Temporal Dynamics of the Intestinal Microbiome Following Short-Term Dietary Restriction

Abstract

Short-term dietary restriction has been proposed as an intriguing pre-operative conditioning strategy designed to attenuate the surgical stress response and improve outcomes. However, it is unclear how this nutritional intervention influences the microbiome, which is known to modulate the systemic condition. Healthy individuals were recruited to participate in a four-day, 70% protein-restricted, 30% calorie-restricted diet, and stool samples were collected at baseline, after the restricted diet, and after resuming normal food intake. Taxonomy and functional pathway analysis was performed via shotgun metagenomic sequencing, prevalence filtering, and differential abundance analysis. High prevalence species were altered by the dietary intervention but quickly returned to baseline after restarting a regular diet. Composition and functional changes after the restricted diet included the decreased relative abundance of commensal bacteria and a catabolic phenotype. Notable species changes included Faecalibacterium prausnitzii and Roseburia intestinalis, which are major butyrate producers within the colon and are characteristically decreased in many disease states. The macronutrient components of the diet might have influenced these changes. We conclude that short-term dietary restriction modulates the ecology of the gut microbiome, with this modulation being characterized by a relative dysbiosis.

Short-Term Dietary Restriction Potentiates an Anti-Inflammatory Circulating Mucosal-Associated Invariant T-Cell Response

“…Bacteria belonging to the Bacteroidetes and Proteobacteria phyla are among the most potent MAIT stimulators in vitro [ 22 ]. Our previous work showed that 4 days of StDR induced species-level abundance changes that returned to a predietary state 3 days after dietary cessation [ 16 ]. Well-established relationships between gut microbial composition and dietary restriction remain elusive given variations in study design, diet selection, and duration of intervention [ 48 ].…”

“…Stool samples were collected by the patients using a fecal collection kit (Zymo Research, Irvine, CA, USA), and samples were stored at −20 degrees Celsius until processing. As previously described [ 16 ], the ZymoBiomics MagBead DNA kit (Zymo Research, Irvine, CA, USA) was used to isolate DNA from thawed stool samples and shotgun metagenomic sequencing (Zymo Research, Irvine, CA, USA) was performed. Whole-genome sequencing libraries were created with the Nextera DNA Flex Library Prep Kit (Illumina, San Diego, CA, USA), pooled in equal abundance, and sequenced with NovaSeq (Illumina, San Diego, CA, USA).…”

“…We have previously described our methods for taxonomic and functional pathway analysis [ 16 ]. Briefly, low-prevalence species were filtered from the dataset using a machine learning algorithm to identify an ideal prevalence filtering cutoff.…”

“…The gut microbiome influences systemic immunity, and its modification represents an important area for translational therapeutic development [ 10 , 11 , 12 , 13 , 14 , 15 ]. Our group has previously shown a relative gut microbial dysbiosis after 4 days of protein-calorie restriction with a rapid return to baseline after resuming a normal diet [ 16 ]. However, characterization of the gut microbiome alone after StDR does not describe its influence on systemic immunity.…”

Molecular Mechanisms and Pathophysiological Pathways of High-Fat Diets and Caloric Restriction Dietary Patterns on Pain

“…123,125 More recent studies have demonstrated caloric restriction dietary patterns as a potent environmental force to induce dramatic changes in the gut microbiome, especially in its composition, structure, and physiology. [125][126][127][128][129][130] Both preclinical and human studies have proved that CR and VLCD could decrease the richness and diversity of the gut microbiota, 123,124 which effects linked with delayed immune senescence induced by naive T and B cell compartment shifts. 131 Furthermore, the decreased gut microbial level was able to mitigate neuropathic pain.…”