This project explored the functional role of the gut microbiome in producing amino acids used by the host organism to maintain protein homeostasis. Combining compound-specific stable isotope analysis and meta-omics allowed us to investigate how animals utilize dietary nutrients, the role of microbial communities in this process, and specific biochemical pathways that enable these reactions. We have not only identified the critical interactions between animals and their associated microbiomes, but also how these interactions can be particularly beneficial in mammals facing seasonal or persistent dietary protein limitation. Wild omnivorous and herbivorous mammals often consume diets deficient in the amount of protein required for growth, reproduction, and maintenance. Mammals must obtain crucial nutrients like essential amino acids (AA_ESS), from either their diet or associated gut microbiome. Prior work has focused on the gut microbiome’s role in host carbohydrate metabolism, but its role in subsidizing host protein metabolism is poorly understood. We executed a series of controlled feeding experiments on wild derived captive deer mice (Peromyscus maniculatus) to quantify the extent intestinal bacteria are supplying AA to their mammalian host and determine how gut microbial community composition changes in response to host diet. 

We quantified the contribution of microbially synthesized AA_ESS to the skeletal muscle of deer mice (Peromyscus maniculatus) fed diets differing in protein quantity and quality, including a synthetic diet rich in simple sugars (sucrose) and highly digestible protein (casein), and a semi-natural diet containing complex carbohydrates (cornmeal and cornstarch) and natural protein (cricket powder) that better mimic what mice consume in the wild. Our work showed that dietary macromolecular type and content influences the degree to which mice assimilate microbially derived AA_ESS into their skeletal muscle. More specifically, mice fed low protein synthetic diets, or more complex dietary substrates in the semi-natural diets regardless of protein content, received greater contributions of AA_ESS of microbial origin and gut microbial populations with the genetic potential for AA_ESS biosynthesis were more abundant in mice with larger contributions of microbially derived AA_ESS in their skeletal muscle. These initial estimates of the relative proportion of microbial AA_ESS used to synthesize mice muscle tissue only considered the contribution of AA_ESS synthesized de novo from dietary carbohydrates. However, gut microbes can synthesize AA_ESS from a diverse pool of metabolite precursors, including non-essential AA (non-AA_ESS), and therefore likely contribute even more microbially synthesized AA_ESS to their host than previously appreciated. The extent mammals assimilate microbially synthesized AA_ESS from dietary non-AA_ESS precursors is currently unknown. To test this, we fed mice low (2.5%) and medium (5%) protein semi-natural diets enriched with a 2% 13C-enriched non-essential amino acids, ¹³C-glutamic acid or ¹³C-alanine. We found significant isotopic enrichment of AA_ESS phenylalanine, isoleucine, threonine, and lysine in the tissues of mice fed ^13-C glutamic acid, but minimal enrichment in mice fed ^13-C alanine, suggesting only certain non-essential AAs are readily used as a substrate by the gut microbiome for AA_ESS synthesis. Lastly, we used meta-omics to identify key microbial taxonomic groups capable of amino acid synthesis and likely responsible for the provisioning of these compounds to their host. We have made significant progress towards combining flow cytometry (FACS) that targets these microbial groups of interest with amino acid isotope analysis because different types of microbes are likely more efficient at synthesizing different suites of essential and non-essential amino acids. Together, these results demonstrate an important role for the gut microbiome in the protein metabolism of its host, especially in the supply of essential nutrients the host cannot synthesize.

Broader Impacts: This project has supported significant participation of underrepresented groups including Hispanic and African American undergraduate women, support for two postdoctoral scientists (both women), three graduate students (all women, one Hispanic), and one postbaccalaureate research education program (PREP) student (African American woman). This work has produced 3 publications to date with several in preparation and has been presented at numerous podium and poster presentations by undergraduate and graduate students. All data were submitted to NCBI’s Sequence Read Archive.

Last Modified: 12/20/2024
Modified by: Seth D Newsome