Principles in Microbiome Engineering. Группа авторов

Africa

      The geographic location of the African continent results in limited access to proper nutrition among individuals. These are further complicated by years of poverty and geopolitical issues within the continent that prevents agricultural activities in the region. For instance, a study of the populations in the North West Province, Southern Africa, showed barely adequate energy and protein intake and low micronutrient intake among the general population. This includes limited access to green vegetables and fruits that are probiotic‐rich needed to cultivate a healthy microbiome [152]. It was also found that children in Africa showed a lower Firmicutes/Bacteroidetes ratio and low abundance of Enterobacteriaceae (Shigella and Escherichia) [153]. The dominant genera of Bacteroides of African children comprise xylan‐ and cellulose‐degrading microbes (Prevotella and Xylanibacter) that assist in the digestion of fibrous foods found in tubers like yam and sweet potatoes that are present in the rural African children diet.

      1.2.4.5 South America

      South America adopts a wide variety of dietary patterns. The primary source of polysaccharide in South American diet includes wheat, corn, rice, and tubers. Yucca and bananas are also part of the daily diet in most Latin American countries. Access to a sugar‐rich diet, and low administrative tax on sugar‐sweetened products resulted in quicker absorption of energetics in the human body [154]. This impacts pre‐adolescents and teenagers, in particular, who were in Latin America have shown an estimated overweight prevalence of approximately 7% in children younger than 5 years. This is further complicated by the high intake of cookies, dairy products, and fruit juices [155, 156].

      1.2.4.6 North America

Similar to certain Asian diets, the dietary habit of North Americans is regulated by public health policies [157]. Based on this, the Diet Quality Index was used in evaluating trends of the US population and found significant improvements from 1965 to 1991 [158]. This is further promoted by the Alternate Healthy Eating Index 2010 [159]. It was found that North Americans have a border range of dietary factors, broad macronutrients, multiple food sources, and nutrients [160]. It was shown that US adults consumed more grains from a study conducted from 1999 to 2012, with a stable intake of unprocessed red meat and poultry consumption. Despite the access to a large variety of foods, it was found that the US adults have the least diverse fecal microbiota, showing an abundance of 23 groups (an average non‐US adult have 73 groups) with the major constituent in the Prevotella genus [161].

1.3 Dietary Modulation of Microbiome for Disease Treatment

In subchapter 1.2, the role of dietary habits and the nutritional composition evidently play a role in both short‐term regulation of the microbiome and long‐term shaping of the microbiota landscape [54, 96, 162]. The microbiome changes facilitate various health‐benefiting properties to the host, such as regulating the host immune system, perturbing host growth, and development, altering the host biochemistry and affecting the microbiome in other parts of the human host [163, 164]. It is often unclear whether it is the change of the host biochemistry that perturbs the microbiota population or the changes of the microbiota population that alters the host biochemistry (Figure 1.4). However, certainly these changes can positively influence the hosts' health by boosting the immune system or negatively impacting the host through dysbiosis, resulting in the pathogenesis of various diseases. Through shaping the host's dietary pattern, it is possible to encourage the growth of the desired microbiota population through the use of prebiotics and nutrients or to eliminate antagonistic competitors of the health‐conferring commensals using probiotics.

      1.3.1 Infection

Infections in the human host occur resulting from microbiome dysbiosis, where there is a change in the interactions between the various members of the microbiota and the human host cells. These changes can be transient and may restore to a state of equilibrium as the host recovers from the ailment or might result in a permanent perturbation that results in an altered microbiome state. The following section will look at the various dietary‐related approaches used to restore balance in the microbiota.

      1.3.1.1 Fecal Microbiota Transplantation (FMT)

The concept of fecal microbiota transplantation (FMT) is to import the colonic microbiome from a healthy person, and transferring it to the intestine of a diseased patient to restore the microbiota (Figure 1.5) [165–167]. FMT is used in the treatment of Clostridium difficile infection (CDI), IBD, insulin resistance, and other diseases [168]. In this section, we will discuss the role of FMT in tackling CDI.

Figure 1.4 Dietary perturbation of the microbiome to improve human health. The healthy microbiome results from an equilibrium of host biochemistry and its microbiota (a). During dysbiosis, the population of certain disease‐causing microbes increases, resulting in pathogenesis (b). Using diet, it is possible to help restore balance in the host biochemistry and establish a balanced microbiota in the host. This can be achieved using prebiotics, probiotics, and nutrition to perturb the host microbiome (c). However, sustained dysbiosis will result in disease pathogenesis, resulting in the manifestation of the disease symptoms (d).

Figure 1.5 Protocol of FMT. Stool from healthy donors are screened and tested. The acceptable stool is homogenized and filtered to obtain stool slurry [165]. Fecal suspensions were given via oral capsules, through nasogastric and nasoduodenal tubes into the upper gastrointestinal tract (top), or through a colonoscope or a retention enema catheter into the colon (bottom).

      Source: Based on Bakken [166].

CDI results from excessive use of antibiotics or gastrointestinal surgery, resulting in the loss of the local microbiota. Such local microbiota includes the loss of essential groups from the Lachnospiraceae and Enterobacteriaceae communities. These changes in the structure and functions of the resident microbiota reduce the resistance for intestinal pathogens, such as Clostridium difficile, to localize and propagate in the gut [169, 170]. While other pathogens can be treated with other antibiotic treatments, C. difficile can exist in three different lifestyles (planktonic, biofilm, and spore) that complicate the process of eliminating these pathogens from the gut. The ability of the microbe to evade antibiotic treatment by regulating its lifestyle often leads to recurrent CDI, where the intestinal microbiota fails to recover and thus establishing a new homeostatic balance within the host post‐initial insult. Left untreated, the pathogen can manifest in different forms including diarrhea, pseudomembranous colitis, toxic mega colon, and other symptoms, even rarely resulting in death [171, 172].

      Tremendous amount of research links bacterial dysbiosis in both human and mice showed the depletion of Bacteroidetes and enrichment of Proteobacteria that are linked to a higher risk rate of acquiring CDI [173–176]. The use of FMT to treat CDI showed lower rates of recurrent CDI, leading to the recovery of