as Alzheimer’s disease [29].

3. Effect of Insecticides on Gut Microbiota

Insecticides, a crucial factor in increasing agricultural output, are used to kill problematic insects. However, these pesticides often exhibit off-target effects due to prolonged exposure [5]. According to recent research, they are hazardous to non-target creatures in the environment. Furthermore, the amount or concentration of insecticides increases as they go up the food chain, posing a concern to human health. Multiple studies have recently discovered pesticides in the human body [30]. Once inside the human body, traces of pesticides may also exhibit adverse effects on the gut microbiota, which can negatively impact human health and behavior [31]. Various exposure studies in this regard have shown that exposure to xenobiotics such as pesticides can lead to alterations in the gut microbial composition, leading to dysbiosis, which further leads to altered functions and behavior impairments in the host, as demonstrated by using animal models [32]. These changes in the gut microbiota can result in various health effects, including metabolic and endocrinal disorders, dysregulation of the immune system, inflammations, and impact on the gut–brain–blood axis as well [33]. Given the extensive employment of pesticides in modern agricultural practices, and the active or passive responses of gut microbiota to such xenobiotics, broader insights must be gained with regard to the interaction between the gut microbiome and pesticides and their long-term collateral effects on gut microbiota composition and function.

3.1. Organophosphate Pesticides (OPPs)

Amides and phosphoric acid are the sources of this class of insecticides. OPPs are the most widely used pesticide worldwide because of their biodegradable nature. These chemicals’ remnants are present in the air, on plant surfaces, and in soil. These chemicals leach into the human system through water and soil. OPP residues have been discovered to be strongly correlated with diabetes in samples of human plasma. When gut microbes break down OPP, the esterase activity and acetate are changed, which leads to gluconeogenesis and glucose intolerance [34]. According to a prior study, mice exposed to OPPs for 180 days developed glucose intolerance. This condition is brought on by the gut microbiome’s breakdown of organophosphate into acetic acid, which is then used as a substrate for gluconeogenesis [35].
Frequently found in fruits and vegetables, chlorpyrifos (O, O-diethyl, O-(3,5,6-trichloro-2-pyridyl)-phosphorothioate) is a widely used organophosphorus insecticide. Several earlier research studies have shown the effects of CPF (chlorpyrifos) in both in vitro and in vivo settings. In the SHIME® model, which mimics the intestinal environment in vitro, there was an observed decrease in the levels of beneficial bacteria such as Bifidobacterium and Lactobacillus, along with an increase in the abundance of Enterococcus and Bacteroides. This shift in microbial composition may lead to alterations in pH levels or the stimulation of short-chain fatty acids (SCFAs), which in turn can inhibit the colonization of potentially harmful bacteria in the gut [36]. When CPF is applied alone to Caco-2/TC7 cell models of the intestinal mucosa, this can disrupt the mucosal barrier, cause the release of the chemokine IL-8, and cause inflammation. However, as mentioned earlier, the two models do not account for microbiota–host crosstalk [37]. Prolonged exposure appears to have effects on the gut in addition to the levels of the gonadotropin’s follicle-stimulating hormone, luteinizing hormone, and testosterone in the blood, as well as the inflammatory cytokines IL-6, monocyte chemoattractant protein-1, and TNF- in rats, suggesting a potential role in the development of colitis and infertility [38]. The effects of CPF on oxidative stress and gut microbiota dysbiosis in zebrafish have been emphasized by other scientists. In comparison to the control group, researchers found that zebrafish exposed to CPF exhibited an increase in Proteobacteria abundance alongside a decrease in the Bacteroidetes phylum [39]. In contrast to mice treated for 30 days with 1 mg/kg body weight of CPF, which caused changes in the gut microbiota and urine metabolites, it was found that amino acids, metabolites, SCFAs, and bile acids caused intestinal inflammation and aberrant permeability of the intestine [40]. Last but not least, exposure to CPF reduced hepatic glucose and lipid metabolism in an animal model through oxidative stress and microbiota dysbiosis [40].
Due to its widespread use in agriculture, diazinon is another OPP that has caused public health issues. Drinking water, the main method of exposure to diazinon for people, has a substantial traceability in its amount [41][42]. Male mice exposed to 4 ppm diazinon concentrations in drinking water for 13 weeks showed changes in bacterial populations and composition, as well as significant impairments in the energy metabolism of the gut flora. Additionally, exposure to diazinon activated several stress response pathways [42]. Rats exposed to diazinon for 14 days exhibited histological alterations and an upsurge in the Bacteroidetes, Firmicutes, and Fusobacteria phyla in their guts [33].

3.2. Organochlorine Pesticides (OCPs)

OCPs have been frequently identified in the environment even though several nations prohibited them in the 1970s and 1980s due to their chronic build-up in the body and hazard to human health [43]. The presence of methanobacteriales in the gut, serum OCP concentrations, and obesity in the general population may all be connected, intriguingly. The most well-known and harmful OCPs are p,p’-dichlorodiphenyldichloroethylene (p,p’-DDE) and b-hexachlorocyclohexane (b-HCH), which are the primary breakdown products metabolized from dichlorodiphenyltrichloroethane (DDT) and hexachlorocyclohexane (HCH) [44]. Changes in the gut microbiota composition of mice exposed to DDE for eight weeks increased Bacteroidetes and decreased Proteobacteria, Deferribacteres, and Cyanobacteria [45]. Another analysis revealed that chronic HCH and DDT exposure in mice led to a modification of the relative abundance and stoichiometry of gut microbiota by boosting Bacteroidetes and lowering Proteobacteria, Deferribacteria, and Cyanobacteria, with an increased quantity of the Lactobacillus strain being observed with bile salt hydrolase activity. These variations substantially impact the hydrophobicity of hepatic and bile acid.

3.3. Permethrin (PEM)

PEM is a pyrethroid compound frequently employed in agricultural, public health, and residential pest management. PEM exposure in the gut microbiota may result from contaminated food [46]. Previous research has found that following exposure to low-dose PEM, the numbers of Bacteroides, Prevotella, and Porphyromonas were decreased. At the same time, the quantity of Enterobacteriaceae and Lactobacillus in the feces rose after the 4-month follow-up [47]. PEM inhibited both potential pathogens like Staphylococcus aureus and Escherichia coli and helpful bacteria like Bifidobacterium and Lactobacillus paracasei in an in vitro investigation [47]. Overall, postnatal exposure to PEM at low doses had a deleterious impact on the gut microbiota in rats, which may play a significant role in the development of illnesses; hence, more research is needed. In conclusion, pesticides have detrimental impacts on the gut microbiota in several animal models and have an effect on the host’s health. Research that lends credence to the theory found that aldicarb exposure enhanced the pathogenicity of gut bacteria in mice and disrupted their metabolism [36]. As a result, researchers have begun paying closer attention to gut bacteria when assessing the toxicity of pesticides.


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