Guided dietary fibre intake as a means of directing short-chain fatty acid production by the gut microbiota

ABSTRACT

The human colon contains a complex microbial community (the microbiota), composed mostly of bacteria, that degrades and ferments indigestible polysaccharides known collectively as dietary fibre. Acting as a co-operative society and using specialised biochemical mechanisms, the microbiota processes the dietary fibre and produces short-chain (volatile) fatty acids (SCFAs) as fermentation products. Mucosal and immune cell receptors and signalling molecules important in maintaining gut homeostasis respond to the presence of these bacterial metabolites. This article provides a perspective on the potential use of dietary fibre to modulate the functioning of the microbiota and hence stimulate health-supporting processes in guided food interventions. Major problems to be solved in developing this approach include the lack of detailed knowledge of the assemblage and functioning of bacterial consortia in the gut microbiota, the relatively large quantity of dietary fibre that might be needed to produce consistent outcomes in humans, the possibility that bacterial species that could utilise more exotic dietary fibres present in ancestral foods may be missing from Western microbiotas, the variation in response to dietary modification because high diversity microbiotas are resistant to change, and the need to develop new forms of dietary fibre supplements that are palatable and tolerable when ingested in efficacious amounts.

KEYWORDS:

• Microbiota
• dietary fibre
• SCFA
• dysbiosis
• prebiotic

The ecology of the gut microbiota of humans with respect to fermentative activities

The human colon provides an anaerobic habitat for a microbial community (the gut microbiota), largely composed of bacterial species, which assembles and develops during the first few years of life, reaching a mature (climax) state after about three years of age (Yatsunenko et al. 2012). Although the presence of the gut microbiota and its associated fermentative capacity, as well as the impact on animal physiology, were described long ago (Tannock 2017), more detailed information about the taxa and biochemical capacity of the microbiota has been obtained during the last two decades. This has been due to the use of culture-independent methods based on high throughput sequencing of DNA extracted from human faeces. Advanced bioinformatics analysis of the genetic information has enabled taxonomic and biochemical details of the microbiota to be described and summarised (Franzosa et al. 2015; Knight et al. 2018). The results of shotgun sequencing of bulk DNA extracted from faeces, which allows the analysis of much of the information contained in microbiota genomes, have been particularly useful because they provide reliable descriptions of the bacterial species comprising microbiotas, as well as the biochemical capacity of the community (Gill et al. 2006). The gut microbiota is individualistic in taxonomic composition but constant in biochemical capacity because microbiota genomes contain biochemical pathways that can be induced or repressed as required in accordance with availability of fermentable substrates (Turnbaugh et al. 2009). Moreover, different taxa of bacteria contain similar biochemical pathways (metabolic redundancy), which means that microbiotas, although distinct in composition, can carry out the same metabolic functions (Turnbaugh et al. 2009; Flint et al. 2015).

Because of the anaerobic nature of colon contents, the microbiota members obtain energy from the fermentation of substrates (organic molecules, not oxygen, are the terminal electron acceptors). Knowledge of gut fermentations associated with mammalian microbiotas, particularly of ruminants, began long ago (Hungate 1966). Rumen microbiologists understand in detail how complex substrates are degraded and fermented by bacteria in the foregut of cows and sheep and how this is essential to the well-being of the host animal (Russell 2002). Extrapolations from these systems have helped establish knowledge of what occurs in the human colon (a hindgut fermentation). In brief, plant polysaccharides in the diet are indigestible to processes in the human stomach and small bowel and pass to the colon where they provide food for the microbiota. Cellulose, hemicelluloses, and resistant starch are common indigestible polysaccharides originating from plants and, together, they are described as dietary fibre (Table 1) (White et al. 2014). Eighty per cent of dietary fibre ingested by humans is degraded and fermented by the colon microbiota (Cummings and Stephen 1980). The fermentation products (the principal ‘emergent properties’ of the community) are mainly SCFAs (mostly acetate, propionate, butyrate) as well as gases (hydrogen, carbon dioxide, methane), minor amounts of branched-chain fatty acids (isobutyrate, isovalerate) derived from fermentation of amino acids in the distal colon, a minor amount of the SCFA valerate, and pungent volatiles such as indoles (derived from tryptophan), hydrogen sulphide, and thiols (derived from sulphur-containing amino acids such as methionine) that give faeces a distinctive odour (Cummings and Macfarlane 1991; Yadav et al. 2018). The release of ‘phytochemicals’ (polyphenols, anthocyanins, phenolics, flavins) through the degradation of plant-derived substances by the microbiota also occurs (O’Keefe 2019). Ninety-five per cent of acetate, propionate, and butyrate produced by the microbiota are absorbed from the colon and have caloric value (Høverstad 1986; Cummings and Macfarlane 1991). The metabolites absorbed in the colon are carried by the portal vein to the liver where they are often chemically transformed (a means of detoxification, for example conversion of ammonia to urea). Acetate passes to the peripheral circulation and can be detected throughout the body and is an important source of acetyl-CoA that supports fatty acid synthesis (Ballard et al. 1969). Propionate is transformed to glucose in the liver (gluconeogenesis) and is therefore also an energy source (Morrison and Preston 2016). Butyrate seems mostly to be used as energy source by the cells forming the gut mucosa (butyrate provides up to 70% of colonocyte energy source) (Zeng et al. 2014). Faeces contain undigested dietary fibre, bacterial metabolites, transformed molecules derived from host secretions such as deconjugated bile salts, and biomass (50% of faecal mass is comprised of bacterial cells) (Stephen and Cummings 1980). Overall, the microbiota harvests about an extra 10% of calories per day from the food (Bergman 1990). This energy would otherwise be unobtainable to the human host and was likely to have been important in times past when food sources were sometimes scarce, and malnourishment and starvation frequent.

Table 1. Codex definition of dietary fibre (Jones 2014).

Dietary fibre means carbohydrate polymers^a with 10 or more monomeric units^b, which are not hydrolysed by the endogenous enzymes in the small intestine of humans and belong to the following categories: Edible carbohydrate polymers naturally occurring in the food as consumed. Carbohydrate polymers, which have been obtained from food raw material by physical, enzymatic or chemical means and which have been shown to have a physiological effect of benefit to health as demonstrated by generally accepted scientific evidence to competent authorities. Synthetic carbohydrate polymers, which have been shown to have a physiological effect of benefit to health as demonstrated by generally accepted scientific evidence to competent authorities.

^aWhen derived from a plant origin, dietary fibre may include fractions from lignan and/or other compounds associated with polysaccharides in the plant cell walls, These compounds also may be measured by certain analytical method(s) for dietary fibre.

^bDecision on whether to include carbohydrates of 3–9 monomeric units should be left up to national authorities.

Hemicelluloses present in plant cell walls contain a diversity of chemical constituents and range from xylans to glucans. As will be described later, the chemical structures within these complex polysaccharides are, in themselves, diverse and include branched-chain structures that are amenable to hydrolysis by only certain specialised bacterial species. For example, Bacteroides species have differential growth patterns on xylans, and also on pectins (Centanni et al. 2017; Bell et al. 2018). These observations may lead to opportunities to manipulate the composition and functioning of the gut microbiota in cases where a ‘dysbiosis’ (variation from normal microbiota patterns) occurs in certain diseases or conditions (Brüssow 2016). However, simple rectification of the problem by alteration of the dietary fibre content of the food of individual humans will be difficult without a more comprehensive knowledge of how the microbiota functions as an ecological and metabolic entity.

The gut microbiota contains bacterial species that can degrade (hydrolyse) complex carbohydrate molecules. These species may not be numerically dominant in the community, but they carry out a function critical (keystone species) to the life of other organisms (Power et al. 1996). As alluded to earlier, they may have large genomes that encode a variety of biochemical pathways that can be switched on or off according to current needs. These species form the nucleus of multi-member consortia that, working together, sequentially degrade and ferment polysaccharides (Flint et al. 2015). The hydrolytic products liberated by the primary degraders become nutrients for other species, so a system of ‘leakage’ and ‘cross-feeding’ (syntrophy) of nutrients can be envisioned as underpinning the metabolic features of the community (Morris 2015). Consortia may contain both strong and weak associations that give flexibility to the bacterial assembly so that the membership of consortia will be able to change in response to a variety of substrates (which will probably change from day to day) delivered to the colon by the food that the host has consumed (Tannock 2017). The molar ratios of short-chain fatty acids may be influenced by the composition of the consortia according to whether particular members contain the pathways for propionate or butyrate production. There are only three biochemical pathways by which propionate can be produced by bacterial species, and two for the production of butyrate (Louis et al. 2014). These fatty acids are often produced from fermentation ‘intermediates’ such as lactate or succinate (Louis et al. 2014). The organic acids lactate and succinate are produced by some bacterial species in pure culture, but they are not detected in rumen contents or human faeces because they are converted to propionate or butyrate by other bacteria in the community as soon as the acids become available in the habitat. Hydrogen gas is also an intermediate because it is utilised together with carbon dioxide to form methane by the archaeal species, Methanobrevibacter smithii (Miller and Wolin 1983; Eckburg et al. 2003). Lowering the partial pressure of hydrogen by means of inter-species hydrogen transfer improves the energetics of the community and fermentative species produce more acetate (and ATP) as a result (Wolin 1974). In the absence of the methanogen, and maybe in its presence as well, acetogens and sulphate reducers (such as Desulfovibrio piger) contribute to the interactive process of hydrogen production and transfer within the microbiota (Rey et al. 2013).

As demonstrated by the epidemiological studies conducted by Painter, Walker, Trowell and Burkitt in Africa decades ago, dietary fibre is clearly important in regulating intestinal transit time through bulking effect and water retention, and influences the prevalence of some non-communicable diseases of humans (Cummings and Engineer 2018). Recent research has indicated that transit time has an impact on gut microbiota composition, at least as judged by the comparison of the appearance and consistency of faeces (Bristol Stool Chart) and the abundances of some bacterial species. In theory, a more rapid transit time selects for bacterial species with a shorter doubling time so that they avoid ‘wash out’ from the colon (Tigchelaar et al. 2016; Vandeputte et al. 2016). Longer transit times in the proximal colon should provide more time for fermentation of dietary fibre, and the development of a more diverse bacterial community under these conditions would increase the stability of the microbiota. Longer transit time in the distal colon would also permit greater absorption of SCFAs. This discussion raises the question as to how much dietary fibre humans should consume each day to promote good health. A recent meta-analysis of prospective studies and clinical trials showed that higher intakes of dietary fibre or whole grains are associated with a reduction in the risk of mortality and incidence of a wide range of non-communicable diseases and their risk factors (Reynolds et al. 2019). The analysis indicated that it would be beneficial to use whole, rather than refined, grains in the diet, and to aim for a dietary fibre intake of 25–29 grams per day. There is a need to encourage the consumption of fruit and vegetables as well as stimulating the food industry to provide attractive products containing appropriate forms of dietary fibre even in processed foods; things that people will like to eat, and can afford. Moreover, from a microbial ecology viewpoint, the kinds of dietary fibre that are ingested need to be carefully considered. Differences in carbohydrate chemistries will influence the assembly and activities of gut consortia and therefore the emergent properties of the microbiota.

This article provides a perspective of the diversity of the major plant polysaccharides found in foods that humans eat, the specialised biochemical features of some members of the microbiota that degrade dietary fibre, the effect of changing the human diet with respect to dietary fibre content on SCFA production by the microbiota, and the prospect of changing SCFA production through dietary fibre consumption in relation to improving health.

Structural and chemical diversity of dietary fibre is reflected in the specialised biochemical attributes of hydrolytic members of the microbiota

The gut microbiota of humans is comprised of a variety (diversity) of bacterial species. Although individual microbiotas are more limited in diversity (about 100 bacterial species or less), it is estimated that, overall, about 1500 species are capable of residence in the human gut (Qin et al. 2010). The potential for the development of species-rich communities relies on the availability of ecological niches that provide nourishment to the bacteria and underpin the functioning of a co-operative microbial society (Gause and Witt 1935; Hardin 1960). In turn, the variety of plant polysaccharides contained in the human diet plays a large role in forming ecological niches. Chemical structures of plant polysaccharides (dietary fibre) dictate which bacterial species can flourish through hydrolysis of the polymers and fermentation of liberated mono- and oligosaccharides (Hamaker and Tuncil 2014). Syntrophic interactions between hydrolytic and non-hydrolytic bacteria ensure that the resources of the habitat are shared, enabling the maintenance of a stable, diverse community in the gut (Tannock and Taylor 2017). Knowledge of the preferential use of particular substrates by bacterial species forms the basis for the prebiotic concept: non-digestible food ingredients can improve health by selectively stimulating the growth and/or activity of particular bacteria (Roberfroid 2007). In other words, ‘a substrate that is selectively utilized by host microorganisms conferring a health benefit’ (https://isappscience.org/prebiotic-definition-updated-isapp/). Commonly, ‘prebiotics’ refers to inulin, fructo- and galacto-oligosaccharides that are used as food additives to cause an augmentation of bifidobacterial and Lactic Acid Bacteria numbers (Gibson and Roberfroid 1995). A new appraisal of the prebiotic action of dietary fibre contained in fruit, vegetables, nuts and grains would better fit recent evaluations of diet in relation to human health (Carlson et al. 2017). However, it should be noted that there are current limitations on the estimation of specific kinds of dietary fibre in food due to changing definitions as well as use of new, internationally approved, technical assays that affect the completeness and accuracy of food composition databases (Westenbrink et al. 2013; Rainakari et al. 2016).

Plant cell walls and resistant starch provide the principal dietary fibre that gut bacteria use for growth (White et al. 2014). Plant cell walls are formed by a matrix of lignocellulosic polymers that, even for bacteria, are difficult to degrade. The most desirable carbohydrates for fermentation by bacteria (such as glucose, xylose) are integral components of cellulose, hemicelluloses, pectin, and glycoproteins. In general, cellulose constitutes 40%, hemicelluloses 30%, and lignin 20% of plant cell walls (White et al. 2014). Lignin is not a polysaccharide but is a hydrophobic polymer composed of aromatic phenolic residues. Oxygen is required for its degradation, so not much hydrolysis of it occurs in the anaerobic environment of the gut. Cellulose is a linear polymer made up of repeating units of glucose. Although cellulose is composed exclusively of glucose, the repeating unit in the structure is the disaccharide cellobiose, with each glucose residue linked to its counterpart rotated 180°. Cellulose is a straight-chain polymer that contains from 100 to 10,000 glucose residues. It forms tightly packed sheets or microfibrils due to hydrogen bonding within and between lengths of the polymer. These highly organised and tightly packed microfibrils make cellulose difficult to hydrolyse (White et al. 2014).

Hemicelluloses provide the matrix in which cellulose fibrils are embedded within the plant cell wall. These non-cellulosic, structural polysaccharides are composed of a variety of different carbohydrate monomers. Examples are provided by galacto-glucomannan, xylan, arabinogalactan, mixed-link (β1-3,1-4) glucans, xyloglucan, and glucomannan. Many side-chain constituents, including arabinofuranosyl, acetyl, feruloyl, and methylglucuronyl groups, branch off the main backbone of non-cellulosic structural polysaccharides. Thus, the chemical complexity of hemicelloses is much greater than that of cellulose (White et al. 2014). As summarised by Kim et al. (2019), pectin is the most complex polysaccharide found in plant cell walls, consisting of structurally heterogeneous components, such as homogalacturonan (HG), rhamnogalacturonan-I (RG-I), and rhamnogalacturonan-II (RG-II) (Mohnen 2008). HG is a homogenous polymer of α-1,4-linked-d-galacturonic acid (d-GalpA) which constitutes the majority of uronic acid contents of pectin, and 65%–70% of the total pectin mass (Ridley et al. 2001; Mohnen 2008). Approximately half of d-GalpA residues present in HG are either methyl-esterified at C-6 or acetyl-esterified at O-2 and/or O-3 (Ridley et al. 2001). Non-esterified d-GalpA residues carry a negative charge, enabling the formation of a gel-like texture by chelating Ca²⁺ ions (Caffall and Mohnen 2009). The RG-I and RG-II regions of pectin are compositionally heterogeneous, containing diverse neutral sugars. Depending on the plant species, up to 20%–80% of l-rhamnose (l-Rhap) residues in RG-I are branched by arabinan (polymers of α-l-1,5-arabinofuranose [l-Araf] units branched at O-2 and O-3 with α-l-Araf residues), galactan (unbranched polymers of β-d-1,4-galactopyranose [d-Galp] residues), and arabinogalactan (a linear β-1,4-galactan substituted with α-l-1,5-Araf oligosaccharides) (Mohnen 2008). Some arabinan and galactan are substituted with ferulic acid side chains, which can dimerise to strengthen the pectin network (Zykwinska et al. 2005). The backbone of RG-I consists of alternating diglycosyl units of α-d-GalpA and α-l-Rhap G-II is made of a linear α-1,4-l-GalpA residues, and does not contain l-Rhap units as a part of the basal structure (Yapo 2011a). The RG-II is less abundant than RG-I, but shows a higher degree of structural complexity as it contains at least 13 glycosyl residues covalently linked together by more than 21 different types of glycosidic linkages (O’Neill et al. 2004; Ndeh et al. 2017). In the primary cell wall, RG-II predominantly occurs as a dimer crosslinked by a borate diester (Yapo 2011b).

Starch is an energy storage polymer produced by many plants and consists of two types of molecules: linear and helical amylose and branched amylopectin. Depending on the plant, starch generally contains 20%–25% amylose and 75%–80% amylopectin by weight. Amylose is more resistant to digestion by human amylase than is amylopectin. Starch present in whole or partly milled grains or seeds (corn, peas, beans, cracked grains), is often inaccessible to digestion. Starch, when cooked, undergoes a process of gelatinisation in which the crystal structure is broken down and the molecules become accessible to amylase. However, cooling, drying, and freezing starch cause changes in starch structure (retrogradation), which makes it resistant to the action of pancreatic amylase (Table 2) (Englyst et al. 1992). The manufacture of convenience foods influences the amount and kinds of starch that are ingested, as well as other kinds of oligosaccharides that reach the large bowel: galacto- and fructo-oligosaccharides, synthetic non-nutritive sweeteners (such as saccharin) and texturizers (such as carrageenan, alginate, gum arabic, guar gum) (Lewis and Abreu 2017). They may have a small but growing influence on the bowel fermentation in modern life (Ruiz-Ojeda et al. 2019).

Table 2. Categories of starch.

Category	Examples	Digestion in small bowel by pancreatic amylase
Readily digestible starch	Freshly cooked starchy foods	Rapid
Slowly digestible starch	Most raw cereals	Slow but complete
RS1: physically inaccessible	Partly milled grains and seeds	Resistant
RS2: native granular structure	Raw potato and banana	Resistant
RS3: retrograded	Cooled cooked potato, bread, and corn flakes	Resistant

Note: After Englyst et al. (1992).

Bacteroides species provide good examples of the differential use of a wide range of plant polysaccharides (plant glycans) for growth. They belong to the Bacteroidetes phylum whose members have the greatest capacity of gut bacteria to utilise complex carbohydrates (White et al. 2014). Thus, they tend to be generalists in that they can degrade a wide spectrum of glycans in contrast to the Firmicutes that tend to be specialists for a smaller set of polysaccharides. Bacteroidetes genomes encode large numbers of carbohydrate-active enzymes (CAZymes; glycosyl hydrolases [GHs] and polysaccharide lyases [PLs]), averaging 137 of this type of gene per genome compared to 39 in members of the phylum Firmicutes (El Kaoutari et al. 2013; Cockburn and Koropatkin 2016). The majority (81%) of Bacteroidetes GH and PL genes have signal sequences indicating that initial catabolism of dietary fibre occurs extracellularly/within the periplasm of the bacterial cell (El Kaoutari et al. 2013).

The genus Bacteroides contains the most expanded glycolytic gene repertoires that target xylan degradation (Zhang et al. 2014). As summarised by Mendis et al. (2018), xylans consist of a backbone of β-(1→4)-linked xylopyranose units onto which 4-O-methylglucuronic acid (MeGlcA) groups, O-acetyl groups, or other sugars, such as arabinose, can be substituted at C(O)-2 and/or C(O)-3 positions. Ferulic acid can be found attached to the C(O)-5 position of these arabinose. Arabinoxylans are xylans with arabinose substitution at C-2 and/or C-3 positions of the xylan backbone. Arabinoxylans are prevalent in many cereal grains: wheat (5.5%–7.2%), barley (3.9%–5.4%), maize (1%–2%), and rice (2%–3%). Arabinoxylans can be hydrolysed into xylo-oligosaccharides (XOS) and arabinoxylo-oligosaccharides (AXOS). Differential growth of Bacteroides based on the utilisation of specific xylans with differing structural complexity is shown by laboratory experiments with Bacteroides ovatus, Bacteroides xylanisolvens and Bacteroides cellulosilyticus strains (Centanni et al. 2017). While all three species can use wheat arabinoxylan and beechwood xylan for growth, only B. ovatus and B. xylanisolvens can grow on a more highly branched xylan obtained from New Zealand (NZ) flax. The dynamics of the utilisation of NZ flax xylan differs between B. ovatus and B. xylanisolvens: B. ovatus completely hydrolyses the flax xylan, whereas there is a relatively small reduction in molecular weight of flax xylan by B. xylanisolvens cultures. This suggests that only partial hydrolysis of side-chain moieties occurs. Although these are two closely related Bacteroides species, their ecological behaviour can be predicted to be different: B. ovatus totally degrades and consumes the entire xylan thus leaving nothing for competitors, whereas B. xylanisolvens as a partial consumer of the polymer, leaves substrate that could be used by other gut bacteria. The behaviour of these two species differs according to the type of xylan that is available since both species degrade wheat arabinoxylan with the release (leakage) of significant amounts of AXOS which could serve as growth substrates for gut bacteria (Louis et al. 2014; Rakoff-Nahoum et al. 2014; Rogowski et al. 2015; Centanni et al. 2017). Therefore, supplementing the human diet with different kinds of xylans is likely to have differential ecological outcomes with respect to Bacteroides species.

Members of the Bacteroidetes package CAZyme genes into genomic clusters called polysaccharide utilisation loci (PULs). PULs encode proteins for the capture, degradation, and import of specific glycans, each locus targeting a different carbohydrate structure (Cockburn and Koropatkin 2016). PUL-encoded proteins include Sus-like systems (starch utilisation system, the prototype PUL described for starch as substrate) (Cockburn and Koropatkin 2016). Upon detecting a carbohydrate, a PUL is activated to express surface glycan-binding proteins, outer membrane oligosaccharide transporters, surface/periplasmic CAZymes, and SusC and SusD homologues. This synchronous production of components comprising a complete glycan-foraging unit binds, degrades, sequesters, and transports carbohydrates into the intracellular space. With respect to xylans, a key feature is the presence of genes encoding endo-1,4-beta xylanases belonging to glycoside hydrolase family 10 (GH10). B. ovatus contains two PULs; a large xylan PUL (PUL-XylL, BACOVA_03417-50) implicated in the degradation of structurally complex xylans, and a small xylan PUL (PUL-XylS, BACOVA_04385-94) that acts only on xylans with simpler structures (Rogowski et al. 2015). A search for similar xylan PULs in other members of the Bacteroidetes phylum showed that these were only present in strains of B. ovatus and B. xylanisolvens. Differences in the specificities of the enzymes encoded within these PUL variants may confer ecological advantages for some strains over others, dependent on both xylan availability and structural complexity (Despres et al. 2016).

Cellulosomes are multi-enzyme complexes at the bacterial cell surface that facilitate the degradation of cellulose and hemicelluloses by bacteria in the rumen and soil (Bayer et al. 2004). One species, Ruminococcus champanellensis, with this property has been detected in the human gut microbiota (Ben David et al. 2015). Cellulosomes bring hydrolytic enzymes, carbohydrate-binding domains, substrate, and cell surface into close proximity, facilitated by molecules called ‘dockerins’ and ‘cohesins’ (Bayer et al. 2004). A simpler type of multi-enzyme complex (the ‘amylosome’) is present on the cells of the starch-degrading species Ruminococcus bromii (Ze et al. 2015). This species has an exceptional ability to degrade particulate resistant starches when compared with other amylolytic bacterial species inhabiting the gut. The importance of starch in the life of R. bromii is confirmed by analysis of the genome sequence of strain L2-63: it encodes 21 glycosyl hydrolases of which 15 belong to the family GH13 (amylases, pullulanases) (Ze et al. 2012).

Cell surface-associated complexes that mediate pectin degradation are present in the species Monoglobus pectinilyticus, recently cultured from human faeces (Kim et al. 2017). M. pectinilyticus, compared to other pectinolytic bacteria, possesses relatively large numbers of genes for carbohydrate esterases (CEs) and PLs predicted to be involved in the initiation of pectin degradation (Kim et al. 2019). Unusually, there seems to be a larger share of pectinolytic activity from PLs relative to GHs that focus on pectin degradation. Abundant production of CEs could mediate an initial removal of methyl and acetyl groups to facilitate rapid access by PLs, which in turn hydrolyse HG and RG backbones (Hugouvieux-Cotte-Pattat et al. 2014). All of the PLs, and most of the CEs, contain signal peptide sequences, suggesting pectin degradation occurs extracellularly. Indeed, the extracellular catabolism of pectin seems to be facilitated by cell surface S-layer homology (SLH) domain-containing proteins that anchor pectin-active enzymes to the bacterial cell surface. Proteomics analysis shows that SLH are differentially expressed in response to pectin. S-layer protein-mediated glycan degradation differentiates M. pectinilyticus from the PUL system of Bacteroides, PULs associated with the Roseburia/Eubacterium rectale group (Sheridan et al. 2016) and the cellulosome/amylosome organisations in R. champanellensis (Moraïs et al. 2015; Cann et al. 2016) and R. bromii (Ze et al. 2015).

In summary, dietary fibre is composed of insoluble and soluble polysaccharides of greatly varying chemical composition and complexity of structure. This molecular diversity is reflected in the specialised fibre-degrading biochemical attributes that are encoded by bacterial genomes within the gut microbiome. Some examples of these sophisticated molecular mechanisms are given above. Expanding this knowledge of the catabolism of particular dietary fibres by specific bacterial taxa could form the basis of interventions to modify the functioning of the gut microbiota, providing a new generation of prebiotics for use in correcting dysbiosis.

Feasibility of changing outputs of SCFAs by changing dietary fibre consumption

Radical changes in the composition of human diets cause shifts in microbiota composition and associated emergent properties of the bacterial community. David et al. (2014) showed that changing the usual diet of 10 American volunteers to one that was ‘plant-based’ (rich in grains, legumes, fruits, vegetables) or one that was ‘animal-based’ (meats eggs, cheeses) modified taxonomic composition and emergent properties of the faecal microbiota. The diets were consumed ad libitum for five consecutive days. The diets changed macronutrient intake: animal-based diet increased average dietary fat from 32% to 69% kcal, and average protein from 16% to 30% kcal. Dietary fibre intake was nearly zero. In contrast, plant-based diet increased fibre intake to average 25 grams/1000 kcal from baseline value of 9 grams/1000 kcal. Fat and protein intake decreased to 22% and 10% kcal respectively. These marked changes in dietary intake did not affect the variety of bacteria present (alpha diversity) but changes in microbiota composition based on differences in phylogeny, relative abundances of ‘species’ and variety (beta-diversity) could be detected between animal-based diet and other groups just one day after the food reached the colon. This was confirmed by detection of 22 taxonomic clusters that differed in relative abundance when the animal-based diet was consumed, whereas only 3 clusters showed significant changes with the plant-based diet relative to baseline samples. The most common clusters associated with the animal-based diet were composed of bile-resistant bacteria, which correlated with the known increase of bile acids in the gut when there is a high fat intake. Macronutrient intake affected the output of SCFAs by the microbiota. Faeces from volunteers consuming the animal-based diet had much lower concentrations of SCFAs originating from the fermentation of carbohydrates (acetate and butyrate) but higher concentrations of SCFAs originating from the fermentation of amino acids (isobutyrate, isovalerate), relative to baseline and plant-based diet samples. In summary, this work showed that radical changes to the diet in an experimental setting produce changes in both composition and fermentative activities of the gut microbiota.

In a natural setting, De Filippo and colleagues (2010) compared the compositions of the faecal microbiotas of children living in a rural village in Burkina Faso, Africa, with those of Italian children living in Florence. There were nine boys and six girls (aged 1–6 years) in each group. The children in rural Africa ate food high in dietary fibre, possibly resembling the diet that humans consumed millennia ago, relative to the ‘modern Western diet’ of urban Italians. The faecal microbiota of Burkina Faso children was rich in Bacteroidetes (57.7% compared to 22.4% relative abundance), but depleted in Firmicutes (27.3% versus 63.7%), with abundant members of the genera Prevotella and Xylanibacter that had genetic capacity to hydrolyse cellulose and xylan. These bacteria were lacking in the microbiota of Italian children. As a consequence of fibre degradation and fermentation, there was a higher concentration of SCFAs in the faeces of Burkina Faso children. The authors considered that the composition of the faecal microbiotas of rural African children reflected consumption of a polysaccharide-rich diet from which they were able to achieve maximal energy harvest through bacterial fermentation.

A further appreciation of the link between dietary fibre intake and the gut microbiota of humans can be obtained by considering the results of studies with African hunter-gatherers, the Hadza, who are one of the last such communities in the world (Schnorr et al. 2014). They are nomadic, living in small camps from which they forage plants and hunt animals to provide most of their subsistence. Their lifestyle probably resembles that of Palaeolithic humans. A comparison of the faecal microbiota of 27 Hadza and 16 Italians showed a greater diversity of bacteria in the Hadza microbiota which included many Bacteroidetes, Clostridiales, Bacteroidales, and Lachnospiraceae that did not resemble previously detected families and genera. These unassigned bacteria comprised 22% of the microbiota. This observation fits with the report that there are many more bacterial types capable of inhabiting the human gut than has been revealed by past studies of humans in Northern Hemisphere countries (Almeida et al. 2019). By extending the scope of microbiota studies to more countries and nationalities, more gut inhabitants are discovered. The Hadza faecal microbiota differs between men and women, probably reflecting the different diets of the groups stemming from different community roles. Women are the gatherers and tend to consume more dietary fibre than men, sourced especially from tubers, which is associated with increases in the relative abundance of spirochaetes (Treponema) in the microbiotas of women. These bacteria are rare in Western microbiotas. Hadza men consume more meat while on hunting expeditions. Their microbiota has increased abundances of Eubacterium and Blautia relative to that of women. No such gender differentiation of Italian microbiotas was apparent. Emergent properties of the microbiotas differed between Hadza and Italians, probably reflecting the relative amounts and types of dietary fibre that was consumed. Italians had more butyrate in the faeces than Hadza who had more propionate. Lower concentrations of butyrate were associated with lower content of Clostridium clusters IV and XIVa (butyrate producers) whereas more propionate was associated with greater relative abundance of Prevotella (Schnorr et al. 2014).

Subsequent investigations of the Hadza faecal microbiota during annual wet or dry periods showed seasonal variations in microbiota composition (Smits et al. 2017). These periods are associated with marked changes in dietary intake: hunting is best in the dry period, foraging for berries and honey is more frequent in the wet season. Phylogenetic diversity was greater during the dry season, mainly due to the decline in abundance of Prevotellaceae during the wet season. Based on data collected from eight Hadza, members of the Succinivibrionaceae, Paraprevotellaceae, Spirochaetaceae, and Prevotellaceae were among the most variable according to seasons. Seasonal changes in the functional capacity of the microbiota were revealed by comparison of metagenomic data with a focus on carbohydrate-active enzymes (CAZymes) encoded by the microbiotas. Hadza had a more diverse collection of CAZymes relative to Americans, with the greatest diversity in the dry season microbiotas.

In summary, microbiota studies in human populations consuming dietary fibre of different types and amounts to those ingested by Westerners have different gut communities in terms of composition and functional capacity. Together with evidence of seasonal cycling of microbiota features, the intake of dietary fibre clearly impacts the bacterial community both in composition and SCFA production. Changing consumption of dietary fibre by humans in Western countries to modulate microbiota composition and function (correct dysbiosis) is therefore feasible, but will depend on accruing knowledge of what dietary polymers can produce the changes deemed to be beneficial.

Intervention studies to influence SCFA production by the gut microbiota

To date, studies to measure the effects of dietary fibre on the human gut microbiota have been driven mostly by commerce to obtain evidence to support health claims (for example, Guglielmetti et al. 2013; Costabile et al. 2016) and often utilise experimental animals (for example, Tian et al. 2017; Drew et al. 2018) or in vitro batch or continuous cultures inoculated with human faeces (for example, Duncan et al. 2003; Ho et al. 2018; Poeker et al. 2018; Alexander et al. 2019). A plant fructan, inulin, and its degradation products (fructo-oligosaccharides), as well as galacto-oligosaccharides, feature prominently in the prebiotic literature mainly with respect to increasing the relative abundance of the bifidobacterial population of the gut microbiota (for example, Davis et al. 2010; Watson et al. 2013). While these kinds of studies are interesting, they are divorced from the fundamental aspects of the human gut ecosystem. It is difficult to extrapolate findings from experimental animals whose gut microbiota is different in distribution and composition from that of humans (Savage 1977; Ley et al. 2008), or to relate culture-based studies using purified substrates to the complexity of in vivo ecosystems in which dietary fibre is presented to the bacteria as complex mixtures of polysaccharides in the form of particulate material.

Much of the dietary fibre in Western diets is derived from intact cereal grain fibres, including wheat bran (which contains arabinoxylans). Jefferson and Adolphus (2019) systematically reviewed the effects of intact cereal grain fibres on the gut microbiota of healthy adults based on the results of 40 studies. In general, increasing the amount of intact cereal grain fibres consumed per day resulted in increased concentrations of SCFAs in the faeces. Resistant starches and AXOS (produced in bread by including endoxylanase enzyme) tend to raise butyrate concentrations in faeces, although whether these increases are biologically meaningful is not clear. For example, a human trial compared the effects of consuming 25 grams of non-starch polysaccharides (NSP) or 25 grams of NSP plus 22 grams of resistant starch (high amylose starches, RS2) per day during a 4-week period in 46 healthy adults. Faecal butyrate concentrations varied among the participants at baseline (3.5–32.6 mmol/kg). In general, acetate, butyrate and total SCFA concentrations were higher when participants consumed RS compared with baseline and NSP diet (average butyrate increase 2.7 mmol/kg), but individual responses varied (McOrist et al. 2011). Similarly, a human trial with 40 healthy adults assessed the impact of consumption of breads containing AXOS. Consumption of AXOS-enriched breads led to increased faecal butyrate, also with an average increase of 2.7 mmol/kg (Walton et al. 2012).

Many human trials have been carried out in relation to dietary fibre intake and morbidity and mortality of non-communicable diseases. Dreher (2018) summarised meta-analyses of these trials in relation to specific human diseases or conditions. The observed statistical associations between certain diseases and dietary fibre intake provide the focus for microbiota studies. Amongst these trials, attention has been given to a relatively modern dietary pattern (1940s–1950s) – The Mediterranean diet – inspired by the eating habits of people in Greece, Southern Italy, and Spain in those decades. The Mediterranean diet is characterised by fruits, vegetables, fish and whole grains, and limited saturated fats. It has low energy content obtained mostly from carbohydrates rather than from proteins and fats, complex carbohydrates compared to simple carbohydrates, and unsaturated rather than saturated fats (Fava et al. 2018). The Mediterranean diet is associated with reduced risk of heart disease (Sofi et al. 2010). It is not clear whether the gut microbiota is important in influencing this outcome, but Italians that adhere closely to ‘The Mediterranean diet’ have higher SCFA concentrations in faeces than do those with lesser adherence (De Filippis et al. 2016). Collectively, therefore, this work supports the view that the more dietary fibre is consumed, the greater the fermentative activity in the colon.

Human trials that test the effect of varying doses (dose–response trials) of different chemically/structurally defined dietary fibres on the production of SCFAs do not seem to have been pursued to any extent (Graf et al. 2015; Maier et al. 2017; Shortt et al. 2018). A major problem is the quantity of dietary fibre that needs to be included in the diet over and above baseline level to produce consistently measurable effects in humans. The amount of dietary fibre that might need to be consumed daily, long term, in order to produce a sustainable outcome could be beyond the tolerance of modern-day humans in Western countries. Daily intakes of 80–150 grams of dietary fibre per day would equate to that consumed by the Hadza (Pontzer et al. 2018), but it is difficult to persuade Westerners to consume even 15–20 grams per day. Changing quality rather than quantity is an attractive proposition but ‘exotic’ dietary fibre not currently included in Western diets might have little effect in promoting a modified, highly diverse microbiota because the microbial community lacks the species with appropriate biochemical attributes that would proliferate and/or affect emergent properties of the community (‘missing microbes’) (Deehan and Walter 2016). Microbiotas that are already relatively high in diversity do not respond to increased intake of dietary fibre even at a level of 40 grams per day (Tap et al. 2015). Thus screening the gut microbiotas of potential participants in intervention studies is probably necessary to identify individuals with low diversity communities so that there would be some hope of obtaining ‘improvement’. Individualism of gut microbiotas may make a general, ‘one diet fits all’ approach unlikely to succeed (Martínez et al. 2010; Walker et al. 2011; Brahma et al. 2017; Johnson et al. 2019).

In summary, although there are many publications that report the outcomes of in vitro fermentations of specific polysaccharides present in the dietary fibre component of food, there has been little effort to test dietary fibre per se (structurally complex mixtures), or pure or defined mixtures of polysaccharides in varying doses (dose–response trials) to observe in vivo shifts in SCFA outputs. This is clearly a topic that needs substantial experimental input. Mechanistic concepts of how consortia assemble within the microbiota in response to structurally and chemically diverse polysaccharides need to be developed. This is not a simple proposition even for multidisciplinary teams. However, understanding the ecology of the gut microbiota in relation to dietary fibre should be priority research. We have a lot of taxonomic knowledge about the predominant members of the microbiota, but we need to learn about how communities assemble and how they function together in a concerted way to degrade and ferment dietary fibre. Phylogenetic, compositional studies alone will not reveal this information.

Changing SCFA production by the microbiota to improve human health

The metabolic products of the gut microbiota are probably instrumental in the maintenance of gut homeostasis, regulation of some aspects of host metabolism, and immune cell development and function (Roediger 1980; Arora et al. 2011; Cani 2014; Thorburn et al. 2014). Maintenance of epithelial integrity (barrier function) has been associated with butyrate, the main energy source for colonocytes (Dupaul-Chicoine et al. 2010). Colonocytes and immune cells associated with the gut mucosa have receptors that bind SCFAs (Table 3) (Thorburn et al. 2014). These G-protein-coupled receptors (GPCR) are associated with functions both in immunity and metabolism, but promoting the up-regulation of anti-inflammatory pathways and regulating appetite may be of most significance in reducing the prevalence of non-communicative diseases such as obesity, diabetes, cancer, and cardiovascular disease in Western countries.

Table 3. Metabolite-sensing G-protein-coupled receptors (GPCR) and associated ligands and functions.

GPCR	Ligands	Function in Immunity	Function in metabolism
GPR41 (FFAR3)	Formate, acetate, propionate, butyrate, pentanoate	Dendritic cell (DC) maturation, anti-inflammatory	Leptin production, regulation of energy balance
GPR43 (FFAR2)	Formate, acetate, propionate, butyrate, pentanoate	Anti-inflammatory, gut homeostasis, tumour suppression	Insulin-mediated fat accumulation, control of body energy
GPR109A (NIACR1, HM74)	Butyrate, nicotinic acid (niacin)	DC trafficking, gut homeostasis, anti-inflammatory, tumour suppression	Intracellular triglyceride lipolysis in adipocytes

Note: After Thorburn et al. (2014).

Through liver gluconeogenesis, propionate is an important source of glucose for ruminants: as much as 90% of glucose in adult ruminants is derived by this method (Nafikov and Beitz 2007). Ruminant studies also showed a marked decrease in appetite following intravenous infusion with propionate (Bergman 1990; Farningham and White 1993; Arora et al. 2011). A liver-brain axis mechanism was suggested because blockading the vagus nerve close to the liver prevented the propionate-induced hypophagia (Anil and Forbes 1980). Propionate probably has much less importance as a source of glucose in humans than in ruminants (Morrison and Preston 2016). However, delivery of propionate directly to the human colon in the form of inulin-propionate ester resulted in increased release of anorectic gut hormones (peptide YY [PYY] and glucagon-like peptide 1 [GLP-1]) and reduced energy intake by the participants by about 14% (Chambers et al. 2015). The use of inulin-propionate ester ensured delivery of most of the propionate to the colon where the propionate was released by bacterial action. Long-term (24 weeks) delivery prevented further weight gain and reduced intra-abdominal fat accretion in overweight participants (Chambers et al. 2015). In rodents, GLP-1 release is due to stimulation of GPR43 (FFAR2) on endocrine cells in the gut mucosa (L cells) (Tolhurst et al. 2012). Administration of PYY or GLP-1 to humans enhances satiety and reduces food intake (Turton et al. 1996; Batterham et al. 2003). Using a similar approach in another human study, functional NMR showed reductions in blood oxygen level-dependent signals in brain regions associated with reward processing during food picture testing (Byrne et al. 2016). The participants also had reduced energy intake during an ad libitum meal. These changes, however, were independent of plasma PYY and GLP-1 levels (Byrne et al. 2016). Adverse influences of calcium propionate (used in bread as a preservative) ingested with food by mice (glycogenolysis, hyperglycaemia) are unlikely to be relevant in the context of dietary fibre (Tirosh et al. 2019); the propionate in food is quickly absorbed in the small bowel whereas in situ production by the microbiota leads to binding to colonic receptors.

Inflammatory bowel diseases (IBD; Crohn’s disease, CD; ulcerative colitis, UC) are disorders that have genetic predispositions, environmental modifiers, and chronic immune-mediated tissue damage (Xavier and Podolsky 2007). The gut microbiota has been invoked as a major environmental factor in IBD. This is based mainly on evidence obtained from experimental animal models of gut inflammation in which colitis only occurs if genetically predisposed germfree animals are colonised by a gut microbiota (Sartor 2005). Chronic inflammation possibly occurs because bowel barrier function is compromised, permitting continual access of luminal bacterial antigens to sub-epithelial tissue and chronic activation of inflammatory processes because a bacterial invasion appears to be occurring (Macdonald and Monteleone 2005). A single bacterial species has not been identified as the causative agent of IBD. Rather, dysbiosis is associated with CD in particular, where human studies indicate that the diversity of species comprising the microbiota is less than in health (Ott et al. 2004; Frank et al. 2007; Cao et al. 2014; Kostic et al. 2014). In general, there is a depletion of members of clostridial cluster IV (Clostridum leptum cluster) that characteristically produce butyrate. Interest has also been placed on Faecalibacterium prausnitzii and Roseburia species (clostridial cluster XIVa, Clostridium coccoides cluster) because there is an inverse correlation between abundance of these species and disease activity (Laserna-Mendieta et al. 2018). Although a causative effect of dysbiosis has not been established in IBD, butyrate is an energy source for colonocytes and has anti-inflammatory effects. Thus correction of the dysbiosis by guided dietary intervention may be an attractive treatment option. Particular kinds of dietary fibre may be useful in this respect, assuming that bacterial species that can utilise the specific fibre and produce butyrate are still present in, or can gain access to, the diseased gut. IBD patients tend to have low fibre intakes despite recommendations that dietary fibre not be restricted except where there is a presence of bowel strictures (potential for blockage) (http://www.ccfa.org/asets/pdf/diet-nutrition-2013.pdf). This lower intake of dietary fibre may be the actual reason for the reduced capacity of IBD-associated microbiotas to produce butyrate.

The best, current nutrition-based treatment for IBD (mainly paediatric CD) is exclusive enteral nutrition (EEN) in which patients consume a liquid diet that provides all of their energy and nutrient needs (Heuschkel et al. 2000; Lewis and Abreu 2017; MacLellan et al. 2017). Although there is sometimes poor compliance by patients, clinical improvement has been reported with reduced symptoms of disease, which may be due to improved mucosal healing (Borrelli et al. 2006). Ironically, EEN results in lower butyrate production by the gut microbiota because the diet does not contain dietary fibre (Gerasimidis et al. 2014). As indicated previously, the Hadza people have lower concentrations of butyrate (Clostridium clusters IV and XIVa less abundant) in the faeces than Italian counterparts. It is possible, therefore, that the importance of butyrate in gut health has been over-stated, but further research may show that smaller quantities can still be therapeutic. It should be noted moreover that SCFAs, in general, may mitigate colorectal cancer through anti-inflammatory effects (Louis et al. 2014).

In summary, increased intake of selected dietary fibre might be a useful adjunct in the management of chronic diseases such as obesity (propionate and appetite) and IBD (butyrate and inflammation). Quality of dietary fibre, not necessarily the quantity, may be important in promoting health. Development of these therapeutic prospects will require much more information about the capacity of the microbiota to utilise different kinds of dietary fibre. Moreover, the dietary fibre will need to be in a palatable form and ingested in efficacious amounts that can be easily tolerated and enjoyed by the consumer.

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No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors were supported wholly (YL) or in part (GWT) by National Science Challenge High Value Nutrition grant ‘A good night’s sleep’.