A chronic lack of dietary fibre has been found to reduce the diversity of bacteria in the guts of mice. This effect is not fully reversed when fibre is reintroduced, and increases in severity over multiple generations. See Letter p.212

People living in industrialized nations routinely consume much less than the recommended amount of 25–38 grams of dietary fibre per day. Physicians and nutritionists have been imploring us for decades to bolster our fibre intake to help stave off maladies ranging from heart disease to intestinal disorders. The mechanisms through which fibre consumption modulates health are manifold, including a role in maintaining our resident gut microorganisms. On page 212 of this issue, Sonnenburg et al.1 reveal that a lack of dietary fibre leads to a substantial loss of diversity in this microbial community, and influences the ability of gut bacteria to be transferred from parents to their offspring. Furthermore, it seems that simply restoring fibre consumption is not enough to reverse this effect once it has been passed to subsequent generations.

The 'fibre' that we see quantified on food labels is a catch-all category encompassing dozens of different molecules, mostly complex carbohydrates (linear and branched chains of simple sugars such as glucose). But the human genome encodes only around a dozen digestive enzymes that target complex carbohydrates. Technically speaking, dietary fibre comprises the polymeric molecules that cannot be broken down by these enzymes. However, these nutrients do not go to waste. Instead, the diverse microorganisms that have evolved to inhabit the human intestine — collectively called the gut microbiota — produce thousands of enzymes that specifically target dietary fibre2,3,4. Some individual bacteria produce more than 300 such enzymes5. These organisms ferment the released sugars into short-chain fatty acids, which are used as fuel for intestinal cells and which influence systemic physiology and the development of immune responses6.

The gut microbiota of each person typically contains hundreds of different bacterial species. We do not each harbour exactly the same community members; rather, the composition of our microbiota is drawn from a larger set of potential colonizers on the basis of parental and environmental exposure that begins at birth. Many microorganisms that live in the human gut exist only in this niche, and thus rely on successful transfer between generations to avoid extinction.

Sonnenburg et al. posed the question: what happens to the microbiota when dietary fibre is withheld for prolonged periods? The researchers colonized the intestines of germ-free mice (those that lack any resident microorganisms) with a human faecal sample, which contains a representative complement of the gut microbiota members. They then fed the mice a diet rich in dietary fibre or one that contained only low fibre, in a form poorly accessible to the microbiota. After several weeks of fibre deprivation, the microbiota showed a reduction in the abundance of many bacterial groups that had been previously present (Fig. 1). These bacteria continued to thrive in the mice that were fed a high-fibre diet. When the fibre-starved mice were returned to a normal diet and allowed to recover for several weeks, many of these groups came back, but some failed to return to their previous levels, revealing that prolonged diet shifts can inflict changes that persist after dietary intervention. Figure 1: Loss of diversity. Sonnenburg et al.1 found that mice fed a low-fibre diet had a lower species diversity in their gut microbiota than mice fed a high-fibre diet. In first-generation mice, most (but not all) of this diversity was recoverable when mice on the low-fibre diet were switched to a high-fibre diet. However, the authors found that diversity loss was greater in each subsequent generation maintained on a low-fibre diet, and that the degree of recovery also decreased, implying extinction of some microbial species. Full size image

The authors next investigated how fibre consumption affects the microbiota over multiple generations. They allowed the mice colonized with human bacteria, from both the high- and low-fibre cohorts, to breed within their cohorts, and for natural microbial colonization of the offspring to occur through maternal contact. Offspring born to parents fed the low-fibre diet had reduced microbiota diversity irrespective of whether they were weaned onto the same diet as their parents or onto a high-fibre diet. Strikingly, the reduction in gut bacterial diversity that was observed in the first generation was compounded over each of four subsequent generations. Moreover, the inferred genomic content of the bacteria that remained after four generations suggested that the abundance of several fibre-degrading enzyme families had been reduced. But further work is required to find out whether a loss in fibre-degrading capacity occurred.

To assess whether dietary change might ameliorate these deficiencies, Sonnenburg et al. placed some of the mice from each generation of fibre-deprived mice on a high-fibre diet. The inability to recover lost diversity was a consistent characteristic at each generation (Fig. 1). However, transplanting the fibre-starved mice with a faecal sample from mice fed a high-fibre diet successfully restored most of the missing bacteria.

It is becoming increasingly apparent that the gut microbiota of people in cultures that eat less-processed and higher-fibre diets differ from those of people in industrialized countries, and often contain a higher diversity of microorganisms7,8,9. Humans have co-evolved with symbiotic bacteria, and these microbial partners shoulder most of the burden of digesting complex carbohydrates. It remains to be determined whether some of this functionality has already been lost in some people and, if so, to what extent. However, in the future, we may turn to probiotic formulations, possibly derived from humans or animals that have not yet restricted their gut microbiome through a low-fibre diet, to restore essential functions that have been lost.

Carbohydrates frequently get a bad rap in fad diets, largely owing to simple carbohydrates such as glucose and fructose that permeate Western diets and provide us with an excess of easy calories. However, their complex cousins that are naturally present in plants, whole grains and a variety of other sources are worth consuming in greater amounts. Two authors of this study last year published a book for the popular press, The Good Gut10, which chronicles the interaction between diet, the microbiome and health, and is replete with high-fibre recipes. You just might consider choosing a salad at lunch today or an extra serving of beans at dinner. Future generations may thank you, too.Footnote 1

Notes

References 1 Sonnenburg, E. D. et al. Nature 529, 212–215 (2016). 2 Martens, E. C. et al. PLoS Biol. 9, e1001221 (2011). 3 Larsbrink, J. et al. Nature 506, 498–502 (2014). 4 Cuskin, F. et al. Nature 517, 165–169 (2015). 5 El Kaoutari, A. et al. Nature Rev. Microbiol. 11, 497–504 (2013). 6 Smith, P. M. et al. Science 341, 569–573 (2013). 7 De Filippo, C. et al. Proc. Natl Acad. Sci. USA 107, 14691–14696 (2010). 8 Clemente, J. C. et al. Sci. Adv. 1, e1500183 (2015). 9 Schnorr, S. L. et al. Nature Commun. 5, 3654 (2014). 10 Sonnenburg, E. & Sonnenburg, J. The Good Gut (Penguin, 2015). Download references

Author information Affiliations Eric C. Martens is in the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA. Eric C. Martens Authors Eric C. Martens View author publications You can also search for this author in PubMed Google Scholar Corresponding author Correspondence to Eric C. Martens.

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