| Abstract: | The concept that gut microbiome-expressed functions regulate ponderal growth has important implications for infant and child health, as well as animal health. Using an intergenerational pig model of diet restriction (DR) that produces reduced weight gain, we developed a feature-selection algorithm to identify representative characteristics distinguishing DR fecal microbiomes from those of full-fed (FF) pigs as both groups consumed a common sequence of diets during their growth cycle. Gnotobiotic mice were then colonized with DR and FF microbiomes and subjected to controlled feeding with a pig diet. DR microbiomes have reduced representation of genes that degrade dominant components of late growth-phase diets, exhibit reduced production of butyrate, a key host-accessible energy source, and are causally linked to reduced hepatic fatty acid metabolism (β-oxidation) and the selection of alternative energy substrates. The approach described could aid in the development of guidelines for microbiome stewardship in diverse species, including farm animals, in order to support their healthy growth.Undernutrition afflicts over 200 million children worldwide and accounts for 45% of mortality in children under 5 y (1). Children with acute malnutrition exhibit wasting (impaired ponderal growth), often accompanied by stunting (reduced linear growth), deficits in bone development, neurodevelopment, and immunity, as well as perturbed metabolism (2, 3). Epidemiologic studies indicate that acute malnutrition in children is not due to food insecurity alone and that perturbed gut microbial community development is a contributing factor; children with severe acute malnutrition (SAM) and moderate acute malnutrition (MAM; weight-for-length z-scores are, respectively, 2 to 3 and >3 SDs below World Health Organization mean values) have microbiota that appear “younger” (more immature) compared to those of chronologically aged-matched healthy children (4–6). Studies in gnotobiotic mice colonized with microbiota from healthy and undernourished children have provided evidence that immature microbiota can transmit features of undernutrition (5, 7). These tests of causality inspired development of microbiota-directed complementary foods (MDCFs) designed to repair the microbiota of undernourished children. A controlled feeding study, involving a small group of 12- to 18-mo-old Bangladeshi children with MAM, identified an MDCF formulation that repaired their microbiota; repair was associated with a marked change in their plasma proteome characterized by alterations in levels of key mediators of bone growth, metabolism, immune function, and neurodevelopment toward a healthy state (5). A larger, longer randomized controlled study showed that this MDCF produced a superior effect on ponderal growth compared to a ready-to-use supplementary food even though the caloric density of the MDCF was 20% lower (8).These observations prompted us to examine the influence of the gut microbiome on weight gain in the domestic pig, Sus scrofa domesticus. We focused on this species for several reasons. First, pigs account for ∼35% of global meat intake, second only to poultry (9, 10). Production costs are heavily influenced by how efficiently feed is transformed into body mass, as well as the degree of growth uniformity across animals (11). Second, pigs have been used as a model for studying human nutrition and metabolism because of the many ways in which they are anatomically, physiologically, and metabolically similar to humans (12, 13). Third, most of the commercial pig industry raises animals in highly controlled farming systems engineered to promote efficient and consistent growth phenotypes. These systems typically include phased feeding programs that transition animals from early, more costly, readily digestible, nutrient-rich diets to later, less-expensive diets with less nutrient fortification where energy/nutrient extraction is more dependent on expressed metabolic activities encoded in the gut microbiome. A central premise of the current study is that in order to more fully realize the goal of predictable robust weight gain at affordable prices, additional knowledge is needed regarding codevelopment of the gut microbiome and host; this knowledge could allow diets to be formulated based on greater understanding of which components (features) of the community play key roles in transforming dietary components to products that the animals use to satisfy their growth requirements (14). The environmentally controlled settings for raising pigs provide great opportunities for performing longitudinal studies designed to delineate these interactions between diet, microbiome features, and host physiology. Finally, the need to focus on whether/how the gut microbiome contributes to growth is made more pressing by international mandates to eliminate use of subtherapeutic antibiotics for growth promotion of farm animals because of the spread of antibiotic-resistant organisms (15, 16).In the present study, we developed an algorithm (entropy-based method for microbial ecology research, EMMER), based on the von Neumann entropy calculation from quantum information theory (17, 18), to identify representative characteristics of fecal microbiomes serially sampled from litters of pigs that were or were not subjected to maternal diet restriction (DR) in utero and then provided either ad libitum access to, or restricted amounts of, a sequence of diets commonly given to farm-reared pigs as they complete their growth cycle. A 45% lower weight was attained by DR compared to full-fed (FF) pigs by the third postnatal month and this difference was sustained for the remainder of the 5-mo-long study. DR microbiomes exhibited a significantly reduced representation of genes encoding enzymes involved in the degradation of polysaccharides from dominant components of diets administered after postnatal day 70. These differences in the DR microbiome were associated with diminished fecal levels of butyrate, a major source of host energy, and significant increases in plasma levels of triglycerides, glucogenic amino acids, and urea cycle precursors. Functional features of DR and FF fecal microbiomes, collected during the period of consumption of the corn/soy-rich “finisher” diet (the last given during the feeding program), were subsequently assayed in gnotobiotic mice under controlled feeding conditions where all animals were provided the same amount of the finisher phase pig diet. The results confirmed the reduced capacity of the DR microbiome to generate butyrate. Moreover, mice colonized with the DR microbiome also exhibited reduced fatty acid oxidation in the liver, a metabolic effect that could explain the redirection of amino acids from protein synthesis to replenish hepatic energy reserves in DR pigs. Marrying longitudinal studies of farm animal gut microbiome development and function, conducted in well-engineered farming systems, with gnotobiotic mouse models that incorporate the microbial communities and diets of the farm animals, provides an opportunity to develop an informed set of practices for microbiome husbandry that promotes healthy growth. The results could have substantial economic and societal impact during this time of increasing global food insecurity and when producing sufficient amounts of high-quality protein to feed a rapidly expanding human population is a major challenge (9). |
