Microbiome, dysbiosis and use of probiotics in various diseases

Abstract

The community of microorganisms that colonize certain areas of the human body is called microbiota. Microorganisms such as bacteria, fungi and viruses make up the microbiota. The sum of the genomes of these microorganisms and microorganisms refers to the microbiome. It has been shown that microbiota has important effects such as protecting the organ from pathogens, contributing to metabolic functions (such as vitamin synthesis, carbohydrate digestion) and providing immunoregulation. Dysbiosis refers to compositional and functional changes in the microbiota. At the beginning of the 21^st century, numerous studies have investigated the human microbiota and its imbalance in relation to various diseases and found that dysbiosis is associated with many diseases. The aim of this mini-review article is to provide brief information about dysbiosis and its care and to raise awareness.

Key Words: Microbiota; Microbiome; Probiotics; Prebiotics; Fecal microbiota transplantation; Dysbiosis; Dysbiosis-related diseases

Core Tip: Dysbiosis refers to compositional and functional changes in the microbiota that cause disruption of the resistance and resilience of the microbial ecosystem. Correction of dysbiosis by beneficial bacteria such as probiotics can be a useful treatment for allergic diseases.

INTRODUCTION

Certain areas of the human body are colonized by trillions of host-specific microorganisms such as bacteria, fungi, viruses and protozoa living in symbiosis. This community of microorganisms is called the microbiota. Human microbiota is a complex, dynamic and symbiotic ecosystem[1]. The most important and largest microbial community in the human body is found in the intestines. Oral microbiota is the second largest microbial community after the intestines. The microbiota is also localized in other regions such as the lung, skin and vagina[2]. The composition of the microbiota varies according to the region. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria and Verrucomicrobia are the major microorganisms constituting the intestinal microbiota[3]. The main bacteria found in the oral microbiota are Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria[4]. Again, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria are the main components of the lung microbiota[5].

It has been shown that the microbiota has effects such as protecting the organ against pathogens, contributing to metabolic functions and providing immune regulation and thus protecting host homeostasis[6]. Gastrointestinal microbiota is known to play a role in supporting the digestion and absorption of complex carbohydrates, utilization of energy sources such as short-chain fatty acids, synthesis of important vitamins such as vitamin B and vitamin K, and regulation of the metabolism of essential substances such as bile acids and sterols. In addition, intestinal microbiota prevents colonization by competing with pathogenic microorganisms and ensures the protection of intestinal epithelial barrier integrity[7,8]. In recent years, it has been shown that the gut and brain interact strongly through endocrine, neural and immunologic mechanisms and has been named as the brain-gut axis[9].

Dysbiosis refers to compositional and functional changes in the microbiota that cause disruption of the resistance and resilience of the microbial ecosystem[10]. Today, thanks to advances in molecular biological techniques (16S ribosomal RNA targeting analysis, metagenomic analysis), intestinal microbiota can be analyzed at the DNA and RNA level without the need for culture. With these developments, the relationship between gut microbiota and various diseases has been extensively reported[11-14]. Recent studies have linked dysbiosis with many diseases such as inflammatory bowel diseases, liver diseases, obesity, type 2 diabetes, atherosclerotic heart diseases, neurological diseases, immune defects, allergic diseases, depression and autism[12-16]. Therefore, studies examining the effect of microbiota and dysbiosis correction in the treatment of these diseases have gained value in recent years.

ROLE OF DYSBIOSIS IN SPECIFIC DISEASES AND THERAPEUTIC TARGETS

In this section, the use of probiotics in diseases of different systems due to dysbiosis and its effects on disease will be discussed.

Inflammatory bowel diseases

The initiating cause of inflammatory bowel diseases (IBD) is not known exactly. Genetic and environmental factors (such as diet, stress, antibiotic use, sleep patterns, smoking, hygiene) are thought to play a role in the development of these diseases[13]. Dysbiosis, which refers to the loss of beneficial bacteria and increase in pathogenic bacteria, is thought to be involved in the pathogenesis of IBD[17]. In many studies, a relative increase in Proteobacteria, especially Escherichia coli (E. coli), has been defined in IBD patients[18-20]. In the intestinal microbiota of patients with ulcerative colitis or Crohn's disease, it was found that Roseburia and Phascolarctobacterium levels decreased and Clostridium levels increased. Roseburia is associated with anti-inflammatory regulatory T cell production in the gastrointestinal system[21]. In IBD patients and animal models with intestinal inflammation, it was found that the amount of Faecalibacterium prausnitzii bacteria producing butyrate and other short-chain fatty acids in the intestine decreased in relation to dysbiosis[22]. In a small-scale study in children with ulcerative colitis, Limosilactobacillus reuteri (L. reuteri) in combination with mesalazine was shown to increase remission and improve clinical, endoscopic and histologic scores compared to the placebo group[23]. On the other hand, a recent Cochrane review involving mostly adults with ulcerative colitis found that the effect of probiotics on the maintenance of remission was unclear[24]. A randomized control trial (RCT) with Lacticaseibacillus rhamnosus (LGG) showed also no benefit in Crohn's disease[25].

Probiotic studies in IBD have frequently been conducted with Lactobacillus and Bifidobacterium species. According to current data, there is no evidence that a specific strain will be beneficial in the treatment of Crohn's disease. There is also insufficient evidence to recommend systematic administration of a specific strain in the treatment of ulcerative colitis, but there are studies showing that L. reuteri and VSL 3 [Lactobacillus acidophilus (L. acidophilus), Lactobacillus delbrueckii subsp. delbrueckii (L. delbrueckii subsp. bulgaricus), Lactobacillus casei (L. casei), Lactobacillus plantarum, Bifidobacterium longum, Bifidobacterium breve, Bifidobacteria infantis and Streptococcus salivarius subsp. thermophilus] may be beneficial[26]. Although there are many studies on IBD and probiotics, there are limitations in the studies conducted so far. The most recent studies on dysbiosis and gut microbiota are ongoing with new generation probiotics such as Faecalibacterium prausnitzii[27].

Colorectal cancer

It has been found that butyrate produced by symbiotic bacteria beneficial to the intestine directly stimulates macrophages, T cells and dendritic cells and suppresses colonic inflammation and carcinogenesis by increasing interleukin (IL)-10 production. In case of dysbiosis, butyrate-producing bacteria in the intestine have been shown to decrease[28]. It has been found that dysbiosis, which causes an increase in bacteria such as E. coli and Bacteriodes fragilis, leads to disruption of the intestinal mucosal barrier and causes more bacteria to be transported to the submucosal tissue. This is thought to lead to chronic tissue inflammation and thus predispose to the development of colorectal cancer[29]. Understanding the mechanisms behind dysbiosis cycles and clearly identifying the bacteria or bacterial groups responsible for dysbiosis will play an important role in the prevention and treatment of IBD and colorectal cancers that will develop on this basis in the future. The most recent research on the treatment of these diseases is related to fecal microbial transplantation (FMT).

Liver diseases

The liver is the first organ supplied by portal blood flow originating from the gut. Therefore, liver diseases are thought to be strongly affected by intestinal bacteria and metabolites[30]. Hepatic macrophages and stellate cells are important cells affected by gut bacteria and metabolites in the development of chronic liver diseases. Stellate cells transform into myofibroblast-like cells with alpha smooth muscle actin expression, produce high levels of cell matrix and induce liver fibrosis. Activation of these cells by various stimuli such as reactive oxygen species, cytokines and chemokines is thought to induce angiogenesis and fibrosis, leading to the formation of a cancer microenvironment that supports the growth and development of cancer cells[31]. Liver macrophages induce the influx of bone marrow-derived monocytes and neutrophils and contribute to the formation of fibrosis by activating stellate cells[32]. In addition, liver macrophages produce matrix metalloprotease, an extracellular matrix-degrading enzyme, and express tumor necrosis factor-related apoptosis-inducing ligand, which induces apoptosis in liver parenchymal cells[33].

It has been reported that patients with chronic hepatitis C virus infection have decreased diversity of intestinal microbiota[34]. In the intestinal microbiota of patients with chronic hepatitis B virus (HBV) infection and HBV-related cirrhosis, a decrease in lactic acid bacteria and Bifidobacteria and an increase in Enterococcus and Enterobacteriaceae have been reported[35,36]. Wei et al[37] compared the intestinal microbiota of HBV-related cirrhosis patients with healthy subjects and reported a decrease in Bacteroidetes and an increase in Proteobacteria compared to healthy subjects. It was reported that intestinal microbial diversity decreased in autoimmune hepatitis patients and Bifidobacterium, which is associated with disease activity in autoimmune hepatitis, decreased[38]. It has also been shown to play a role in autoimmune hepatitis exacerbation through IL-18 induced by toll like receptor (TLR) ligands produced by gut microbiota[39]. Dysbiosis is known to cause the formation and progression of nonalcoholic fatty liver disease [nonalcoholic steatohepatitis (NASH), steatohepatitis][40]. As a result of the association of microbiota with liver diseases, intestinal microbiota has been targeted in the treatment of liver diseases in recent years. In a meta-analysis on the effects of probiotics on NASH, it was reported that probiotic treatment decreased alanine aminotransferase (ALT), total cholesterol and tumour necrosis factor-alpha and improved insulin resistance in patients[41]. Again, it has been observed that ALT level and fatty liver in NASH patients improved significantly with the combined use of probiotics and prebiotics[42,43]. There are various studies on FMT in liver diseases. In a study conducted with 8 male patients with severe alcoholic hepatitis, FMT was found to be effective in the treatment of hepatic damage within the first 1 week, and even 1 year after FMT, a decrease in severe hepatic damage and improvement in survival were observed[44]. Further clinical trials are ongoing to determine the effects of FMT in the treatment of chronic liver diseases.

Allergic diseases

Human cohort studies have shown that individuals with food allergy have different gut microbiomes compared to healthy control subjects. Study results suggest that dysbiosis in allergic individuals occurs before the development of food allergy. Accumulating evidence supports a potential role for the gut microbiome in the pathogenesis and course of food allergy[45-49]. In a United States-based study, 141 children with proven egg allergy and a control group without food allergy were compared. It was found that microorganisms from the Lachnospiraceae, Streptococcaceae and Leuconostocaceae families were quite high in the microbiome of allergic children[49]. In an Italy-based study conducted in children with milk allergy, it was shown that the intestinal microbiome of infants with milk allergy contained a higher proportion of Lachnospiraceae and Ruminococcaceae compared to healthy control subjects[50]. Mouse experiments to test the role of the microbiota in food allergy have used germ-free mice receiving broad-spectrum antibiotics to reduce the bacterial load in the gut or completely devoid of a normal commensal microbiota. Studies have shown that the microbiota provides a suppressive signal to prevent the development of peanut or milk allergy[51,52].

Evidence from clinical and mouse studies that gut microbiota may influence the pathogenesis and course of food allergy has led to investigations into the effects of microbial therapeutics (probiotics, prebiotics, synbiotics and FMT) in the prevention or treatment of food allergies. Although the efficacy of microbial therapeutics in food allergy has not yet been proven, advances in molecular biological techniques hold promise for the future. After oral administration, probiotics interact with intestinal epithelial cells via TLRs and stimulate cytokine synthesis. Macrophage chemoattractant protein 1 is released by intestinal cells, leading to an increase in the number of immunoglobulin A-secreting cells of mucosal tissues. In addition, probiotics stimulate Treg cells and increase the release of the anti-inflammatory cytokine IL-10[53-55].

There are many studies in which different probiotics have been administered for the prevention and treatment of atopic dermatitis. Although the results are controversial, it has been demonstrated that probiotic administration in the last 3 months of pregnancy and around 6 months postpartum prevents/delays the development of eczema[56]. Again, it has been demonstrated that different probiotics reduce atopic dermatitis disease scores (Severity Scoring of Atopic Dermatitis) in therapeutic administration[57].

In patients with allergic rhinitis, some probiotic strains have been shown to prevent disease complaints and improve quality of life[58-61]. Similarly, many studies have been conducted on the use of probiotics in children with asthma. Our conclusion from these studies is that the routine use of probiotics in the treatment of asthma is not recommended. However, especially some strains have shown beneficial effects on respiratory tract symptoms and attacks in asthmatic patients[62,63].

Neurological diseases

Recent studies have demonstrated the pathogenic role of intestinal dysbiosis in many diseases related to the central nervous system. These diseases range from neuropsychiatric disorders to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease[64], frontotemporal degeneration and autoimmune neurological diseases such as amyotrophic lateral sclerosis and multiple sclerosis[65-69].

The ratio of total body levels of various neurotransmitters is significantly higher in the gut than in the brain. Short-chain fatty acids modulate the levels of excitatory and inhibitory neurotransmitters essential for brain functioning, such as dopamine, epinephrine, norepinephrine, serotonin, gamma-aminobutyric acid (GABA), glutamate and histamine, mainly by regulating amino acid catabolism. It has been found that various bacterial species can alter the levels of neurotransmitter precursors in the gut and even independently synthesize neurotransmitters such as GABA, dopamine, serotonin and noradrenaline. These neurotransmitters are important in diseases such as depression, anxiety, autism and schizophrenia[70]. Increased intestinal and blood brain barrier permeability due to intestinal dysbiosis is thought to affect the host's immune homeostasis through translocation of intestinal microorganisms and neuroactive metabolites and trigger a toxic inflammatory environment that alters brain morphology[71]. Recent preclinical and clinical studies have provided scientific evidence for the role of gut microbiota disruption in the pathology of neurological diseases. These results suggest that correction of gut dysbiosis through prebiotics, probiotics and synbiotics may be an effective strategy for the treatment of symptoms of psychiatric, neurodevelopmental and neurodegenerative disorders[72]. In one study, it was observed that probiotic (L. acidophilus) supplementation administered to children with autism for two months improved the ability to concentrate and the ability to follow a command[73]. Another study showed that the correct use of probiotics alleviated the symptoms of autism[74]. The results of these studies are promising for the future (Table 1)[23,25,57,61,63,74].

Table 1 Use and effects of probiotics in various diseases.

Disease	Probiotics	Dose/duration	Conclusion	Ref.
Ulcerative colitis	L. reuteri +meselazin	1010/8 weeks	Increase in remission, improvement in clinical, histologic and endoscopic scores	Oliva et al[23]
Crohn's disease	LGG	2 × 1010/2 years	Ineffective	Bousvaros et al[25]
Atopic dermatitis	Various (LGG/LGG + L.reuteri)/(rhamnosus + Bifidobacterium lactis)	Variable	Improvement in Severity Scoring of Atopic Dermatitis	Michail et al[57]
Allergic rhinitis	Various	Variable	Improvement in nasal symptoms and eye symptoms, improved quality of life	Chen et al[61]
Asthma	L. reuteri	108/2 months	Decreased FeNO and IL-2, increased IL-10	Miraglia Del Giudice et al[63]
Autism	VSL 3	Not known	Alleviation of autism symptoms	Grossi et al[74]

IL: Interleukin; LGG: Lacticaseibacillus rhamnosus; L. reuteri: Limosilactobacillus reuteri.

Cardiovascular diseases

The gut microbiota is thought to play an important role in the control of blood pressure. Impairment in microbiota may be associated with hypertension. In a study by Kawase et al[75] in which hypertensive rats were compared with normotensive rats, it was observed that microbial enrichment was impaired in hypertensive animals, the Firmicutes/Bacteroidetes ratio increased and the presence of a significant dysbiosis. There are also studies reporting that Lactobacillus probiotics are beneficial in the regulation of blood pressure[76-78]. A meta-analysis showed a significant decrease in blood pressure in patients treated with probiotics[79]. Recent studies have shown that the risk of cardiovascular disease is related not only to gut microbiota but also to oral microbiota. In a study conducted in patients with acute coronary syndrome, a higher subgingival bacterial load was shown compared to controls. In this study, Streptococcus intermedius, S. sanguis, Streptococcus anginosus, Tannerella forsythensis, Treponema denticola and Porphyromonas gingivalis were the most increased species[80].

Obesity and type 2 diabetes

It is thought that increased plasma lipopolysaccharides in case of dysbiosis lead to the release of proinflammatory cytokines by binding to TLR-4 and triggering macrophage aggregation or activation of nuclear factor kappa B signaling pathway and this interaction is thought to cause diabetes development as a result of inhibition of insulin secretion[81,82]. In addition to causing the development of insulin resistance, dysbiosis is thought to be effective in the development of obesity and metabolic disease by inhibiting the production of satiety-related gastrointestinal peptides[83]. In one study, FMT was performed from normal-weight donors to insulin-resistant patients with metabolic syndrome and this transplantation was shown to increase insulin sensitivity in recipients[84].

Infectious diseases and diarrhea

Acute gastroenteritis (AGE) is a picture of dysbiosis caused by an increased number of microorganisms such as pathogenic bacteria, viruses and parasites in the intestines. Most of the existing probiotic studies are related with the use of probiotics in gastroenteritis[59]. Microorganisms e.g., LGG, Saccharomyces boulardii, Enterococcus, L. reuteri are the most common microorganisms evaluated for AGE treatment. As a common result of various studies conducted with these microorganisms, it was found that the number of days of diarrhea was shortened by 1 day on average with the use of probiotic in appropriate duration and dose[85-87]. A Cochrane review of 39 RCTs concluded that probiotics reduced Clostridium difficile diarrhea by approximately 60% when administered with antibiotics in diarrhea associated with antibiotic use. This beneficial effect of probiotics is even more pronounced in patients at high risk[88].

CONCLUSION

Due to the fact that previous studies on microbiota were culture-based, the gut microbiota could not be fully analyzed until recent years. Today, thanks to advances in molecular biological techniques (16S ribosomal RNA targeting analysis, metagenomic analysis), the gut microbiota can be analyzed at the DNA and RNA level without the need for culture. With these advances, the relationships between gut microbiota and various diseases have been elucidated and dysbiosis has been associated with more diseases. As dysbiosis has been shown to play a role in the pathogenesis of many diseases, researchers have focused on the principles of treatment of these diseases based on correction of dysbiosis. Although there are studies showing that FMT with appropriate prebiotic or probiotic use is successful in some diseases, more extensive research is needed to develop effective treatments for dysbiosis.