Isotopic and genetic methods reveal the role of the gut microbiome in mammalian host essential amino acid metabolism.

Intestinal microbiota perform many functions for their host, but among the most important is their role in metabolism, especially the conversion of recalcitrant biomass that the host is unable to digest into bioavailable compounds. Most studies have focused on the assistance gut microbiota provide in the metabolism of carbohydrates, however, their role in host amino acid metabolism is poorly understood. We conducted an experiment on Mus musculus using 16S rRNA gene sequencing and carbon isotope analysis of essential amino acids (AAESS) to quantify the community composition of gut microbiota and the contribution of carbohydrate carbon used by the gut microbiome to synthesize AAESS that are assimilated by mice to build skeletal muscle tissue. The relative abundances of Firmicutes and Bacteroidetes inversely varied as a function of dietary macromolecular content, with Firmicutes dominating when mice were fed low-protein diets that contained the highest proportions of simple carbohydrates (sucrose). Mixing models estimated that the microbial contribution of AAESS to mouse muscle varied from less than 5% (threonine, lysine, and phenylalanine) to approximately 60% (valine) across diet treatments, with the Firmicute-dominated microbiome associated with the greatest contribution. Our results show that intestinal microbes can provide a significant source of the AAESS their host uses to synthesize structural tissues. The role that gut microbiota play in the amino acid metabolism of animals that consume protein-deficient diets is likely a significant but under-recognized aspect of foraging ecology and physiology

Dietary Protein Content and Digestibility Influences Discrimination of Amino Acid Nitrogen Isotope Values in a Terrestrial Omnivorous Mammal

RATIONALE: Ecologists increasingly determine the δ15N values of amino acids (AA) in animal tissue; source AA typically exhibit minor variation between diet and consumer, while trophic AA have increased δ15N values in consumers. Thus, trophic-source δ15N offsets (i.e., Δ15NT-S) reflect trophic position in a food web. However, even minor variation in δ15Nsource AA values may influence the magnitude of offset that represents a trophic step, known as the trophic discrimination factor (i.e., TDFT-S). Diet digestibility and protein content can influence the δ15N values of bulk animal tissue, but the effects on AA Δ15NT-S and TDFT-S in mammals are unknown. METHODS: We fed captive mice (Mus musculus) either (A) a low-fat, high-fiber diet with low, intermediate, or high protein; or (B) a high-fat, low-fiber diet with low or intermediate protein. Mouse muscle and dietary protein were analyzed for bulk tissue δ15N using elemental analyzer-isotope ratio mass spectrometry (EA-IRMS), and were also hydrolyzed into free AA that were analyzed for δ15N using EA-IRMS. RESULTS: As dietary protein increased, Δ15NConsumer-Diet slightly declined for bulk muscle tissue in both experiments, increased for AA in the low-fat, high-fiber diet (A), and remained the same or decreased for AA in the high-fat, low-fiber diet (B). The effects of dietary protein on Δ15 NT-S and on TDFT-S varied by AA but were consistent between variables. CONCLUSIONS: Diets were less digestible and included more protein in Experiment A than in Experiment B. As a result, the mice in Experiment A probably oxidized more AA, resulting in greater Δ15 NConsumer-Diet values. However, the similar responses of Δ15 NT-S and of TDFT-S to diet variation suggest that if diet samples are available, Δ15 NT-S accurately tracks trophic position. If diet samples are not available, the patterns presented here provide a basis to interpret Δ15 NT-S values The trophic-source offset of Pro-Lys did not vary across diets, and therefore may be more reliable for omnivores than other offsets (e.g., Glu-Phe)

Environmental harshness mediates the relationship between aboveground and belowground communities in Antarctica

Linkages between aboveground and belowground communities are a key but globally under-researched component of responses to environmental change. Given the logistical complications to studying these relationships, much of our knowledge derives from laboratory experiments and localized field studies which have so far yielded inconsistent results. Because environmental factors may alter relationships between above- and belowground communities, there is a need for broad-scale field studies testing these interactions. The Antarctic Peninsula provides an ideal test setting, given the relatively simple communities both above- and belowground. The Peninsula is also experiencing rapid environmental changes, including alterations in species diversity and distribution both above- and belowground. Thus, an improved understanding of the broad-scale consequences of altered environments and vegetation communities for the soil microbiome is of high priority. To determine the nature and strength of the relationship between in situ plant and soil communities across a broad spatial scale and range of environmental conditions, we sampled soil communities at 9 locations (spanning 60–72°S along the Scotia Arc and Antarctic Peninsula) beneath the major aboveground habitats (moss, grass, lichen, algae and bare soil). We measured a comprehensive suite of soil physicochemical properties, microbial (bacterial and fungal) diversity and composition, and invertebrate abundance and community composition to determine the relationships between plant and soil communities. Our results suggest that, with increased environmental severity, plant cover types become more important for influencing the physicochemical soil environment, and therefore the soil microbial communities. Although we found site-specific relationships, broad-scale patterns reveal significant differences among bare soils and vegetated soils, particularly soils beneath grass and moss. This suggests that expansion of vegetation communities under current climate warming projections will be accompanied by shifts in the soil microbiome, with important implications for the ecosystem functioning with which they are associated

Solutions in microbiome engineering: prioritizing barriers to organism establishment.

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions