Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets

Ketogenic Diet in Steatotic Liver Disease: A Metabolic Approach to Hepatic Health

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a major cause of chronic liver dysfunction worldwide, characterized by hepatic steatosis that may progress to nonalcoholic steatohepatitis and cirrhosis. Owing to its strong association with metabolic disorders, current management focuses on weight reduction via lifestyle modifications. Recently, the very-low-calorie ketogenic diet (VLCKD) has emerged as a promising intervention due to its potential for rapid weight loss and reduction in liver fat. This review aims to evaluate the clinical evidence regarding the impact of ketogenic diets on hepatic steatosis. We conducted an extensive MEDLINE literature search in databases including PubMed, Scopus, and Web of Science up to December 2024. Studies assessing the effects of ketogenic or low-carbohydrate high-fat diets on liver fat, evaluated by imaging, histology, or biochemical markers, were included. The analysis indicates that ketogenic diets significantly reduce hepatic fat content and improve metabolic parameters, including insulin sensitivity and liver enzyme levels. Evidence further suggests that substituting saturated fats with unsaturated fats or replacing carbohydrates with proteins may enhance these benefits. However, considerable variability exists among studies and long-term data remain limited. Although short-term outcomes are encouraging, potential adverse effects such as dyslipidaemia, gastrointestinal disturbances, and transient 'keto flu' symptoms require careful clinical monitoring. Future research should focus on elucidating underlying mechanisms, optimizing dietary composition, and assessing long-term safety to establish ketogenic diets as a robust strategy for managing MASLD.

The microbiome's influence on obesity: mechanisms and therapeutic potential

In 2023, the World Obesity Atlas Federation concluded that more than 50% of the world's population would be overweight or obese within the next 12 years. At the heart of this epidemic lies the gut microbiota, a complex ecosystem that profoundly influences obesity-related metabolic health. Its multifaced role encompasses energy harvesting, inflammation, satiety signaling, gut barrier function, gut-brain communication, and adipose tissue homeostasis. Recognizing the complexities of the cross-talk between host physiology and gut microbiota is crucial for developing cutting-edge, microbiome-targeted therapies to address the global obesity crisis and its alarming health and economic repercussions. This narrative review analyzed the current state of knowledge, illuminating emerging research areas and their implications for leveraging gut microbial manipulations as therapeutic strategies to prevent and treat obesity and related disorders in humans. By elucidating the complex relationship between gut microflora and obesity, we aim to contribute to the growing body of knowledge underpinning this critical field, potentially paving the way for novel interventions to combat the worldwide obesity epidemic.

The role of the microbiota-gut-brain axis and artificial intelligence in cognitive health of pediatric obstructive sleep apnea: A narrative review

Pediatric obstructive sleep apnea (OSA) is a prevalent sleep-related breathing disorder associated with significant neurocognitive and behavioral impairments. Recent studies have highlighted the role of gut microbiota and the microbiota-gut-brain axis (MGBA) in influencing cognitive health in children with OSA. This narrative review aims to summarize current knowledge on the relationship between gut microbiota, MGBA, and cognitive function in pediatric OSA. It also explores the potential of artificial intelligence and machine learning in advancing this field and identifying novel therapeutic strategies. Pediatric OSA is associated with gut dysbiosis, reduced microbial diversity, and metabolic disruptions. MGBA mechanisms, such as endocrine, immune, and neural pathways, link gut microbiota to cognitive outcomes. Artificial intelligence and machine learning methodologies offer promising tools to uncover microbial markers and mechanisms associated with cognitive deficits in OSA. Future research should focus on validating these findings through clinical trials and developing personalized therapeutic approaches targeting the gut microbiota.

Global deletion of the immune cell transcription factor, T-bet, alters gut microbiota and insulin sensitivity in mice

The gut microbiota plays a role in energy homeostasis: its composition differs in lean and obese mice and may impact insulin sensitivity. The immune system has co-evolved with the gut microbiota, but direct regulation of microbial communities by the immune system and its metabolic impact is unclear. Mice lacking the immune cell specific transcription factor T-bet (Tbx21) are insulin sensitive. Compared with wild-type mice, T-bet deficient mice were found to have a higher proportion of colonic regulatory T cells despite significantly fewer colonic T cells, B cells and NK cells. Microbiota deletion by administration of antibiotics, increased colonic immune cell numbers. Furthermore, we report that T-bet -/- mice have an altered gut microbial composition and fecal short-chain fatty acid content, with an increase in butyrate production, compared with wild-type mice. Finally, in a proof-of concept study, we show that the enhanced insulin sensitivity observed in T-bet -/- mice is temporarily transmissible to antibiotic-treated wild-type mice through fecal transfer. Immune regulation of the gut microbiota by T-bet may be a novel pathway modulating insulin sensitivity.

Direct and indirect effects of estrogens, androgens and intestinal microbiota on colorectal cancer

Sex differences in colorectal cancer (CRC) has received considerable research attention recently, particularly regarding the influence of sex hormones and the intestinal microbiota. Estrogen, at the genetic and epigenetic levels, directly inhibits CRC cell proliferation by enhancing DNA mismatch repair, regulating miRNAs, blocking the cell cycle, and modulating ion channels. However, estradiol's activation of GPER promotes oncogene expression. Conversely, androgen contributes to epigenetic dysregulation and CRC progression via nuclear receptors while inducing apoptosis through membrane receptors. Specific gut microorganisms produce genotoxins and oncogenic metabolites that damage colonic cell DNA and contribute to cancer induction. Regarding the tumor microenvironment, estrogen mitigates intestinal inflammation, reverses immunosuppression, increases gut microbiome diversity and commensal bacteria abundance, and decreases pathogen enrichment. On the contrary, androgen disrupts intestinal microecology, diminish immunotherapy efficacy, and exacerbate colonic inflammation and tumor growth. The impact of estrogen and androgen is closely tied to their receptor status, elucidating their dual roles in CRC pathogenesis. This review comprehensively discusses the direct and indirect effects of sex hormones and the intestinal microbiota on CRC, considering environmental factors such as diet and lifestyle to propose novel prevention and treatment strategies.

Purified diets containing high levels of soluble fiber and grain-based diets promote similar gastrointestinal morphometry yet distinct microbial communities

Dietary fibers play a crucial role in shaping the gut microbiome and influencing gastrointestinal (GI) physiology. Grain-based diets (GBDs) are widely used in rodent studies, but their utility is limited due to batch-to-batch variability resulting from inconsistent ingredients. Purified diets (PDs) are composed of only known and refined ingredients and offer a solution to the constraints of GBDs. This study aimed to identify a combination of dietary fibers in a purified diet (PD) that promotes optimal murine gut morphometry and a diverse intestinal microbial community. Male C57BL/6J mice were fed either two grain-based diets (GBDs) or four PDs with varying fiber compositions for 28 days. Mice consuming PDs lacking soluble fiber had more gonadal fat (P < 0.05), shorter small intestines (P < 0.05), and lighter ceca (P < 0.05) compared with those fed the LabDiet 5001 GBD. Increasing the proportion of soluble fibers in PDs progressively reduced microbial diversity in the cecum and colon. Multidimensional scaling analysis revealed distinct microbial communities in the cecum and colon between mice fed GBDs and PDs (P < 0.05). Differential abundance analysis identified relatively more Family XII UCG 001 and less Lactococcus in mice fed GBDs relative to mice consuming PDs (P < 0.05). While no PD recapitulated the gut microbial composition of GBDs, PDs with high soluble fiber content best preserved GI morphometry. These findings underscore the importance of considering diet as an experimental variable and highlight the need for a PD formulation that combines the benefits of GBDs on GI health and microbial richness.

IMPORTANCE

Dietary fibers are essential for maintaining gut health. Insoluble fibers aid in fecal bulking and water retention while soluble fiber is a fermentative substrate for intestinal microbial communities. Grain-based diets (GBDs) are commonly used in preclinical research but the variability in ingredients across batches impedes reproducibility. Purified diets (PDs), which are composed of highly refined ingredients, pose a potential solution but the most widely used low-fat control PDs contain no soluble fiber. This study intended to identify a PD with a combination of fibers that promotes murine gut health and microbial diversity. A PD with optimal fiber composition would aid in the standardization and reproducibility of studies investigating intestinal physiology and the gut microbiota.

Albumin binding domain fusion improved the therapeutic efficacy of Inhibitor of Differentiation-2 protein in colitis mice

AIMS

The human Inhibitor of Differentiation-2 (hID2) protein is a promising candidate for the treatment of colitis. However, its relatively low molecular weight limits its clinical application. To extend the therapeutic half-life, an albumin-binding domain (ABD), known for its high affinity for human serum albumin (HSA), was fused to hID2, resulting in a recombinant ABD-hID2. The anti-colitis bioactivity of ABD-hID2 than that of hID2 was evaluated in this study.

MAIN METHODS

Western blotting, size-exclusion high-performance chromatography, HSA binding assay, and pharmacokinetic studies were used to characterise ABD-hID2, which was induced by dextran sulfate sodium salt (DSS), Citrobacter rodentium (CR), and ABD-hID2 and hID2. The Disease Activity Index, histological pathologies, inflammatory response, Alcian blue or tuft cell staining, and tight junction proteins were determined. Alterations in the intestinal microbiota after ABD-hID2 treatment were analysed via 16S rRNA gene sequencing.

KEY FINDINGS

Compared with hID2, ABD-hID2 exhibited a decreased dimer complex, bound to HSA with high affinity, and demonstrated an extended blood retention time in vivo. Consequently, ABD-hID2 exhibited increased therapeutic efficacy in both DSS- and CR-induced colitis mouse models, as evidenced by the alleviation of colitis symptoms, preservation of goblet and tuft cell functions, restoration of the intestinal mucus barrier, and suppression of abnormal immune-inflammatory responses. Additionally, the modulation of the gut microbiota may play a role in the protective effects of ABD-hID2 in mice with CR-induced ulcerative colitis.

SIGNIFICANCE

ABD-hID2 enhances the bioactivity of hID2 and has the potential for further development as a treatment for colitis.

Exploring the Spatial Variation in the Microbiota and Bile Acid Metabolism of the Compound Stomach in Intensively Farmed Yaks

Yaks are one of the important livestock on the Qinghai-Tibet Plateau, providing abundant dairy and meat products for the local people. The formation of these dairy and meat products mainly relies on the microbiota in their gastrointestinal tract, which digests and metabolizes plant feed. The yak's gastrointestinal microbiota is closely related to the health and production performance of the host, but the molecular mechanisms of diet-induced effects in intensively farmed yaks remain to be elucidated. In this study, 40 chyme samples were collected from the four stomach chambers of 10 intensively farmed yaks, and the bacterial diversity and bile acid changes in the rumen (SFRM), reticulum (SFRC), omasum (SFOM), and abomasum (SFAM) were systematically analyzed using 16S rRNA sequencing and bile acid metabolism. Our results showed that the gastrointestinal microbiota mainly distributes in the four-chambered stomach, with the highest microbial diversity in the reticulum. There is a highly negative correlation among the microbiota in the four chambers. The dominant bacterial phyla, Bacteroidota and Firmicutes, were identified, with Rikenellaceae_RC9_gut_group being the dominant genus, which potentially helps maintain short-chain fatty acid levels in the stomach. In contrast, the microbiome within the four stomach chambers synergistically and selectively altered the content and diversity of bile acid metabolites in response to intensive feeding. The results of this study provide new insights into the microbiota and bile acid metabolism functions in the rumen, reticulum, omasum, and abomasum of yaks. This can help uncover the role of gastrointestinal microbiota in yak growth and metabolic regulation, while also providing references for improving the production efficiency and health of ruminants.

KRAS mutations promote the intratumoral colonization of enterotoxigenic bacteroides fragilis in colorectal cancer through the regulation of the miRNA3655/SURF6/IRF7/IFNβ axis

KRAS mutations are associated with poor prognosis in colorectal cancer (CRC). Although the association between the gut microbiota and CRC has been extensively documented, it is unclear whether KRAS mutations can regulate the gut microbiota. Metagenomics has identified changes in the diversity of the gut microbiota in CRC due to KRAS mutations. Specifically, KRAS mutations positively correlate with the abundance of the bacteroides. Understanding how to regulate the classic carcinogenic bacterium within the bacteroides, such as enterotoxigenic bacteroides fragilis (ETBF), to enhance treatment efficacy of tumors is a key focus of research. Mechanistically, we found that the reduction of miR3655 is indispensable for KRAS mutation-promoted proliferation of CRC and the abundance of ETBF. miR3655 targets SURF6 to inhibit its transcription. Further transcriptomic sequencing revealed that SURF6 promotes intratumoral colonization of ETBF in CRC by inhibiting the nuclear translocation and transcription levels of the IRF7, affecting the activation of the IFNβ promoter. Regulating miR3655 and SURF6 can promote IFNβ secretion in CRC, directly killing ETBF. These data indicate that KRAS mutations affect the intratumoral colonization of ETBF in CRC through the miR3655/SURF6/IRF7/IFNβ axis. This provides new potential strategies for treating CRC associated with KRAS mutations or high levels of ETBF.

Metabolomic Profiling of Obese Patients with Altered Intestinal Permeability Undergoing a Very Low-Calorie Ketogenic Diet

A healthy intestinal permeability facilitates the selective transport of nutrients, metabolites, water, and bacterial products, involving cellular, neural, hormonal, and immune factors. An altered intestinal permeability indicates pathologic phenotypes and is associated with the exacerbation of obesity and related comorbidities. To investigate the impact of altered permeability in obese patients undergoing a calorie-restrictive dietary regimen (VLCKD), we collected urinary and fecal samples from obese patients with both normal and altered permeability (determined based on the lactulose/mannitol ratio) before and after treatment. The analysis of volatile organic compounds (VOCs) aids in understanding the metabolites produced by the intestinal microbiota in this unique ecological niche. Furthermore, we examined clinical and anthropometric variables from the cohort and compared them to significant VOC panels. Consequently, we identified specific markers in the metabolomics data that differentiated between normal and altered profiles before and after the diet. These markers indicated how the variable contribution specifically accounted for interleukins and lipopolysaccharides (LPS). The targeted metabolomics experiment detected no differences in measured short-chain fatty acids (SCFA). In summary, our study evaluated metabolomic markers capable of distinguishing low-grade inflammation conditions, exacerbated in more advanced stages of obesity with altered intestinal permeability.