Key points

Introduction: what is the microbiome?

There are several extant definitions of the term “microbiome,” a field of research that has become principally associated with the technological advances in DNA/RNA sequencing and computational biology. As such, the microbiome is still commonly defined as the collective genomic content of all microbes recovered from a habitat or ecosystem (eg, saliva and stool samples, skin swabs). However, although such a definition captures the functional potential inherent to the microbiota (micro-), there is a need to place this knowledge in context with the interactions and processes contingent on the physicochemical attributes of their surrounding environment (-biome). This more holistic definition of the microbiome is applied throughout this article, in recognition of diet as a major influence on microbiome dynamics. By doing so, the concept of nutritional ecology is introduced: how the nutrient and its variations across temporal and spatial scales affect the gut microbiota. We contend that nutritional ecology will provide the mechanistic bases for understanding “diet and the microbiome,” which will translate into improved diagnoses and treatments for functional and organic diseases.

Introduction: what is the microbiome?

There are several extant definitions of the term “microbiome,” a field of research that has become principally associated with the technological advances in DNA/RNA sequencing and computational biology. As such, the microbiome is still commonly defined as the collective genomic content of all microbes recovered from a habitat or ecosystem (eg, saliva and stool samples, skin swabs). However, although such a definition captures the functional potential inherent to the microbiota (micro-), there is a need to place this knowledge in context with the interactions and processes contingent on the physicochemical attributes of their surrounding environment (-biome). This more holistic definition of the microbiome is applied throughout this article, in recognition of diet as a major influence on microbiome dynamics. By doing so, the concept of nutritional ecology is introduced: how the nutrient and its variations across temporal and spatial scales affect the gut microbiota. We contend that nutritional ecology will provide the mechanistic bases for understanding “diet and the microbiome,” which will translate into improved diagnoses and treatments for functional and organic diseases.

General concepts and approaches of microbiome studies

For the interested reader, Morgan and Huttenhower present a well-structured and illustrated general overview of the techniques and approaches underpinning microbiome studies. Over the last two decades, microbiome studies have emphasized the use of polymerase chain reaction techniques targeting regions within the gene encoding 16S ribosomal RNA in prokaryotes (ie, bacteria principally, and archaea). When combined with the rapid advances in DNA sequencing technologies and a combination of ecologic, biostatistical, and computational methods, these 16S rRNA profiling methods have resulted in a taxonomy-based assessment of gut microbial communities resident in different regions of the gastrointestinal tract. Importantly, these approaches have afforded the differentiation of the microbiota to reveal specific microbes and microbial consortia indicative of alterations to gut homeostasis, which are generically referred to as “dysbiosis.” During the same period the National Institutes of Health Human Microbiome Project has augmented these studies by producing the “reference genomes” of individual microbial species, which has supported the inference of the functional attributes inherent to the 16S rRNA profiles by such methods as PICRUSt. However, and because of the continued advances in sequencing technologies, the time and cost constraints to “shotgun metagenome sequencing” are being relaxed, which affords a scale and depth of sequence coverage that provides an actual (rather than inferred) representation of the functional attributes inherent to the microbiota.

These studies have also substantiated that the microbial communities of the gut are readily differentiated according to their microbial (and gene) density, diversity, and distribution; as affected by anatomic structure, host secretions, and digesta residence times at different sites. Although the esophageal, stomach, and small intestinal microbiota have now been characterised, most studies that have advanced the mechanistic understanding of diet-microbiome interactions have been undertaken using stool/fecal samples and/or tissue samples collected from the large bowel. As such, the term “gut microbiome” has come to define this (terminal) region of the gastrointestinal tract. During the last 5 years in particular, shotgun metagenome sequencing of stool microbiota and the associated metagenome-wide association studies has revealed that the form and function of the stool microbiota is altered in patient cohorts with type-2 diabetes, cirrhosis, and colorectal cancer. These differences have not only provided insights of how microbial metabolism contributes to disease, but the identification of candidate gene and organismal biomarkers of health and disease.

Critically, these methods have also shown the gut microbiota of humans (and other animals) is rapidly altered by changes in habitual or available diet, leading to the perception that diet may exert a stronger selective pressure on the gut microbiota than host genetics. A particular focus in the last 10 years has related to obesity research, with Turnbaugh and colleagues reporting an enrichment of microbial genes involved in carbohydrate, lipid, and amino acid metabolism in the obese adult gut. More recent studies have revealed that non-obese and obese individuals are characterized by variations in gene richness: subjects with a low gene count are characterized by increased adiposity, insulin resistance, and inflammation. The difference in gene richness has been suggested to be predictive of previous weight gain and in mice, could be partially reversed following a dietary intervention for weight loss. The links between diet and microbiome have also been further substantiated via fecal transplant studies in animal models. For instance, Turnbaugh and colleagues were among the first to show how the transfer of an obese (or lean) phenotype to a naive host (ie, germ-free mice) can be effectively recapitulated using diet to exert the necessary selective pressure to sustain the microbiome. This type of an approach is being increasingly used to establish how either specific microbes or microbial consortia contribute to the onset of non-communicable metabolic and immune-mediated diseases. Additionally, the benefits of existing and candidate next-generation probiotic strains, in terms of their capacity to attenuate inflammation and/or positively affect barrier function and host metabolism (eg, Bifidobacterium spp, Faecalibacterium prausnitzii and Akkermansia muciniphila ), are being examined by their introduction to either germ-free or conventionally reared mice.

Table 1 provides a summary of some recent advances in the understanding of how diet and the gut microbiome, from ecologic, metabolic and immunomodulatory contexts, can affect gut function and health. In addition to the other contributions provided in this issue, there are numerous books and reviews of the topic, especially as it pertains to diet-microbiome (diet × microbiome) interactions during pregnancy and early life, obesity and metabolic diseases, and immune development and immune-mediated diseases. Indeed, these interrelationships are now being defined from conception to grave: from their influences on fetal and infant developmental biology and homeostatic processes, to triggering a plethora of acute and chronic (extra) intestinal diseases, through to defining rules for microbiome restoration to better treat diseases and prevent relapse. Here, as a primer for gastroenterologists, we provide two examples of how diet has been used as a primary intervention that affects the microbiome: exclusive enteral nutrition (EEN) and diets with reduced fermentable oligo-, di-, monosaccharides and polyols (FODMAP) as induction therapies for Crohn’s disease (CD) and irritable bowel syndrome (IBS), respectively. These two examples provide insights into how the microbiota is affected by these conditions, how diet can be managed to produce positive health outcomes, the consequences of these interventions on the microbiome, and why improved knowledge of diet × microbiome interactions is needed.

The microbiome and inflammatory bowel disease

The cause of inflammatory bowel disease (IBD) remains elusive because it is a multifactorial disease influenced by the complex interplay between host genetic susceptibilities, environmental, and lifestyle choices (eg, habitual diet, smoking). With the global incidence and prevalence of IBD increasing, and reaching across to historically low-risk ethnic groups and countries, the microbiome is widely perceived to represent the functional interface among these three components precipitating disease. Indeed, Sartor proposed variations in the balance of the gut microbiota as a trigger for disease, and a large number of case-control and observational studies of the stool and mucosa-associated microbiota from patients with new-onset and chronic IBD now show an overall decrease in bacterial diversity of adult and pediatric patients with IBD during active disease, when compared with healthy control subjects. Reductions in bacterial lineages associated with the Gram-positive Clostridium leptum and Clostridium coccoides clusters are consistently reported in patients with IBD. Members of these lineages are recognized to produce short chain fatty acids including butyrate during active growth in the large bowel, and at least some are implicated in driving the expansion of regulatory T-cell populations in the gut that suppress the inflammatory response. Furthermore, reductions in the abundance of F. prausnitzii , which in healthy subjects may comprise approximately 5% of the total population, are frequently reported for patients with CD and ulcerative colitis (UC). Longitudinal studies have also revealed that these changes are coincident with the onset of disease and that the restoration of these bacterial taxa is prognostic of better health outcomes. Conversely, an increase in the relative abundance of pro-inflammatory Gram-negative bacteria principally affiliated with the Proteobacteria has been consistently identified in IBD, and some Bacteroides spp have also been implicated in the onset of IBD and flares. Much less is known about the diversity of the non bacterial members of the healthy gut microbiota. Our own studies revealed a strong signal for methane-producing archaea associated with colonic tissue, although reductions in the absolute counts and taxonomic composition of archaea and fungi have been reported for patients with IBD compared with healthy subjects. These findings strongly suggest that although the anti-inflammatory factors produced by such bacteria as F. prausnitzii are sustained and robust in healthy subjects, the growth, persistence and metabolic activity of these bacteria can be challenged by not-yet-identified factors that change within the gut milieu during active disease episodes. At the same time, pro-inflammatory bacteria seem to thrive in these same conditions but whether inflammation is the cause, or the consequence of these interrelationships still needs to be established.