Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
Microbiota and infant development
Malnutrition in children is a persistent challenge that is not always remedied by improvements in nutrition. This is because a characteristic community of gut microbes seems to mediate some of the pathology. Human gut microbes can be transplanted effectively into germ-free mice to recapitulate their associated phenotypes. Using this model, Blanton et al. found that the microbiota of healthy children relieved the harmful effects on growth caused by the microbiota of malnourished children. In infant mammals, chronic undernutrition results in growth hormone resistance and stunting. In mice, Schwarzer et al. showed that strains of Lactobacillus plantarum in the gut microbiota sustained growth hormone activity via signaling pathways in the liver, thus overcoming growth hormone resistance. Together these studies reveal that specific beneficial microbes could potentially be exploited to resolve undernutrition syndromes.
Science, this issue p. 10.1126/science.aad3311, p. 854
Structured Abstract
INTRODUCTION
As we come to appreciate how our microbial communities (microbiota) assemble following birth, there is an opportunity to determine how this facet of our developmental biology relates to the healthy or impaired growth of infants and children. Childhood undernutrition is a devastating global health problem whose long-term sequelae, including stunting, neurodevelopmental abnormalities, and immune dysfunction, remain largely refractory to current therapeutic interventions.
RATIONALE
To test the hypothesis that perturbations in the normal development of the gut microbiota are causally related to undernutrition, we first applied random forests (RF), a machine learning method, to bacterial 16S ribosomal RNA data sets generated from fecal samples that were collected serially from healthy Malawian infants and children during their first 3 postnatal years. Age-discriminatory bacterial taxa were identified with distinctive time-dependent changes in their relative abundances; they were used to construct a sparse RF-derived model describing a program of normal postnatal gut microbiota development that is shared across biologically unrelated individuals. A metric based on this model (microbiota-for-age Z-score) was used to define the state of development (maturation) of fecal microbiota from infants and children with varying degrees of undernutrition. Fecal samples obtained from 6- and 18-month-old children with healthy growth patterns or with varying degrees of undernutrition were transplanted into young germ-free mice that were fed a representative Malawian diet. The recipient animals’ rate of lean body mass gain was characterized by serial quantitative magnetic resonance, their metabolic phenotypes were determined by targeted mass spectrometry, and their femoral bone morphologic features were delineated by microcomputed tomography.
RESULTS
Undernourished children in the Malawian birth cohort that we studied have immature gut microbiota. Unlike microbiota from healthy children, immature microbiota transmit impaired growth, altered bone morphology, and metabolic abnormalities in the muscle, liver, and brain to recipient gnotobiotic mice. The representation of several age-discriminatory taxa in the transplanted microbiota harbored by recipient animals correlated with their growth rates. Microbiota from 6-month-old infants produced greater effects on growth than did microbiota from 18-month-old children, although in each age bin, the growth effects produced by a healthy donor’s community were greater than those produced by an undernourished donor’s community. Cohousing coprophagic mice shortly after they received microbiota from healthy or severely stunted and underweight 6-month-old infants resulted in the invasion of age- and growth-discriminatory taxa from the former into the latter microbiota in the recipient animals, with associated prevention of growth impairments. Introducing cultured members from this group of invasive species ameliorated growth and metabolic abnormalities in recipients of microbiota from undernourished donors.
CONCLUSION
These preclinical findings provide evidence that gut microbiota immaturity is causally related to childhood undernutrition. The age- and growth-discriminatory taxa that we identified should help direct studies of the effects of host and environmental factors on gut microbial community development, and they represent therapeutic targets for repairing or preventing gut microbiota immaturity.
Preclinical evidence that gut microbiota immaturity is causally related to childhood undernutrition.
(A) A model of normal gut microbial community development in Malawian infants and children, based on the relative abundances of 25 bacterial taxa that provide a microbial signature defining the “age,” or state of maturation, of an individual’s (fecal) microbiota. (Hierarchical clusterings of operational taxonomic units are indicated on the left.) (B) Fecal samples from healthy (H) or stunted and underweight (Un) infants and children were transplanted into separate groups of young germ-free mice that were fed a Malawian diet. The immature microbiota of Un donors transmitted impaired growth phenotypes to the mice. (C) Evidence that a subset of age-discriminatory taxa are also growth-discriminatory. Cohousing mice shortly after they received microbiota from 6-month-old healthy or undernourished donors resulted in the invasion of taxa from the healthy donor’s microbiota (HCH) into the undernourished donor’s microbiota (UnCH) among recipient animals and prevented growth impairments. Adding cultured invasive growth-discriminatory taxa directly to the Un donor’s microbiota (Un+) improved growth.
Abstract
Undernourished children exhibit impaired development of their gut microbiota. Transplanting microbiota from 6- and 18-month-old healthy or undernourished Malawian donors into young germ-free mice that were fed a Malawian diet revealed that immature microbiota from undernourished infants and children transmit impaired growth phenotypes. The representation of several age-discriminatory taxa in recipient animals correlated with lean body mass gain; liver, muscle, and brain metabolism; and bone morphology. Mice were cohoused shortly after receiving microbiota from healthy or severely stunted and underweight infants; age- and growth-discriminatory taxa from the microbiota of the former were able to invade that of the latter, which prevented growth impairments in recipient animals. Adding two invasive species, Ruminococcus gnavus and Clostridium symbiosum, to the microbiota from undernourished donors also ameliorated growth and metabolic abnormalities in recipient animals. These results provide evidence that microbiota immaturity is causally related to undernutrition and reveal potential therapeutic targets and agents.
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Supplementary Material
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Materials and Methods
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Information & Authors
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Published In
Science
Volume 351 | Issue 6275
19 February 2016
19 February 2016
Copyright
Copyright © 2016, American Association for the Advancement of Science.
Submission history
Received: 28 August 2015
Accepted: 23 December 2015
Published in print: 19 February 2016
Acknowledgments
We are indebted to the parents and children from Malawi for their participation in this study. We thank S. Wagoner, D. O’Donnell, M. Karlsson, and J. Serugo for their assistance with gnotobiotic mouse husbandry; D. Leib and M. Silva for their assistance with bone morphology assays; J. Guruge for help with anaerobic microbiology; B. Dankenbring for assistance with maintenance of the biospecimen repository; and M. Meier, S. Deng, and J. Hoisington-Lopez for their contribution to various facets of the DNA sequencing pipeline. This work was supported by the Bill and Melinda Gates Foundation and the NIH (grant DK30292). Additional funding was provided by the Office of Health, Infectious Diseases and Nutrition, Bureau for Global Health, U.S. Agency for International Development under the terms of cooperative agreement no. AID-OAA-A-12-00005, through the Food and Nutrition Technical Assistance III Project managed by FHI 360. Data management and statistical analysis for theiLiNS-DYAD-M clinical study were also funded by the Academy of Finland (grant 252075) and the Medical Research Fund of Tampere University Hospital (grant 9M004). Micro-CT analysis was performed in the Washington University Musculoskeletal Research Center, which is supported by NIH grant P30 AR057235. L.V.B. received stipend support from NIH predoctoral training grants NIH T32 AI007172 and T32 GM007067 and from the Lucille P. Markey Special Emphasis Pathway in Human Pathobiology. D.A.R. and S.A.L. were supported by the Russian Science Foundation (grant 14-14-00289). Collection of the human specimens included in this study was approved by the University of Malawi College of Medicine Research Ethics Committee. Specimens were provided to Washington University in St. Louis under a materials transfer agreement (MTA) between the University of Malawi and Washington University, and their collection and use for this study was approved by the Washington University Human Research Protection Office (Federalwide Assurance no. FWA00002284). 16S rRNA sequences, generated from fecal samples in raw format before post-processing and data analysis, and shotgun sequencing data sets, generated from the R. gnavus TS8243C and C. symbiosum TS8243C genomes, have been deposited in the European Nucleotide Archive under accession number PRJEB9853. J.I.G. is a cofounder of Matatu, a company characterizing the role of diet-by-microbiota interactions in animal health. A.L.O. is an adjunct vice president for research for Buffalo BioLabs. L.V.B., M.R.C., and J.I.G. designed the gnotobiotic mouse studies; L.V.B. and M.R.C. performed the experiments with gnotobiotic animals; I.T. and M.J.M. designed and implemented the clinical monitoring and sampling for the twin study and participated in patient recruitment, sample collection and preservation, and/or clinical evaluations; K.M.M., Y.F., J.M.J., K.G.D., and P.A. designed and oversaw the clinical studies, sample collection and processing, and/or clinical monitoring and evaluations in the iLiNS-DYAD-M study; L.V.B. generated the 16S rRNA data; L.V.B., M.R.C., S.V., and O.I. generated the metabolomics data; T.S. and L.V.B. cultured bacterial isolates; B.H., D.A.R., S.A.L., and A.L.O. performed metabolic reconstructions of the R. gnavus and C. symbiosum genomes; L.V.B., M.R.C., M.J.B., S.S., C.B.N., and J.I.G. analyzed the data; and L.V.B. and J.I.G. wrote the paper.
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