Bacterial pathogens have developed exquisite virulence mechanisms to survive in the host cells. These virulence mechanisms help them bind and internalize into host cells, replicate, and evade the host immune response. The mammalian host itself has developed its own repertoire of weapons to prevent this from happening. One important component of host response in preventing infections in the gut lumen is the diverse commensal microbiota present. Dysbiosis of the gut microbiota has been implicated in the development of many gastrointestinal diseases. A potential therapeutic pathway to solve these diseases would be by providing probiotics and/or prebiotics to help stimulate growth of the beneficial commensal bacteria. Here, we will present evidence of commensal microbiota imbalance in the development of disease as well as potential therapies to restore gut harmony.
- bacterial infections
Probiotic microorganisms have been extensively studied for their beneficial effects in not only maintaining the normal gut mucosa but also protection from allergens, pathogens, and toxins [1, 2]. The gastrointestinal tract (GI) and its associated microbiota is a complex system that allows for the digestion and absorption of critical nutrients. Additionally, the presence of the commensal bacteria leads to the development and regulation of the mucosal immune system . It is believed that 60% of all fecal matter mass in humans consists of bacteria and that there are between 1010 and 1012 colony-forming units per gram of intestinal content in the colon . The intestinal epithelium is a physical and biochemical barrier that seeks to protect mammalian cells from infection and injury from contaminants such as toxins, pathogenic bacteria, commensal bacteria, and even other luminal contents. Specialized intestinal epithelial cells (IECs) are able to sense and respond to these stimuli with appropriate responses such as increasing their barrier function to activation of anti-pathogenic immune mechanisms .
The International Scientific Association for Probiotics and Prebiotics (ISAPP) in 2014 agreed on a consensus definition of probiotics based on the previous Food and Agriculture Organization of the United Nations and World Health Organization (WHO) definition. ISAPP defines probiotics as ‘live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” . Probiotics have been used for the treatment of
The major defensive mechanism of the gut is the intestinal barrier which maintains epithelial integrity and to protect the host from the environment. In defense of this barrier, there exists the mucous layer, antimicrobial peptides, secretory IgA and the epithelial junction adhesion complex . Disruption of these defense mechanisms allows for the bacteria and food antigens to reach the submucosa, which can induce an inflammatory response potentially leading to the intestinal disorders such as inflammatory bowel disease [15, 16].
The most common probiotic strains used are
In regards to maintenance of the gut epithelial barrier, one can upregulate the genes important for this process . Lactobacilli treatment has been shown to affect several genes including E-cadherin and β-catenin that affect adherence cell junctions in a cell culture model. The phosphorylation and abundance of adherence junction proteins including PKCδ  has been seen with Lactobacilli treatment. The probiotic
Another method to promote epithelial barrier function may be to increase mucin production thereby leading to increased barrier function as well as exclusion of pathogens and toxins. There have been contradictory data for both
Prebiotics and their beneficial effects on human health have been of interest in recent years because of their perceived safety since they are derived from dietary products. The definition of prebiotics has changed somewhat from their initial description in 1995 by Glenn Gibson and Marcel Roberfroid . Today, the general consensus is that “dietary prebiotics” are “selectively fermented ingredients that results in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health” . There are many types of prebiotics but they can be segregated into the following groups : (1) fructans, (2) galacto-oligosaccharides (GOS), (3) starch and glucose-derived oligosaccharides, (4) other oligosaccharides, and (5) non-carbohydrate oligosaccharides.
Fructans, such as inulin and fructose-oligosaccharides (FOS)/oligofructose, generally have a linear chain of fructose with a β(2 + 1) linkage usually with terminal glucose units with a β(2 + 1) linkage with variable degrees of polymerization (DP) [33, 34, 35, 36]. GOS is the product of lactose extension that can be classified into two subgroups: (i) excess galactose at C3, C4 or C6 and (ii) derived from enzymatic trans-glycosylation . The product of the enzymatic trans-glycosylation is a mixture of tri-to pentasaccharides with galactose known as trans-galacto-oligosaccharides (TOS) [37, 38]. In addition, there are GOSs derived from lactulose, an isomer of lactose, as well as raffinose family of oligosaccharides (RFO) [33, 37]. Starch that is resistant to the upper gut digestion is known as resistant starch (RS) and is considered a prebiotic along with polydextrose (glucose-derived oligosaccharide) [39, 40]. Pectin derived oligosaccharides (POS) are derived from an extension of galacturonic acid or rhamnose . The carboxyl groups of POS can be modified with methyl esterification as well as acetylated at C2 or C3. Additionally, many different types of sugars (i.e. arabinose, galactose, and xylose) or ferulic acid can be linked to the side chains of POS [41, 42]. Though most of the accepted compounds defined as prebiotics are carbohydrates, there are some non-carbohydrate compounds that are recommended to be classified as prebiotics, i.e. cocoa-derived flavanols [33, 43].
How do prebiotics affect human health? What mechanism(s) are involved? Since prebiotics are derived from dietary products, they provide the metabolic energy for the gut microbiota. This means that they can affect the composition and function of these microorganisms. For example, GOSs can stimulate the growth of
In addition to feeding the gut microbiota, the fermentation of prebiotics can generate metabolites such as short chain fatty acids (SCFA) (i.e. lactic acid, butyric acid, and propionic acid) that have dramatic effects not only on the intestinal environment but can affect distant organ sites as well as the immune system. SCFAs decrease the pH of the gut that can alter the composition of the microbiota [45, 46]. A pH unit decrease affects acid sensitive species such as
2. Bacterial infections and the disruption of gut homeostasis
Bacterial pathogens are microorganisms that have the ability to cause disease due to their specialized virulence factors or that can arise from a dysbiosis such as from antibiotic treatment that can eliminate the normal healthy flora of the gut leading to opportunistic infections from commensals or normally non-pathogenic organisms.
2.1 Bacterial pathogens, virulence factors, and mechanisms of pathogenesis
Some of the best-known bacterial pathogens are
One important growth restriction system on the part of hosts/intestinal flora is the sequestration of iron, which is absolutely required for growth. For example,
2.2 The mammalian host response to bacterial infections
Probiotic strains have been shown to induce the release of defensins, small peptides/proteins active against bacteria, fungi, and viruses but also are able to stabilize the gut barrier from epithelial cells. Host cells are able to mount as a first line of defense against pathogens increased production of antimicrobial proteins (AMPs) such as α- and β-defensins, cathelicidins, C-type lectins and ribonucleases. Many of these proteins disrupt the cell wall structures of the bacterial membrane either through enzymatic (i.e. lysozyme, phospholipase A2) or non-enzymatic mechanisms (i.e. pore formation by defensins and cathelicidins) [56, 57, 58].
The effect of commensal and probiotic bacteria on the host immune system is complex and not fully understood. It is believed that the effect of probiotic bacteria in modulating the immune system lies with its potential interactions with the host innate immune system by activating pattern recognition receptors (PRRs) that recognize common structures called pathogen-associated molecular patterns (PAMPs) shared by the vast majority of pathogens. Of note are the potential interactions with toll-like receptors (TLRs), extracellular C-type lectin receptors (CLRs), and intracellular nucleotide-binding oligomerization domain-containing protein (NOD)-like receptors (NLRs) that recognize PAMPs such as lipopolysaccharide (LPS), peptidoglycan, lipoprotein, flagellin, and CpGDNA. Activation of these receptor complexes will activate multiple downstream signaling pathways that may induce a pro- or anti-inflammatory response. Dysregulation of the pro-inflammatory response has been implicated in Crohn’s disease with human intestinal inflammation as well as human autoinflammatory disease . However, expression levels of some of these PRRs are low in immune cells therefore the ability to rapidly induce the expression of the PRRs such as NLRP3 in response to PAMP stimuli are absolutely critical in the defense against potential pathogens [60, 61, 62, 63, 64].
3. Probiotic mechanisms of antagonism against bacterial growth and gene expression
In 1969, Greenberg  described the phenomena that
Lactobacilli and bifidobacteria have been shown to inhibit a broad range of pathogens including
Lactobacilli have been shown to produce bacteriocins that are active against some foodborne pathogens . Additionally production of various metabolites and low molecular weight products by probiotics have been shown to have antimicrobial and antifungal properties such as low molecular weight species, deconjugated bile acids, and cyclic dipeptides among others [80, 81, 82, 83, 84, 85].
The production of antimicrobial substances such as lactic and acetic acid is one example of probiotics making the host environment hostile for pathogens.
4. Probiotics and inhibition of bacterial toxins
In order to cause disease for foodborne botulism, BoNTs must first be able to survive in the intestinal lumen, bind to and translocate through the intestinal epithelium to reach the bloodstream . Once in the bloodstream, BoNTs bind to peripheral cholinergic neurons to cleave SNAREs and block exocytosis of neurotransmitters hence leading to flaccid muscle paralysis. Similar to other classic A-B chain toxins, the heavy chain (B chain) of BoNTs bind to carbohydrate and protein receptors on their target cell while the light chain (A chain) has the enzymatic function. Therefore, there are two potential therapeutic pathways to block BoNT intoxication: (1) blocking binding/translocation at the intestinal epithelium/target cells and (2) degradation or inactivation of the toxin It has been shown that pre-treatment with probiotics (
Another mechanism to inactivate bacterial toxins would to be to subject them to proteolysis thus rendering them inactive.
5. Probiotics and/or prebiotics as therapeutics to combat gastrointestinal diseases and bacterial infections
Studies in using probiotics as a treatment for a diverse set of diseases ranging from colorectal cancer, traditional gastrointestinal diseases (i.e. IBS/IBD/RCDI), as well as non-gastrointestinal diseases such as arthritis, autism, multiple sclerosis, and Parkinson’s among others  has been undertaken. In this chapter, we will focus mainly on the effect probiotic and/prebiotic treatments on gastrointestinal diseases.
The therapeutic potential of prebiotics has been investigated for some gastrointestinal disorders. Irritable bowel syndrome (IBS) is a gastrointestinal disease characterized by chronic pain and altered bowel movements with no clear cause. Crohn’s disease, a chronic relapsing inflammatory bowel disease (IBD), can affect any part of the gastrointestinal tract. For both conditions, it has been speculated that a shift in the gut microbiota population lays at the foundation of these diseases. It has been shown that the
Therefore, prebiotics were hypothesized as a potential therapeutic because of its known properties to stimulate the growth of beneficial bacteria. In regards to IBS, the results were unclear for 4 clinical trials. Two clinical trials had no improvement [102, 103] whereas two studies using FOS and GOS showed an improvement in IBS symptoms [104, 105]. In the case of Crohn’s disease, one study showed improvement  while two did not [107, 108]. As reviewed in , their analysis of available studies indicated that generally, the conclusions were supportive of probiotic treatment for IBS, however, the exact beneficial strains to be used were unclear. The caveats from these studies were the variabilities in the type of prebiotic(s) used, the dosage, time of supplementation, and patient disease stage. As has been used in the treatment of recurrent
The recurrent infection in humans with recurrent
Another area of medical use that prebiotics may impact is on the health of preterm neonates. These babies are at significant risk of developing the severe gastrointestinal condition necrotizing enterocolitis (NEC), a life-threatening condition. Studies have shown that FOS and GOS prebiotics can help prime the growth of gut bacteria such as
The successful use of probiotics in treating acute infectious diarrhea (AID) in children is well documented and accepted treatment therapy . It has beneficial effects for children at risk (i.e. hospital acquired diarrhea) and should be used early after onset of symptoms. Its usage, however, in healthy populations as a preventive measure to prevent diarrhea in day care centers and communities is currently unknown and not advised.
It has been shown that
The development of synthetic oligosaccharide-based mimics such as Synsorb (inert silica particles-linked to synthetic oligosaccharides) have been developed against a variety of toxins including: Stx1/2-Gb3, Stx2e-Gb4, Ctx-GM1, LT-GM1, epsilon toxin–GM2, TcdA-Lewis X and Lewis Y, botulinum neurotoxin- GD1a, GT1b,
STEC gastroenteritis has not been traditionally treated with probiotics/FMT as has been seen with acute gastroenteritis and RCDI. There has been a plethora of evidence suggesting the role of probiotic strains in having an antimicrobial effect on STEC but the effects were dependent on the strain(s) used as reviewed in . Additionally, recombinant receptor mimics have been targeted against STEC .
In the three studies that mimicked human digestive conditions,
Though there have been many successful and safe uses of probiotics for treatment of multiple conditions, there have been reported side effects linked to their usage especially in vulnerable populations . As reviewed in , there has been movement toward using extracellular vesicles (EVs) derived from probiotic strains (both Gram-negative and Gram-positive) to deliver the same beneficial effects as from using the probiotic strains themselves. There are many different pathways that EVs utilize including bacteria-bacteria communication, affecting host microbial interactions, host immune system, increasing tight junction function, and decreasing inflammatory responses from TLR signaling .
6. Future works and perspectives
It has been shown that the development of gastrointestinal disease is due to an imbalance in the host response (physical, commensal microbiota, adaptive/innate immune systems) to bacterial infections. There has been an increasing accumulation of evidence (
This work was funded by the United States Department of Agriculture, Agricultural Research Service, National Program project NP108, CRIS 2030-42000-049-00D.
Conflict of interest
The authors have no conflict of interest.