doi:10.1038/nindia.2016.48 Published online 18 April 2016
Four decades ago, Indian scientists showed that the guts of ‘normal’ Indian children are different from those in more developed countries, with the presumed nearly-sterile upper gastrointestinal tract colonised with a range of anaerobic and aerobic bacteria1. These findings are more extreme in malnourished children and adults reportedly resulting from high environmental exposure to pathogens, which not only caused overt diarrhoea but also abnormal architecture of the villi and malabsorption of nutrients in a gut colonised by bacteria along its length2. High rate of malnutrition was then common in India. Various feeding programmes had been developed and implemented with varying levels of success.
However, a lot has changed in four decades — the mortality due to diarrhoea decreases every year, in part due to better rehydration methods and better access to care. Many feeding programmes have significantly decreased acute malnutrition — marasmus and kwashiorkor, the forms of severe malnutrition, once common, now rarely occur in most parts of India; but stunting, or reduced height, a sign of chronic malnutrition, is declining much more slowly3. Although nutrition is a matter of eating food and using it for growth, metabolism and repair, new tools to investigate human biology help in understanding possible reasons of why the ingestion of adequate energy and protein does not necessarily result in an acceleration of linear growth in stunted children.
The human gut contains trillions of microbes, which provide several metabolic functions that are not encoded in our own genome. Before the development and application of sequence-based molecular tools for microbiome analysis, culture-based methods were used to identify bacteria and its interaction, significantly underestimating the complexity of the human gut microbial ecosystem. The availability of culture-independent approaches to analyse the structure and function of microbial communities in the gut is now permitting insights that were previously inaccessible.
Recent studies, combining field sample collection from healthy and malnourished children with microbiome analysis and establishment of model systems, have shown that the microbiomes in malnourished children are functionally less mature than that in healthy children of similar age and from similar locations4. Using 16S ribosomal sequencing to identify bacterial taxa in the children’s faecal samples, patterns that differed in key taxa between malnourished and healthy children were detected. Supplementary feeding of these children with commercially available or locally made ‘therapeutic’ foods resulted in some weight gain but not reversal to the level of healthy children or height gain5. The microbiome immaturity in the malnourished children showed some improvement during treatment but regressed within months when the feeding was stopped, indicating that the re-programming of the microbiome maturity would not be easily achieved by diet alone.
The immaturity of the gut microbiome in malnourished children may be responsible, in part, for its inability to play a role in energy harvest and nutrient assimilation and the consequent lack of effect on stunting. The microbial flora functions relevant to growth include fermentation of dietary polysaccharides, anaerobic metabolism of proteins and peptides, biosynthesis of vitamins and possibly, the absorption of ions and regulation of a number of host metabolic pathways.
Data from animal models indicate that the relationship between the microbiome, the immune system and intestinal epithelial cells affects the absorptive capacity of the gut. When B cells, responsible for IgA antibodies acting as defence at mucosal surfaces, are absent (as in B-cell knockout mice), there is lower transcription of a large number of genes involved in metabolism, especially in fat absorption. However, if the gut lacks microbiota, the effect on fat absorption is lost. Normally, controlling and regulating the microbiota are undertaken mainly by IgA but in the absence of IgA this protective response becomes the role of intestinal epithelial cells, with an associated decrease in their metabolic and absorptive functions6. This may explain why children, who have multiple infections or extensive intestinal exposure to microbes, have malnutrition. Thus, the development of a functionally mature microbiome in young children might require lower exposure to potential pathogens as well as a diet that provides nutrients for growth and repair. The window of opportunity for rebalancing the gut microbiota is not yet known but will require interventional studies in order to reduce the consequences of early childhood malnutrition.
This necessary reduction in stunting is not only important to prevent or treat malnutrition, it also has the potential to significantly enhance future human capital. This, given accumulating evidence that stunting, particularly in the first two years of life when brain growth is maximal, affects cognitive development and intelligence. Studies in India and elsewhere using culturally appropriate tools to assess intelligence have shown that children who are stunted have a lower intelligence quotient (IQ) than children with normal growth7, 8. This may affect school performance and future earning capacity.
This is important not only in the context of the individual child and his or her family but also at the level of the population. Although measuring cognitive development, particularly in children, is challenging. Many tools have been adapted and validated. The intelligence quotient (IQ) test is used as a measure of cognitive ability. When average IQs are measured for a country or geographic region, it correlates with many factors including temperature, gross domestic product, secondary education and nutrition.
Newborns expend the majority of the metabolic output in developing the brain. A recent hypothesis has proposed that the absence of infectious diseases allows healthy babies to have more metabolic energy for cognitive development. When a child is sick, the immune system requires metabolic resources to fight the infection in addition to the demands of the multiplying micro-organisms that cause the infection, furthering the nutritional deficit9. Nutrients used to fight disease are not available for brain growth resulting in less cognitive development. It has also been suggested that continued or repeat infections could rewire metabolic pathways, leading to permanent investment of more energy in the immune system.
Thus, even in the absence of an infection, fewer nutrients are available for brain development. Using available datasets around the world, scientists have found that countries with high levels of infectious diseases consistently have lower average IQ scores. Incredibly, this correlation is stronger than any other measure including education. In some settings with high rates of infectious diseases, the IQ is up to 20 points lower than in people in healthier countries. In Asia, for example, Japan, South Korea, Taiwan and Singapore have the highest IQs. In many of these countries, changes in average intelligence have been rapid, increasing by 10–15 points in a single generation, with education certainly contributing but leaving the possibility that decrease in disease and improvement in nutritional status might play a role.
While cleaning up the environment, improving hygiene and food and water safety and education are necessities for any nation striving for the health of its population and economic prosperity, the ability to investigate disease pathogenesis and its reversal through intervention in humans have never been more exciting. This has long been considered challenging because access to the gut, where infection, absorption and secretion happen, requires invasive procedures unethical in young children without major pathology.
New imaging and mass-spectrometric techniques are permitting investigation of intestinal function in health and disease. Stable isotope methods enable tracking water and nutrients from ingestion to body composition10. The complexity of microbial communities and their functions are being resolved through next generation sequencing and bioinformatics analyses11. Multi-modal imaging methods permit quantitative study of structural and functional brain development in neonates and young children.
But why bother studying problems such as malnutrition that we can largely address without necessarily understanding the biology of disease? It is clear that the health problems in the future are going to be significantly related to lifestyle, particularly activity and diet relating to the new form of malnutrition-obesity. Our genomes have been enriched over millennia with alleles favouring energy conservation. Body fat, an energy-dense disposable reserve, accumulates when nutrients are in excess but its loss is defended against vigorously. Although about 25% of obesity is heritable, genome-wide association studies have implicated more than 100 genes that account for a small fraction of obesity12.
While some hormonal and environmental determinants of obesity are clear, the role of the microbiome is being studied in both animals and humans. In animals, eating increases the number of gut bacteria. Some bacteria then produce peptide YY that stimulates the release of satiety hormones, thus sending a signal to the host to stop eating13. Therefore, the growth of the microbiome might participate in appetite regulation. Other studies indicate that short-chain fatty acids produced by colonic microbiota stimulate anorexigenic gut hormones and increase leptin synthesis14. Metagenomic and biochemical analyses show that the microbiome of obese individuals has an increased capacity to harvest energy from the diet. Metabolic studies have demonstrated an alteration of the metabolism of bile acids, branched fatty acids, choline, vitamins (i.e. niacin), purines, and phenolic compounds associated with the obese phenotype.
These associations demonstrate consistently that human gut microbial profiles are altered in malnutrition and metabolic disease, with decreased diversity and functional richness associated with disordered intestinal function and disease (Figure 1). However, validation and the establishment of causality are challenging. Among approaches being considered, system biology combined with new experimental technologies may help to disentangle the complex interactions of diet, microbiota and host metabolism. As in the case of stunting, there are opportunities to explore how sustainable alternations of the microbial flora can affect nutrient assimilation or appetite regulation to control obesity.
There is a change in the scale of the challenges in disease biology that we can begin to address using the technologies now available and in development. Well-designed studies that bring together complementary skills in medicine, science and analytics will generate new insights that offer the opportunity for a deeper understanding of the biology of malnutrition and its consequences. These are large problems that require scientists to harness curiosity and explore the mechanisms by which a pathologic state is created and can be corrected. The consequences of success for science, medicine and society will be tremendous.
*Christian Medical College, Vellore, Tamil Nadu, India.
1. Albert, M. J. et al. Jejunal microbial flora of southern Indian infants in health and with acute gastroenteritis. J. Med. Microbiol. 11, 433–440 (1978)
2. Baker, S. J. Subclinical intestinal malabsorption in developing countries. Bull World Health Organ. 54, 485–494 (1976)
3. Rehman, A. M. et al. Chronic growth faltering amongst a birth cohort of Indian children begins prior to weaning and is highly prevalent at three years of age. Nutr. J. 8, 44 (2009)
4. Ghosh, T. S. et al. Gut microbiomes of Indian children of varying nutritional status. PLoS One.9, e95547 (2014)
5. Subramanian, S. et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 510, 417–421 (2014)
6. Shulzhenko, N. et al. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat. Med. 17, 1585–1593 (2011)
7. Ajjampur, S. S. et al. Effect of cryptosporidial and giardial diarrhoea on social maturity, intelligence and physical growth in children in a semi-urban slum in south India. Ann. Trop. Pediatr. 31, 205–212 (2011)
8. Kvestad, I. et al. Diarrhea, stimulation and growth predict neurodevelopment in young North Indian children. PLoS One. 10, e0121743 (2015)
9. Eppig, C. et al. Parasite prevalence and the worldwide distribution of cognitive ability. Proc. Biol. Sci. 277, 3801–3808 (2010)
10. Borgonha, S. et al. Total body water measurements by deuterium dilution in adult Indian males and females. Indian J. Physiol. Pharmacol. 41, 47–51 (1997)
11. Gupta, S. S. et al. Metagenome of the gut of a malnourished child. Gut Pathog. 3, 7 (2011)
12. Apalasamy, Y. D. et al. Obesity and genomics: role of technology in unravelling the complex genetic architecture of obesity. Hum. Genet. 134, 361–374 (2015)
13. Breton, J. et al. Gut commensal E. coli proteins activate host satiety pathways following nutrient-induced bacterial growth. Cell Metab. pii: S1550–4131(15), 00566–5 (2015)
14. Chakraborti, C. K. et al. New-found link between microbiota and obesity. World J. Gastrointest. Pathophysiol. 6, 110–119 (2015)