The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation. This Review discusses the role of the gut, respiratory tract and vaginal microbiota in susceptibility and resistance to infectious diseases.

The role of the microbiota in infectious diseases

Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis.

Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Associations between Gut Microbiota and Common Luminal Intestinal Parasites

Entamoeba histolytica is a protozoan parasite and the causative agent of amebiasis. It is estimated approximately 1% of humans are infected with E. histolytica, resulting in an estimate of 100,000 deaths annually. Clinical manifestations of amebic infection range widely from asymptomatic to severe symptoms, including dysentery and extra-intestinal abscesses. Like other infectious diseases, it is assumed that only ~20% of infected individuals develop symptoms, and genetic factors of both the parasite and humans as well as the environmental factors, e.g., microbiota, determine outcome of infection. There are multiple essential steps in amebic infection: degradation of and invasion into the mucosal layer, adherence to the intestinal epithelium, invasion into the tissues, and dissemination to other organs. While the mechanisms of invasion and destruction of the host tissues by the amebae during infection have been elucidated at the molecular levels, it remains largely uncharacterized how the parasite survive in the host by evading and attacking host immune system. Recently, the strategies for immune evasion by the parasite have been unraveled, including immunomodulation to suppress IFN-γ production, elimination of immune cells and soluble immune mediators, and metabolic alterations against reactive oxygen and nitrogen species to fend off the attack from immune system. In this review, we summarized the latest knowledge on immune reaction and immune evasion during amebiasis.

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Immune Response of Amebiasis and Immune Evasion by Entamoeba histolytica

Children in developing countries are continually exposed to enteric pathogens [1–4]. This results in high rates of morbidity and mortality, especially in infants [5]. The outcome of an Entamoeba histolytica exposure can be diarrhea, dysentery, or amebic liver abscess, with the latter occurring mainly in men [6]. Disease, however, occurs in a minority of E. histolytica infections (approximately 20%) [6]. While both host and parasite factors contribute to outcome, they do not entirely explain susceptibility [7–9].

A prospective longitudinal study of enteric pathogens in a slum community in Dhaka, Bangladesh, has provided a rich data set to identify parameters important for protection and disease. It has been previously shown that children in this study cohort who are malnourished at birth are more susceptible to amebiasis and in general experience more-severe diarrhea [2]. There is evidence in support of both passive and active acquired immunity. Infants with mothers with high levels of breast milk anti-galactose/N-acetylgalactosamine (Gal/GalNAc) lectin immunoglobulin A (IgA) had fewer E. histolytica infections, and children with fecal IgA anti-Gal/GalNAc lectin IgA also had a lower incidence of new infection [10, 11].

Weaning and the introduction of supplementary food into the diet is known to trigger changes in the bacterial composition of the microbiome that include increases in Prevotellaceae and Bacteroides species [12, 13]. The first 2 years of life in general is a period of rapid immune and microbiome maturation, which, in this population, may be disrupted by malnutrition and environmental insult [13–15].

Here we describe the natural history of amebiasis in the first 2 years of life in infants from an urban slum in Dhaka. The cumulative incidence of amebic infection and diarrhea, the association of protection with anti-Gal/GalNAc lectin IgA, the impact of parasite burden on symptoms, and potential role of Prevotella copri in E. histolytica diarrhea are described.

Role of the Gut Microbiota of Children in Diarrhea Due to the Protozoan Parasite Entamoeba histolytica

BACKGROUND: Cryptosporidiosis is a common cause of infectious diarrhea in young children worldwide and is a significant contributor to under-five mortality. Current treatment options are limited in young children. In this study we describe the natural history of Cryptosporidium spp. infection in a birth cohort of children in Bangladesh and evaluate for association with malnutrition. METHODOLOGY/PRINCIPAL FINDINGS: This is a longitudinal birth cohort study of 392 slum-dwelling Bangladeshi children followed over the first two years of life from 2008 to 2014. Children were monitored for diarrheal disease and stool was tested for intestinal protozoa. Anthropometric measurements were taken at 3-month intervals. A subset of Cryptosporidium positive stools were genotyped for species and revealed that C. hominis was isolated from over 90% of samples. In the first two years of life 77% of children experienced at least one infection with Cryptosporidium spp. Non-diarrheal infection (67%) was more common than diarrheal infection (6.3%) although 27% of children had both types of infection. Extreme poverty was associated with higher rates of infection (chi-square 49.7% vs 33.3% p = 0.006). Malnutrition was common in this cohort 56% of children had stunted growth by age two. Children with Cryptosporidium spp. infection had a greater than 2-fold increased risk of severe stunting at age two compared to uninfected children (odds ratio 2.69 95% CI 1.17 6.15 p = 0.019) independent of sex income maternal body-mass index maternal education and weight for age adjusted z (WAZ) score at birth. CONCLUSIONS/SIGNIFICANCE: Cryptosporidium infection is common (77%) in this cohort of slum-dwelling Bangladeshi children and both non-diarrheal and diarrheal infections are significantly associated with a childs growth at 2 years of age.

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Daniel J. Reichman

Papers

Role of the Gut Microbiota of Children in Diarrhea Due to the Protozoan Parasite Entamoeba histolytica

Natural History of Cryptosporidiosis in a Longitudinal Study of Slum-Dwelling Bangladeshi Children: Association with Severe Malnutrition.