Diet and host–microbial crosstalk in postnatal intestinal immune homeostasis

Abstract

Neonates face unique challenges in the period following birth. The postnatal immune system is in the early stages of development and has a range of functional capabilities that are distinct from the mature adult immune system. Bidirectional immune–microbial interactions regulate the development of mucosal immunity and alter the composition of the microbiota, which contributes to overall host well-being. In the past few years, nutrition has been highlighted as a third element in this interaction that governs host health by modulating microbial composition and the function of the immune system. Dietary changes and imbalances can disturb the immune–microbiota homeostasis, which might alter susceptibility to several autoimmune and metabolic diseases. Major changes in cultural traditions, socioeconomic status and agriculture are affecting the nutritional status of humans worldwide, which is altering core intestinal microbial communities. This phenomenon is especially relevant to the neonatal and paediatric populations, in which the microbiota and immune system are extremely sensitive to dietary influences. In this Review, we discuss the current state of knowledge regarding early-life nutrition, its effects on the microbiota and the consequences of diet-induced perturbation of the structure of the microbial community on mucosal immunity and disease susceptibility.

Key points

• Infant nutrition, including breast-milk, formula milk and solid weaning foods, is a key determinant of early microbial community structure that influences development of protective immunity and seems to affect health throughout life
• Diet-induced dysbiosis changes the species composition of the gut microbiota and leads to immune-mediated inflammatory and metabolic diseases
• Diet influences the postnatal development of innate and adaptive defences at the mucosal barrier surface and affects intestinal barrier function
• A triad of diet, the microbiota and the immune system regulates postnatal intestinal homeostasis and host physiology, which has consequences through to adulthood

Introduction

The 'hygiene hypothesis' proposed that an increased predisposition to allergies and the rise in the incidence of atopic diseases was linked to a lack of exposure to infectious agents, microorganisms and parasites during childhood that resulted in the development of the immune system being suppressed.^{1, 2} In the past few years, epidemiological studies further showed that children growing up on traditional farms with exposure to livestock and consumption of unprocessed cow's milk during their early years are resistant to these diseases.³ That errors in the development of the immune system are connected to improved sanitary conditions and the increased use of antibiotics, among other factors, is now evident. The gut microbiota is central to this phenomenon as it responds to changes in the environment and also affects the maturation and function of the immune system. Fluctuations in the composition of this microbiota are also caused by perturbations in diet.^{4, 5} This observation has led to the proposal of the 'diet hypothesis' that unifies changes in nutrition with gut microbiota and immune health (Figure 1).^{6, 7, 8}

Figure 1: The 'diet hypothesis'.

Diet, gut microbiota and host immunity are intimately connected and their bidirectional communication is central to maintaining intestinal and metabolic homeostasis. The commensal bacteria determine the nutritional value of food by fermenting dietary components to usable energy sources and by affecting nutrient uptake. Specific bacteria and microbial by-products influence the development and function of key components of mucosal immunity. The mucosal immune system shapes the commensal composition and location. Immune–microbial interactions via pattern-recognition receptors (TLRs, NODs) result in secretion of antimicrobial peptides, mucins and IgA, which maintains intestinal homeostasis and barrier function. The mucosal innate immune system also influences dietary energy absorption. Finally, perturbation of microbial community structure leads to dysbiosis, which can precipitate immune-mediated disorders such as IBD and metabolic diseases such as type 2 diabetes. Abbreviations: ILC, innate lymphoid cell; NOD, nucleotide oligomerization domain; T_H17 cell, type 17 T helper cell; TLR, Toll-like receptor; T_REG cell, regulatory T cell.

Figure 2: Diet, gut microbiota and dysbiosis.

Several features regulate the establishment and composition of the microbiota and their effect on the health and immune function of the host. Eubiosis or a normal microflora structure that protects against infections educates the immune system and contributes to nutrient digestion. Energy harvest is established by early intestinal colonization with specific microbes immediately after birth. An ordered process of subsequent colonization and expansion shaped by diet results in the establishment of distinct 'enterotypes', or clusters of microbial communities, that remains fairly stable in adults. Perturbations in the microbial community structure or dysbiosis are induced by factors such as diet, use of antibiotics or infection, which can alter susceptibility to several diseases.

Figure 3: The intestinal barrier.

 The intestinal barrier is made up of a single layer of epithelium consisting of intestinal epithelial cells and specialized Goblet cells, M cells and Paneth cells (present only in small intestine). Peyer's patches (found specifically in the ileum) and mesenteric lymph nodes develop prenatally when LTi are recruited to sites of the developing intestines called cryptopatches. Cryptopatches mature into isolated lymphoid follicles when pattern-recognition receptors (TLRs) are triggered by MAMPs, which then release IgA-producing plasma cells into the lamina propria. Dendritic cells in the Peyer's patches access microbes through M cells or directly from the lumen by extending dendrites through intestinal epithelial cells. These antigen-loaded dendritic cells can induce T-cell differentiation or T-cell-dependent B-cell maturation into germinal centres. Naive T cells (T_H0 cells) can differentiate into effector T_H1, T_H2 or T_H17 cells or into regulatory FOXP3⁺ T_REG cells or Tr1 cells. Microbial sensing by intestinal epithelial cells also marks the release of antimicrobial peptides and stimulation of intestinal epithelial cell proliferation in crypts. Abbreviations: IEL, intraepithelial lymphocyte; LTi, lymphoid tissue inducer cell; MAMP, microbe-associated molecular pattern; M cell, microfold cell; T_H, T helper cell; TLR, Toll-like receptor; Tr1, type 1 regulatory T cell; T_REG, regulatory T cell.



Figure 4: Development and maturation of the intestinal mucosal barrier and mucosal immune system.

Developmental changes in the prenatal, postnatal and adult intestine are summarized. Intestinal microbial colonization, as well as dietary components, induces maturation of the intestinal epithelium and initiates development of the mucosal immune system. Complex bidirectional interactions between gut microbiota, diet and the immune system itself regulate the establishment and maintenance of intestinal homeostasis and barrier function. Abbreviations: CRAMP, cathelin-related antimicrobial peptide; CRS, cryptidin-related sequence; TLR, Toll-like receptor; ±, cells might or might not be present; +, ++, +++, ++++, relative numbers of indicated cells.



Cultural diversity and geographical location contribute to dietary differences that result in distinct patterns of intestinal microbial colonization and disease susceptibility in different populations. The Western diet is generally low in fibre and high in processed foods, which adversely affects the intestinal microbial composition and leads to an obesity-prone metagenome.^{6, 8, 9} Conversely, the Japanese diet, which includes rice, beans and fermented foods,^{10, 11} and the diet of Eskimos in Greenland (which is typically high in fish and omega-3 fatty acids) promote resistance to chronic inflammatory diseases and heart diseases.^{12, 13, 14} In mouse experiments, offspring of mice fed a diet rich in omega-3 fatty acids have an altered gut microbiome and have enhanced production of the anti-inflammatory cytokine IL-10 in the colon and spleen, which protects the mice from an allergic challenge.¹⁵ The influence of nutrition on the microbiome and disease susceptibility is also specific to age. In newborn babies, the establishment and type of feeding has a considerable effect on the composition of the microbial community.¹⁶ In adults, both long-term dietary intake and short-term changes in macronutrients (for example, an animal or plant-product-based diet) influences microbial community structure and microbial gene expression profiles.⁴ The outcomes of the complex dynamic connections between the microbiota and the immune system are most important during the postnatal period and have consequences on host immunity and on metabolic homeostasis that reach well into adulthood.

 

In this Review, we discuss the effect of diet on host–microbial interactions in early life and highlight the key aspects of nutritional programming during the postnatal period in influencing the lifelong function of the immune system in health and disease.

Conclusions

The relationship between diet, microbiota and host immunity is being rapidly unravelled using a combination of epidemiological, immunological, metagenomic and metabolomic approaches. These studies are most pertinent at the postnatal period when dietary intake is closely tied to the development of both the gut microbiota and the immune system. In a study published in 2014, a prenatal placental microbiome was described that could be a source of the infants' first bacterial inoculum via intrauterine seeding.¹⁶⁵ Whether and how this low abundance yet metabolically rich microbiome directs the development of the immune system and the microbial community structure during gestation, as well as the effect of maternal nutrition on these processes, remains to be determined. A systems approach involving both animal studies and analysis of human cohorts are needed to unravel the complexities of microbiota–host crosstalk in early life. Animal models are invaluable and have provided a plethora of information and insights into the interplay between the immune system and host microbiota. However, it is important to caution that a direct correlation from animal studies to humans is not possible, particularly when interrogating immune developmental events in early life. For instance, in humans, αβ TCR⁺ T cells are seen in peripheral tissue at 10–12 gestational weeks; however, in mice, peripheral T cells are undetected in the fetus and their numbers only increase after birth,¹⁶⁶ which is suggestive of distinct developmental cues and immune requirements in human versus mouse neonates.

 

The interdependence of diet, immune and microbiota interactions and communications between the elements of this triad dictate intestinal mucosal homeostasis as well as metabolic well-being. The mechanisms by which these dialogues occur are only now being elaborated on and major gaps remain in our understanding of how specific nutrients and microbial metabolites regulate microbial composition, host metabolism and immunity. The use of specific dietary components in modulating the gut microbiota and subsequent immune function offers an attractive approach to deliver health benefits to a vulnerable population, such as paediatric and geriatric populations. As such, probiotics and prebiotics are being increasingly used to prevent and treat a variety of gastrointestinal and systemic diseases in infants.^{167, 168} Discoveries aimed at establishing specific features of the immune–microbiota crosstalk will provide useful insights for the development of preventive and therapeutic agents of multiple infectious, autoimmune and metabolic disorders.

 

Nature Reviews Gastroenterology & Hepatology | Review

Nitya Jain^1, & W. Allan Walker^2,

Published online 09 September 2014



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Mycobiota in gastrointestinal diseases

Abstract

New insights gained through the use of state-of-the-art technologies, including next-generation sequencing, are starting to reveal that the association between the gastrointestinal tract and the resident mycobiota (fungal community) is complex and multifaceted, in which fungi are active participants influencing health and disease. Characterizing the human mycobiome (the fungi and their genome) in healthy individuals showed that the gastrointestinal tract contains 66 fungal genera and 184 fungal species, with Candida as the dominant fungal genera. Although fungi have been associated with a number of gastrointestinal diseases, characterization of the mycobiome has mainly been focused on patients with IBD and graft-versus-host disease. In this Review, we summarize the findings from studies investigating the relationship between the gut mycobiota and gastrointestinal diseases, which indicate that fungi contribute to the aggravation of the inflammatory response, leading to increased disease severity. A model explaining the mechanisms underlying the role of the mycobiota in gastrointestinal diseases is also presented. Our understanding of the contribution of the mycobiota to health and disease is still in its infancy and leaves a number of questions to be addressed. Answering these questions might lead to novel approaches to prevent and/or manage acute as well as chronic gastrointestinal disease.

Key points

• The mycobiome (the resident fungal community and their genome), is a key component of the human microbiome
• Within a microbiome, there are interactions between and within species or genera among fungi and bacteria
• Alterations within the mycobiota are associated with different diseases
• The mycobiota might directly or indirectly interact with the host immune system
• Interactions between the mycobiota and host immune system can lead to exacerbation of gastrointestinal diseases such as IBD

Introduction

The association between fungi and gastrointestinal disease has been documented since the 18^th century, with a special focus on candidiasis. One of the first observations of this association was the study by Rosen von Rosenstein,¹ who described oral candidiasis that extended to the stomach and intestines. In addition, the first reported case of gastrointestinal candidiasis in an infant was described in this period.¹ Subsequent case reports published in the 19^th century documented Candida infection of the stomach, colon^{2, 3} and ileum.⁴ Candida gastrointestinal infections occur less frequently than oesophageal infection, with the stomach being the most common site of infection in the gastrointestinal tract.¹

 

Historically, fungi such as Candida were considered passive colonizers of the microbial community that could become pathogenic as the result of a change in the environment, for example the loss or reduction of bacterial neighbours (due to use of antibiotics) or suppression of immune defence (as a result of an immunosuppressive drug regimen). However, studies performed in the past decade have demonstrated that fungi have a complex, multifaceted role in the gastrointestinal tract and are active participants in directly influencing health and disease through fungal–bacterial, fungal–fungal and fungal–host interactions.

 

Advances in sequencing technology have provided the ability to profile the microbiome, with emphasis on the bacterial component. However, studies are now beginning to define the fungal component of the human microbiome (the mycobiome). A historical perspective of the interactions between fungi and the gastrointestinal tract and a description of the current state of research on the mycobiota as it pertains to the gastrointestinal tract in health and disease is provided in this Review.

 

Of note, a search of the mycobiome literature shows clear variability between different studies, which can be attributed to the lack of standardized methods to characterize the mycobiome. A multitude of differences occur across studies: sample types; collection times and protocols; DNA extraction methods; varying amplification targets; sequencing methods; differences in algorithms and online database composition; and variation in data cleaning steps and bioinformatics approaches. Therefore, development of standardized methods in microbiome (both bacterial and fungal) analyses is critical. Efforts to address standardization have been initiated and variables that influence microbiome research are being optimized.^{5, 6, 7}

 

Figure 1: Normal and abnormal interactions between fungi and the host immune system in gastrointestinal tissue.

APCs present fungal antigens as MHC class II conjugates to T-cell receptors on naive T cells. T cells then differentiate into T helper cells (T_H1 or T_H17), which secrete different proinflammatory and anti-inflammatory cytokines leading to recruitment of humoral and cellular factors of innate immunity. a | In healthy tissues, immune homeostasis is maintained by interdependent control exerted by T_H1 cytokines and T_REG cells. b | In patients with IBD, dysfunctional regulation of T_H1 or T_H17 pathways triggers an unregulated inflammatory response and recruitment of innate immune cells. Increases in cytokine levels can trigger oxidative tissue damage and recruitment of proteolytic peptides and enzymes, eventually manifesting as gastrointestinal disease. Furthermore, activation of the T_H2 pathway can lead to plasma cells detecting fungal cell wall antigens and producing antiglycan antibodies (ASCA, ALCA and ACCA). Abbreviations: ACCA, anti-chitobioside carbohydrate IgA antibodies; ALCA, anti-laminaribioside carbohydrate IgG antibodies; APC, antigen presenting cell; ASCA, anti-S. cerevisiae antibodies; mac, macrophage; NK, natural killer cell; NO, nitrogen oxide; PAMP, pathogen-associated molecular pattern; PRR, pattern-recognition receptor; ROS, reactive oxygen species; T₀, naive T cell; T_H1, type 1 T helper cell; T_H17, type 17 T helper; T_REG, regulatory T cell.

Conclusions

Studies performed to date on the role of the mycobiota in gastrointestinal diseases have just started to scratch the surface and demonstrate that the fungal community is a critical player in the pathogenesis of these diseases. Although studies performed so far have started to characterize the mycobiome in health and disease, and show potential links, it is important to note that such links reflect association rather than causation. Moreover, most studies have focused on the role of Candida and its effect on the host immune system. Focusing on one microbial kingdom (bacteria or fungi) whilst analysing the microbiome in a sample (for example, oral wash, gut biopsies or faecal pellets) provides limited insight.⁹⁶ To expand our knowledge and obtain deeper insight into the role of the microbiome in health and disease, future studies should also characterize the different microorganisms (bacteria, fungi and viruses) in the same sample types.

 

There is still a long way to go and several questions remain to be answered regarding the contribution of the gut mycobiota to the pathogenesis of gastrointestinal diseases (Box 1). Research funding to address these questions will be instrumental and will lead the way to develop novel approaches to prevent, manage and treat gastrointestinal disease.

Nature Reviews Gastroenterology & Hepatology | Review

Published online 11 November 2014

Pranab K. Mukherjee,^1, Boualem Sendid,^2, Gautier Hoarau,^2, Jean-Frédéric Colombel,^3, Daniel Poulain^2, & Mahmoud A. Ghannoum^1,

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