Human gut microbiome: hopes, threats and promises

Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding

Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.

Analysis of causal effects on metabolic syndrome and inflammatory bowel disease: a Mendelian randomization study

BACKGROUND

Metabolic syndrome (MetS) is a conglomerate of metabolic abnormalities including hypertension, obesity, hyperglycemia, hypertriglyceridemia, and low levels of high-density lipoprotein cholesterol (HDL-C). The relationship between MetS and Inflammatory Bowel Disease (IBD) has received a lot of attention lately. Epidemiological investigation has yet to determine if the two illnesses are causally related. To investigate the causal link between IBD and MetS levels, we screened publically available genome-wide association study (GWAS) data using Mendelian randomization (MR) analysis. The study aimed to comprehensively analyze the causal association of each component of MetS, including fasting blood glucose(FBG), HDL-C, triglyceride(TG), waist circumference(WC), and hypertension, on the risk of IBD and its subtypes via univariate, two-way, and multivariate MR (MVMR) methods.

METHODS

We selected independent genetic variants of MetS and IBD as instrumental variables (IVs) from published data from the IEU OpenGWAS project and IIBDGC (International Inflammatory Bowel Disease Genetic Consortium), used MR to infer potential causal effects between them, and used a variety of methods (random effect inverse variance weighting (IVW), weighted median, MR-Egger regression, etc.) to ensure the robustness of causal effects.

RESULTS

Univariate two-sample MR (TSMR) revealed that WC was significantly linked to the risk of Crohn's disease (CD) (OR = 1.659; 95% CI: 1.144-2.405; p = 0.008) and IBD (OR = 1.383; 95% CI: 1.050-1.822; p = 0.021). However, MVMR did not support this finding. In MVMR analysis, hypertension was predicted to be positively associated with the risk of IBD (OR = 2.322516, 95% CI: 1.097713-4.91392, p = 0.0275365), whereas FBG was confirmed to reduce the risk of CD in MVMR studies (OR = 0.4346427, 95% CI: 0.2685399-0.7034868, p = 0.0006948939). Other elements of the MetS did not significantly correlate with IBD.

CONCLUSION

Although confounding factors cannot be completely ruled out, certain metabolic components, such as WC, may impact the risk of IBD. In addition to highlighting the need for more research to understand the underlying mechanisms and potential indirect effects between MetS components and IBD, this research offers insight into therapeutic treatment decisions for patients with IBD and MetS.

Potential relationship of the gut microbiome with testosterone level in men: a systematic review

The gut microbiome influences the metabolism and health of several organs beyond the gut and has recently gained considerable attention. The gut plays a central role in food digestion, absorption, nutrition, and general health. Hence, the gut microbiome has become a research subject for almost all health conditions. Imbalance or dysbiosis in the gut microbiome can cause different health issues in men, including reproductive and sexual health issues associated with testosterone levels. Several studies have investigated the relationship between the gut microbiome and testosterone levels. In this systematic review, we aimed to examine the relationship between the gut microbiome and testosterone levels in men. Literature searches were conducted by scanning PubMed, ProQuest, EBSCO, Taylor & Francis Online, Wiley Online, Springer Link, Web of Science, Google Scholar, and Science Direct databases for relevant keywords following the preferred reporting items for the systematic review guidelines. This review included cross-sectional, case-control, retrospective, and prospective cohort studies. Quality assessment was conducted using the Newcastle-Ottawa Scale. We found a significant positive correlation between the gut microbiome and testosterone levels in men. Several microbes play substantial roles in testosterone production. Mechanisms have been proposed as factors that contribute to testosterone levels, namely the hypothalamus-pituitary-gonad axis modulation, androgen metabolism, and intestinal homeostasis, by balancing the bone morphogenic protein (BMP) and the Wnt diverse microbiome. Ruminococcus showed a stronger correlation with testosterone levels than other microorganisms. The gut microbiome has complex correlations with testosterone metabolism. However, the microbiome with the most significant influence on testosterone levels cannot be easily identified and requires further research.

The Influence of an AI-Driven Personalized Nutrition Program on the Human Gut Microbiome and Its Health Implications

Background/Objectives: Personalized nutrition programs enhanced with artificial intelligence (AI)-based tools hold promising potential for the development of healthy and sustainable diets and for disease prevention. This study aimed to explore the impact of an AI-based personalized nutrition program on the gut microbiome of healthy individuals. Methods: An intervention using an AI-based mobile application for personalized nutrition was applied for six weeks. Fecal and blood samples from 29 healthy participants (females 52%, mean age 35 years) were collected at baseline and at six weeks. Gut microbiome through 16s ribosomal RNA (rRNA) amplicon sequencing, anthropometric and biochemical data were analyzed at both timepoints. Dietary assessment was performed using food frequency questionnaires. Results: A significant increase in richness (Chao1, 220.4 ± 58.5 vs. 241.5 ± 60.2, p = 0.024) and diversity (Faith's phylogenetic diversity, 15.5 ± 3.3 vs. 17.3 ± 2.8, p = 0.0001) was found from pre- to post-intervention. Following the intervention, the relative abundance of genera associated with the reduction in cholesterol and heart disease risk (e.g., Eubacterium coprostanoligenes group and Oscillobacter) was significantly increased, while the abundance of inflammation-associated genera (e.g., Eubacterium ruminantium group and Gastranaerophilales) was decreased. Alterations in the abundance of several butyrate-producing genera were also found (e.g., increase in Faecalibacterium, decrease in Bifidobacterium). Further, a decrease in carbohydrate (272.2 ± 97.7 vs. 222.9 ± 80.5, p = 0.003) and protein (113.6 ± 38.8 vs. 98.6 ± 32.4, p = 0.011) intake, as well as a reduction in waist circumference (78.4 ± 12.1 vs. 77.2 ± 11.2, p = 0.023), was also seen. Changes in the abundance of Oscillospiraceae_UCG_002 and Lachnospiraceae_UCG_004 were positively associated with changes in olive oil intake (Rho = 0.57, p = 0.001) and levels of triglycerides (Rho = 0.56, p = 0.001). Conclusions: This study highlights the potential for an AI-based personalized nutrition program to influence the gut microbiome. More research is now needed to establish the use of gut microbiome-informed strategies for personalized nutrition.

Sample Size Estimations Based on Human Microbiome Temporal Stability Over 6 Months: A Shallow Shotgun Metagenome Sequencing Analysis

BACKGROUND

Biological factors affect the human microbiome, highlighting the need for reasonably estimating sample sizes in future population studies.

METHODS

We assessed the temporal stability of fecal microbiome diversity, species composition, and genes and functional pathways through shallow shotgun metagenome sequencing. Using intraclass correlation coefficients (ICC), we measured biological variability over 6 months. We estimated case numbers for 1:1 or 1:3 matched case-control studies, considering significance levels of 0.05 and 0.001 with 80% power, based on the collected fecal specimens per participant.

RESULTS

The fecal microbiome's temporal stability over 6 months varied (ICC < 0.6) for most alpha and beta diversity metrics. Heterogeneity was seen in species, genes, and pathways stability (ICC, 0.0-0.9). Detecting an OR of 1.5 per SD required 1,000 to 5,000 cases (0.05 significance for alpha and beta; 0.001 for species, genes, and pathways) with equal cases and controls. Low-prevalence species needed 15,102 cases, and high-prevalence species required 3,527. Similar needs applied to genes and pathways. In a 1:3 matched case-control study with one fecal specimen, 10,068 cases were needed for low-prevalence species and 2,351 for high-prevalence species. For ORs of 1.5 with multiple specimens, cases needed for low-prevalence species were 15,102 (one specimen), 8,267 (two specimens), and 5,989 (three specimens).

CONCLUSIONS

Detecting disease associations requires a large number of cases. Repeating prediagnostic samples and matching cases to more controls could decrease the needed number of cases for such detections.

IMPACT

Our results will help future epidemiologic study designs and implement well-powered microbiome studies.

Porphyromonas gingivalis aggravates alcohol-related liver injury via gut microbiome-HO-1-ACSL4-dependent ferroptosis

Background

Alcoholic liver disease (ALD) is a common liver condition caused by long-term alcohol consumption, and its specific molecular mechanism remains unclear. It may be influenced to some extent by ferroptosis and Porphyromonas gingivalis (P.g), which is an important pathogen of periodontitis.

Materials and methods

C57BL/6 J mice and AML12 cells were selected as the study subjects. The periodontitis model was induced using P.g, and the alcoholic liver model was created. Pathological analysis was performed on the liver, intestine, and periodontal tissues. 16S rRNA sequencing was used to analyze changes in the intestinal flora and intestinal gap junction protein (zonula occludens-1 (ZO-1) and occludin) levels in each group. Ferroptosis indices were detected in the liver tissues and AML12 cells.

Results

Oral exposure to P.g induced mice periodontitis and exacerbated alcohol-related liver injury. Both alcohol and P.g caused intestinal flora disturbance, damage to the intestinal epithelial barrier, increased permeability, and activation of mouse hepatocyte ferroptosis. Furthermore, P.g aggravated such alcohol-induced liver damage.

Conclusion

Both alcohol and P.g can lead to intestinal flora disturbance, damage to the intestinal epithelial barrier, increased permeability, and the activation of mouse hepatocyte ferroptosis, and P.g can aggravate such alcohol-induced liver damage. Acyl-CoA synthetase long-chain family member 4 (ACSL4) and heme oxygenase-1 (HO-1) play important roles in the exacerbation of alcoholic liver injury by P.g.

Fecal microbiome composition in neonates with or without urinary tract infection

BACKGROUND

Most infants with febrile urinary tract infection (UTI) do not have an underlying anatomical risk factor. Thus, other non-anatomical risk factors should be considered. Since the most common pathogens arise from the fecal microbiota, our aim was to investigate whether the gut microbiota composition differs between febrile infants younger than 2 months with or without UTI.

METHODS

In this prospective, case-control, pilot study, we performed 16S ribosomal ribonucleic acid amplicon sequencing to characterize gut microbiota of febrile neonates with and without UTI admitted to the pediatric ward at Shamir Medical Center between February 2019 and May 2021.

RESULTS

The study cohort included 42 febrile neonates: 17 with and 25 without febrile UTI. We found a significant difference in beta diversity (i.e. between-sample/study group similarity indices) between the UTI and non-UTI group (p = 0.016). There were also distinct differences in the relative abundance of the 20 most prevalent genera. Furthermore, several genera were significantly enriched in the UTI group, with others dominating the non-UTI group. Streptococci were underrepresented in the UTI group. There was no difference in alpha diversity (i.e. within-sample diversity/richness) between groups.

CONCLUSION

Febrile neonates with UTI have a different fecal microbiota composition (beta-diversity), but not alpha diversity, in comparison to febrile neonates without UTI. A larger study is warranted to confirm these findings and their potential applications.

The microbiota-gut-brain axis in myalgic encephalomyelitis/chronic fatigue syndrome: a narrative review of an emerging field

The intricate relationship between gut microbiota and the brain has emerged as a pivotal area of research, particularly in understanding Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). This complex condition is characterized by debilitating fatigue, cognitive dysfunction, and a wide array of systemic manifestations, posing significant challenges for diagnosis and treatment. Recent studies highlight the microbiota-gut-brain axis as a crucial pathway in ME/CFS pathophysiology, suggesting that alterations in gut microbial composition may impact immune responses, neurochemical signaling, and neuronal health. This narrative review systematically explores English-language scholarly articles from January 1995 to January 2025, utilizing databases such as PubMed, Scopus, and Web of Science. The findings underscore the potential for targeted therapeutic interventions aimed at correcting gut dysbiosis. As research progresses, a deeper understanding of the microbiota-gut-brain connection could lead to innovative approaches for managing ME/CFS, ultimately enhancing the quality of life for affected individuals.

The Relationship Between Bacterial Flora in Saliva and Esophageal Mucus and Endoscopic Severity in Patients with Eosinophilic Esophagitis

Eosinophilic esophagitis (EoE) is a chronic inflammatory disease characterized by esophageal dysfunction and eosinophilic inflammation of the esophageal mucosa. In this study, we investigated the bacterial flora in saliva and esophageal mucus in patients with EoE and examined the relationship between EoE disease activity and mucosal cytokine expression, involving patients with active and inactive EoE (A-EoE and I-EoE, respectively). A-EoE was defined as a peak eosinophil count > 15/high-power field, according to the 2025 consensus guidelines. Saliva samples were collected from patients before the endoscopic examination. Brushing samples were collected from the distal esophagus of patients with EoE during endoscopic procedures. The degree of EoE inflammation was assessed using the EoE endoscopic reference score (EREFS). The samples were profiled using the Illumina MiSeq platform. The V3-V4 regions of the 16S rRNA gene (460 bp) were amplified using tailed PCR. Fifty-nine patients were enrolled, including eight with I-EoE, seventeen with A-EoE, and twenty-eight non-EoE controls. Major bacterial genera such as Streptococcus, Prevotella, Veillonella, and Haemophilus were detected in both the oral cavity and esophagus. Compared with the control group, the active EoE group had significantly more Prevotella spp. in the saliva and esophageal mucosa. Conversely, significantly fewer Neisseria spp. were found in the saliva and Streptococcus spp. in the esophageal mucosa of patients with active EoE. The EREFS of EoE and Streptococcus were inversely correlated. This study elucidated the characteristics of bacterial flora in the saliva and esophageal mucosa of patients with EoE.

Potential of queen bee larvae as a dietary supplement for obesity management: modulating the gut microbiota and promoting liver lipid metabolism

Queen bee larvae (QBL) have been consumed as both a traditional food and medicine in China for thousands of years; however, their specific benefits for human health, particularly their potential anti-obesity property, remain underexplored. This study investigated the anti-obesity effect of QBL freeze-dried powder (QBLF) on high-fat diet (HFD) induced obesity in mice and explored the underlying mechanisms. Our findings showed that QBLF effectively reduced body weight, fasting blood glucose levels, lipid accumulation, and inflammation in HFD mice. 16S rRNA sequencing revealed that QBLF significantly modulated the gut microbiota disrupted by an HFD, notably increasing the relative abundance of beneficial microbes such as Ileibacterium, Clostridium sensu stricto 1, Incertae sedis, Streptococcus, Lactococcus, Clostridia UCG-014, and Lachnospiraceae UCG-006, which were inversely associated with obesity-related phenotypes in the mice. RNA sequencing analysis further demonstrated that QBLF intervention upregulated the expression of genes involved in liver lipid metabolism, including Pck1, Cyp4a10, Cyp4a14, and G6pc, while downregulating genes associated with the inflammatory response, such as Cxcl10, Ccl2, Traf1, Mapk15, Lcn2, and Fosb. These results suggested that QBLF can ameliorate HFD-induced obesity through regulating the gut microbiota, promoting liver lipid metabolism, and reducing inflammatory response.

The Microbiome and Metabolic Dysfunction-Associated Steatotic Liver Disease

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a condition wherein excessive fat accumulates in the liver, leading to inflammation and potential liver damage. In this narrative review, we evaluate the tissue microbiota, how they arise and their constituent microbes, and the role of the intestinal and hepatic microbiota in MASLD. The history of bacteriophages (phages) and their occurrence in the microbiota, their part in the potential causation of MASLD, and conversely, "phage therapy" for antibiotic resistance, obesity, and MASLD, are all described. The microbiota metabolism of bile acids and dietary tryptophan and histidine is defined, together with the impacts of their individual metabolites on MASLD pathogenesis. Both periodontitis and intestinal microbiota dysbiosis may cause MASLD, and how individual microorganisms and their metabolites are involved in these processes is discussed. Novel treatment opportunities for MASLD involving the microbiota exist and include fecal microbiota transplantation, probiotics, prebiotics, synbiotics, tryptophan dietary supplements, intermittent fasting, and phages or their holins and endolysins. Although FDA is yet to approve phage therapy in clinical use, there are multiple FDA-approved clinical trials, and this may represent a new horizon for the future treatment of MASLD.

The dual role of gut microbiota in pancreatic cancer: new insights into onset and treatment

Pancreatic cancer ranks among the most lethal digestive malignancies, exhibiting a steadily increasing incidence and mortality worldwide. Despite significant advances in cancer research, the 5-year survival rate remains below 10%, predominantly due to delayed diagnosis and limited therapeutic options. Concurrently, the gut microbiota-an integral component of host physiology-has emerged as a crucial player in the pathogenesis of pancreatic cancer. Mounting evidence indicates that alterations in gut microbial composition and function may influence tumor initiation, progression, and response to therapy. This review provides an in-depth examination of the intricate interplay between the gut microbiome and pancreatic cancer, highlighting potential diagnostic biomarkers and exploring microbiome-targeted therapeutic strategies to improve patient outcomes.

Traumatic Brain Injury and Gut Microbiome: The Role of the Gut-Brain Axis in Neurodegenerative Processes

PURPOSE OF REVIEW

A deeper understanding of the communication network between the gut microbiome and the central nervous system, termed the gut-brain axis (GBA), has revealed new potential targets for intervention to prevent the development of neurodegenerative disease associated with tramatic brain injury (TBI). This review aims to comprehensively examine the role of GBA post-traumatic brain injury (TBI).

RECENT FINDINGS

The GBA functions through neural, metabolic, immune, and endocrine systems, creating bidirectional signaling pathways that modulate brain and gastrointestinal (GI) tract physiology. TBI perturbs these signaling pathways, producing pathophysiological feedback loops in the GBA leading to dysbiosis (i.e., a perturbed gut microbiome, impaired brain-blood barrier, impaired intestinal epithelial barrier (i.e., "leaky gut"), and a maladaptive, systemic inflammatory response. Damage to the CNS associated with TBI leads to GI dysmotility, which promotes small intestinal bacterial overgrowth (SIBO). SIBO has been associated with the early stages of neurodegenerative conditions such as Parkinson's and Alzheimer's disease. Many of the bacteria associated with this overgrowth promote inflammation and, in rodent models, have been shown to compromise the structural integrity of the intestinal mucosal barrier, causing malabsorption of essential nutrients and further exacerbating dysbiosis. TBI-induced pathophysiology is strongly associated with an increased risk of neurodegenerative diseases, including Parkinson's and Alzheimer's diseases, which represents a significant public health burden and challenge for patients and their families. A healthy gut microbiome has been shown to promote improved recovery from TBI and prevent the development of neurodegenerative disease, as well as other chronic complications. The role of the gut microbiome in brain health post-TBI demonstrates the potential for microbiome-targeted interventions to mitigate TBI-associated comorbidities. Promising new evidence on prebiotics, probiotics, diet, and fecal microbiota transplantation may lead to new therapeutic options for improving the quality of life for patients with TBI. Still, many of these preliminary findings must be explored further in clinical settings. This review covers the current understanding of the GBA in the setting of TBI and how the gut microbiome may provide a novel therapeutic target for treatment in this patient population.

The association between gut microbiota and accelerated aging and frailty: a Mendelian randomization study

BACKGROUND

The recent observational studies have unveiled the correlation between the composition and dynamic alterations of the gut microbiome and aging; however, the causal relationship remains uncertain.

AIMS

The objective of this study is to investigate the causal relationship between the gut microbiome and accelerated aging as well as frailty, from a genetic perspective.

METHODS

We obtained data on the gut microbiome, intrinsic epigenetic age acceleration, and Frailty Index from published large-scale genome-wide association studies. A two-sample Mendelian randomization analysis was conducted primarily using inverse variance weighting model. We utilized the MR-Egger intercept analysis, IVW method, the Cochran Q test, and the leave-one-out analysis to assess the robustness of the results.

RESULTS

IVW analysis indicated a potential association between Peptococcus (OR: 1.231, 95% CI 1.013-1.497, P = 0.037), Dialister (OR: 1.447, 95% CI 1.078-1.941, P = 0.014) and Subdoligranulum (OR: 1.538, 95% CI 1.047-2.257, P = 0.028) with intrinsic epigenetic age acceleration; while Prevotella 7 (OR: 0.792, 95% CI 0.672-0.935, P = 0.006) was associated with a potential protective effect. Allisonella (OR: 1.033, 95% CI 1.005-1.063, P = 0.022), Howardella (OR: 1.026, 95% CI 1.002-1.050, P = 0.031) and Eubacterium coprostanoligenes (OR: 1.037, 95% CI 1.001-1.073, P = 0.042) were associated with an increased risk of frailty; conversely, Flavonifractor (OR: 0.954, 95% CI 0.920-0.990, P = 0.012) and Victivallis (OR: 0.984, 95% CI 0.968-1.000, P = 0.049) appeared to exhibit a potential protective effect against frailty.

CONCLUSION

The findings of this study provide further evidence for the genetic correlation between gut microbiota and accelerated aging as well as frailty, enhancing the understanding of the role of gut microbiota in aging-related processes. However, the underlying mechanisms and potential clinical applications require further investigation before any targeted interventions can be developed.

Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives

Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.

The gut-masticatory muscles-temporomandibular joint pain axis-a scoping review

Orofacial pain has become the most common debilitating disease resulting in high healthcare costs, and compromising the quality of life, speech, aesthetics and masticatory function of those affected. As its aetiology is multifactorial and as the treatment involves a multidisciplinary holistic approach, arriving at a confirmative diagnosis is challenging. Numerous studies have been published that support the bidirectional link between gut health and other organs like the cardiovascular system, respiratory system, neurological and hormonal. Recent studies indicate a potential link between gut microbiota dysbiosis and chronic orofacial and temporomandibular joint (TMJ) pain. In this review, we enumerate the link between the metabolites released by the gut bacteria and how they regulate the pain mechanism of various types of orofacial pain like chronic, neuropathic and inflammatory in the orofacial and TMJ regions. We also discuss the potential link between pain and gender predisposition. Further, we review the recent non-invasive therapeutic options which can be put forth to use for treating orofacial and TMJ pain.

Pregnancy-specific shifts in the maternal microbiome and metabolome in the BPH/5 mouse model of superimposed preeclampsia

Preeclampsia (PE) is a life-threatening hypertensive disorder of pregnancy with an incidence rate of up to 8% worldwide. However, the complete pathogenesis is still unknown. Obesity increases the risk of developing PE threefold. To better understand the relationship of maternal risk factors, the BPH/5 mouse was described as a model of superimposed PE. Previous research demonstrated that adult BPH/5 female mice have an adverse cardiometabolic phenotype characterized by hypertension, obesity with increased white adipose tissue, and dyslipidemia, exaggerated by pregnancy. We hypothesize that BPH/5 mice have gut dysbiosis characterized by changes in alpha and beta diversity of bacterial community structure as well as perturbed short-chain fatty acids (SCFAs) compared with controls in pregnancy. Fecal samples were used for Illumina sequencing of 16S v4 rRNA amplicons. Microbial community composition of the pregnant BPH/5 mice compared with C57 controls was different using permutational multivariate analysis of variance (PERMANOVA) with Bray-Curtis dissimilarity. Alpha diversity was increased in pregnant BPH/5 dams compared with controls. Alistipes and Helicobacter were increased, whereas Bacteroides, Lactobacillus, Parasutterella, and Parabacteroides were decreased compared with controls. Fecal SCFAs were not different between groups, but BPH/5 serum acetic and butyric acids were decreased, whereas isobutyric and isovaleric acids were increased specifically in pregnancy. BPH/5 pregnant colons had decreased expression of free fatty acid receptor, GPR41. In conclusion, the BPH/5 maternal fecal microbiome demonstrates microbial dysbiosis characterized by community structure and diversity changes before and after the onset of pregnancy. Gut dysbiosis may be a key mechanism linking SCFA signaling and obesity to the BPH/5 PE-like phenotype.NEW & NOTEWORTHY This is the first time the pregnant fecal microbiome has been identified in the BPH/5 spontaneous mouse model of superimposed PE. Community composition changed with the onset of pregnancy in this model. BPH/5 showed an altered colonic signaling with decreased GPR41 expression, suggesting that gut dysbiosis may link SCFA signaling to the PE phenotype. This data highlights the importance of the maternal obesogenic gut microbiome in pregnancy.

The effects of restraint stress and orthodontic tooth movements on the intestinal epithelial structure and metabolic function in rats

Chronic stress and orthodontic treatment have been revealed to trigger systemic stress responses in rats. This study aimed to investigate the effects of restraint stress and orthodontic treatment on the intestinal epithelial structure, barrier function, flora, and metabolism in rats. Twenty 8-week-old male Wistar rats were randomly divided into four groups: sham-stressed non-orthodontic (CC), sham-stressed orthodontic (CO), stressed non-orthodontic (SC), and stressed orthodontic (SO). The stress intervention involved subjecting the rats to restraint stress for 21 days, while the orthodontic intervention consisted of maxillary first molar traction from days 8 to 21. Histological and immunohistochemical staining were used to observe the epithelial structure and barrier function of the colon. The intestinal flora and metabolite alterations were investigated by 16S rRNA high-throughput sequencing and untargeted metabolomics sequencing. Colonic epithelial tissue disruption, mucus cells reduction, and a decreased expression of intestinal tight junction proteins were observed in the CO, SC, and SO groups. Lactobacillus spp. abundance was significantly lower in the CO group than in the CC group. Prevotella spp. abundance was significantly lower in the SC and SO groups than in the CC and CO groups. The differential metabolite enrichment pathways between each inter-group comparison might all be related to amino acid biosynthesis, protein digestion and absorption, and cofactor biosynthesis. Both restraint stress and orthodontic treatment may adversely affect the colonic epithelial structure and barrier function of rats. The intestinal flora structure and types of metabolites were also affected cumulatively.

Gut microbiota therapy in gastrointestinal diseases

The human gut microbiota, consisting of trillions of microorganisms, plays a crucial role in gastrointestinal (GI) health and disease. Dysbiosis, an imbalance in microbial composition, has been linked to a range of GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), celiac disease, and colorectal cancer. These conditions are influenced by the interactions between the gut microbiota, the host immune system, and the gut-brain axis. Recent research has highlighted the potential for microbiome-based therapeutic strategies, such as probiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary modifications, to restore microbial balance and alleviate disease symptoms. This review examines the role of gut microbiota in the pathogenesis of common gastrointestinal diseases and explores emerging therapeutic approaches aimed at modulating the microbiome. We discuss the scientific foundations of these interventions, their clinical effectiveness, and the challenges in their implementation. The review underscores the therapeutic potential of microbiome-targeted treatments as a novel approach to managing GI disorders, offering personalized and alternative options to conventional therapies. As research in this field continues to evolve, microbiome-based interventions hold promise for improving the treatment and prevention of gastrointestinal diseases.

Measuring water pollution effects on antimicrobial resistance through explainable artificial intelligence

Antimicrobial resistance refers to the ability of pathogens to develop resistance to drugs designed to eliminate them, making the infections they cause more difficult to treat and increasing the likelihood of disease diffusion and mortality. As such, antimicrobial resistance is considered as one of the most significant and universal challenges to both health and society, as well as the environment. In our research, we employ the explainable artificial intelligence paradigm to identify the factors that most affect the onset of antimicrobial resistance in diversified territorial contexts, which can vary widely from each other in terms of climatic, economic and social conditions. Specifically, we employ a large set of indicators identified through the One Health framework to predict, at the country level, mortality resulting from antimicrobial resistance related to Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus pneumoniae. The analysis reveals the outstanding importance of indicators related to water accessibility and quality in determining mortality due to antimicrobial resistance to the considered pathogens across countries, providing perspective as a potential tool for decision support and monitoring.

Therapeutic role of gut microbiota in lung injury-related cognitive impairment

Lung injury can lead to specific neurocognitive dysfunction, and the "triple-hit" phenomenon may be the key theoretical mechanism for the progressive impairment of lung injury-related cognitive impairment. The lung and brain can communicate biologically through immune regulation pathway, hypoxic pathway, neural circuit, mitochondrial dysfunction, and microbial influence, which is called the "lung-brain axis." The gut microbiota is a highly complex community of microorganisms that reside in the gut and communicate with the lung via the "gut-lung axis." The dysregulation of gut microbiota may lead to the migration of pathogenic bacteria to the lung, and directly or indirectly regulate the lung immune response through their metabolites, which may cause or aggravate lung injury. The gut microbiota and the brain interact through the "gut-brain axis." The gut microbiota can influence and regulate cognitive function and behavior of the brain through neural pathway mechanisms, immune regulation pathway and hypothalamic-pituitary-adrenal (HPA) axis regulation. Based on the gut microbiota regulation mechanism of the "gut-lung axis" and "gut-brain axis," combined with the mechanisms of cognitive impairment caused by lung injury, we proposed the "triple-hit" hypothesis. It states that the pathophysiological changes of lung injury trigger a series of events such as immune disorder, inflammatory responses, and microbiota changes, which activate the "lung-gut axis," thus forming a "triple-hit" that leads to the development or deterioration of cognitive impairment. This hypothesis provides a more comprehensive framework for studying and understanding brain dysfunction in the context of lung injury. This review proposes the existence of an interactive tandem network for information exchange among the gut, lung, and brain, referred to as the "gut-lung-brain axis." It further explores the potential mechanism of lung injury-related cognitive impairment caused by multiple interactions of gut microbiota in the "gut-lung-brain axis." We found that there are many numerous pathophysiological factors that influence the interaction within the "gut-lung-brain axis." The impact of gut microbiota on cognitive functions related to lung injury may be mediated through mechanisms such as the "triple-hit" hypothesis, direct translocation of microbes and their metabolites, hypoxic pathway, immune modulation, vagal nerve activity, and the HPA axis regulation, among others. As the research deepens, based on the "triple-hit" hypothesis of lung injury, it is further discovered that gut microbial therapy can significantly change the pathogenesis of the inflammatory process on the "gut-lung-brain axis." It can also relieve lung injury and therapeutically modulate brain function and behavior. This perspective provides a new idea for the follow-up treatment of lung injury-related cognitive impairment caused by dysregulation of gut microbiota.

Time Restricted Eating: A Valuable Alternative to Calorie Restriction for Addressing Obesity?

PURPOSE OF REVIEW

In this review, we summarize the molecular effects of time-restricted eating (TRE) and its possible role in appetite regulation. We also discuss the potential clinical benefits of TRE in obesity.

RECENT FINDINGS

TRE is an emerging dietary approach consisting in limiting food intake to a specific window of time each day. The rationale behind this strategy is to restore the circadian misalignment, commonly seen in obesity. Preclinical studies have shown that restricting food intake only during the active phase of the day can positively influence several cellular functions including senescence, mitochondrial activity, inflammation, autophagy and nutrients' sensing pathways. Furthermore, TRE may play a role by modulating appetite and satiety hormones, though further research is needed to clarify its exact mechanisms. Clinical trials involving patients with obesity or type 2 diabetes suggest that TRE can be effective for weight loss, but its broader effects on improving other clinical outcomes, such as cardiovascular risk factors, remain less certain. The epidemic proportions of obesity cause urgency to find dietary, pharmacological and surgical interventions that can be effective in the medium and long term. According to its molecular effects, TRE can be an interesting alternative to caloric restriction in the treatment of obesity, but the considerable variability across clinical trials regarding population, intervention, and follow-up duration makes it difficult to reach definitive conclusions.

Bacteroides Fragilis Exacerbates T2D Vascular Calcification by Secreting Extracellular Vesicles to Induce M2 Macrophages

Vascular calcification (VC) in type 2 diabetes (T2D) poses a serious threat to the life and health of patients. However, its pathogenesis remains unclear, resulting in a lack of effective treatment for the root cause. It is found that both intestinal Bacteroides fragilis (BF) and peripheral M2 monocytes/macrophages are significantly elevated in patients with T2D VC. M2 macrophages are identified as a significant risk factor for T2D VC. Both BF and their extracellular vesicles (EV) promote T2D VC and facilitate macrophage M2 polarization. Macrophages clearance significantly antagonized BF EV-induced T2D VC in mice. Mechanistically, EV-rich double-stranded DNA (dsDNA) activates stimulator of interferon response cGAMP interactor 1 (Sting), promotes myocyte enhancer factor 2D (Mef2d) phosphorylation, upregulates tribbles pseudokinase 1 (Trib1) expression, and induces macrophage M2 polarization. Concurrently, Mef2d activated by the EV targets and upregulates the expression of pro-calcification factor Serpine1, thereby exacerbating T2D VC. Clinical studies have shown that Serpine1 is significantly elevated in the peripheral blood of patients with T2D VC and is closely associated with T2D VC. In summary, this study reveals that intestinal BF promotes Trib1 expression through the EV-Sting-Mef2d pathway to induce macrophage M2 polarization and upregulates serpin family E member 1 (Serpine1) expression, thereby aggravating T2D VC. The findings provide a new theoretical and experimental bases for optimizing the strategies for prevention and treatment of T2D VC.

Free fatty acid receptor 4 modulates dietary sugar preference via the gut microbiota

Sugar preference is a key contributor to the overconsumption of sugar and the concomitant increase in the incidence of diabetes. However, the exact mechanism of its development remains ambiguous. Here we show that the expression of free fatty acid receptor Ffar4, a receptor for long-chain fatty acids, is decreased in patients and mouse models with diabetes, which is associated with high sugar intake. Deletion of intestinal Ffar4 in mice resulted in reduced gut Bacteroides vulgatus and its metabolite pantothenate, leading to dietary sugar preference. Pantothenate promoted the secretion of GLP-1 which inhibited sugar preference by stimulating hepatic FGF21 release, which in turn regulates energy metabolism. These findings uncover a previously unappreciated role of Ffar4 in negatively regulating sugar preference and suggest B. vulgatus-derived pantothenate as a potential therapeutic target for diabetes.

Should we consider microbiota-based interventions as a novel therapeutic strategy for schizophrenia? A systematic review and meta-analysis

Schizophrenia is a chronic psychiatric disorder characterized by a variety of symptoms broadly categorized into positive, negative, and cognitive domains. Its etiology is multifactorial, involving a complex interplay of genetic, neurobiological, and environmental factors, and its neurobiology is associated with abnormalities in different neurotransmitter systems. Due to this multifactorial etiology and neurobiology, leading to a wide heterogeneity of symptoms and clinical presentations, current antipsychotic treatments face challenges, underscoring the need for novel therapeutic approaches. Recent studies have revealed differences in the gut microbiome of individuals with schizophrenia compared to healthy controls, establishing an intricate link between this disorder and gastrointestinal health, and suggesting that microbiota-targeted interventions could help alleviate clinical symptoms. Therefore, this meta-analysis investigates whether gut microbiota manipulation can ameliorate psychotic outcomes in patients with schizophrenia receiving pharmacological treatment. Nine studies (n = 417 participants) were selected from 81 records, comprising seven randomized controlled trials and two open-label studies, all with a low risk of bias, included in this systematic review and meta-analysis. The overall combined effect size indicated significant symptom improvement following microbiota treatment (Hedges' g = 0.48, 95% CI = 0.09 to 0.88, p = 0.004, I2 = 62.35%). However, according to Hedges' g criteria, the effect size was small (approaching moderate), and study heterogeneity was moderate based on I2 criteria. This review also discusses clinical and preclinical studies to elucidate the neural, immune, and metabolic pathways by which microbiota manipulation, particularly with Lactobacillus and Bifidobacterium genera, may exert beneficial effects on schizophrenia symptoms via the gut-brain axis. Finally, we address the main confounding factors identified in our systematic review, highlight key limitations, and offer recommendations to guide future high-quality trials with larger participant cohorts to explore microbiome-based therapies as a primary or adjunctive treatment for schizophrenia.

Functional Significance of Probiotic Bacterial Interactions with Milk Fat Globules in a Human Host

Dairy products often serve as matrices for delivering probiotic bacteria to humans through the diet; however, little is known about the impact of milk fat globules on the growth and survival of probiotic microorganisms. This review discusses current knowledge on the structure and functionality of the milk fat globule membrane (MFGM) and the structural components contributing to the mechanisms of interactions with probiotic bacteria. We analyzed studies published between 2001 and 2025 with reference to earlier foundational research on probiotics and MFGM structure to explore the functional significance of MFGM-probiotic interactions. Recent research indicates that the effects of MFGM interaction with bacteria are species-specific and may influence probiotic activity in the host, including enhancing probiotic viability during intestinal transit and modulating probiotic colonization. In general, research findings suggest that the MFGM holds potential for use as a probiotic carrier to the gut with beneficial health consequences.

Structural characteristics and nonvolatile metabolites of theabrownins and their impact on intestinal microbiota in high-fat-diet-fed mice

This study prepared enzymatic theabrownins (TBs-e), alkaline theabrownins (TBs-a), and Pu-erh tea theabrownins (TBs-f), and investigated whether different preparation processes affected the structures, nonvolatile metabolites, and biofunctional activities of TBs. Structural characterization revealed that TBs were polymeric phenolic compounds rich in hydroxyl and carboxyl groups. Nontargeted metabolomics revealed that amino acids were the primary nonvolatile metabolites in TBs-e and TBs-a, accounting for over 70 % of the total nonvolatile content. TBs-f contained more polyphenols, caffeine, and flavonoids, accounting for 14.2 %, 3.9 %, and 0.8 % of total nonvolatile content, respectively. In vivo, at 560 mg/kg body weight, TBs-f were associated with regulation of blood glucose and lipid concentrations in mice. Moreover, 16S rRNA indicated that at 1120 mg/kg body weight, TBs-a were associated with increased numbers of microbiota linked with hypolipidemic activity. This study explores the impacts of different preparation processes on TBs and provides a theoretical foundation for the understanding of TBs.

The causal relationship of cigarette smoking to metabolic disease risk and the possible mediating role of gut microbiota

BACKGROUND

Cigarette smoking is a leading cause of preventable death worldwide, with its associated diseases and conditions. Emerging evidence suggests that cigarette smoking contributes to a range of pathological metabolic injuries, including diabetes and nonalcoholic fatty liver disease (NAFLD). The impact of gut microbiota on metabolic health and diseases has been observed, but the causality remains uncertain.

OBJECTIVE

To confirm the causal relationship between cigarette smoking and metabolic diseases, and to investigate the possible mediating effect of gut microbiota on these connections.

METHODS

The relationships among cigarette smoking, metabolic diseases, and the gut microbiome were analyzed by Univariate Mendelian randomization (UVMR). Furthermore, to mitigate the impact of confounding factors, adjusted models were conducted via the multivariate Mendelian randomization (MVMR) method, aiming to improve the accuracy of prediction. Ultimately, the study evaluated the effect of the intermediary factor, gut microbiome, on the relationship between cigarette smoke and metabolic diseases.

RESULTS

The phenomenon that a causal relationship between cigarette smoke (249752 individuals) and gut microbiota (7738 individuals), diabetes (406831 individuals), NAFLD (377998 individuals), hypercholesterolaemia (463010 individuals), and obesity (463010 individuals) was observed using UVMR. In the MVMR model, the genetic connection between cigarette smoking, gut microbiota, and type 2 diabetes remained significant. Of note, paraprevotella_clara served an important mediating role in the type 2 diabetes associated with cigarette smoke.

CONCLUSION

This work offered genetic evidence linking cigarette smoke to metabolic diseases, suggesting that the gut microbiota, particularly paraprevotella_clara, might be a crucial mediator in the development of type 2 diabetes caused by cigarette smoke. Our future studies should consider conducting other ethnic groups MR analyses, particularly with larger sample sizes. Still, more in vivo and in vitro work should be carried out to validate the precise effect and molecular mechanisms of the gut microbiome.

Berberine alleviates enterotoxigenic Escherichia coli-induced intestinal mucosal barrier function damage in a piglet model by modulation of the intestinal microbiome

Introduction

Enterotoxic Escherichia coli (ETEC) is the main pathogen that causes diarrhea, especially in young children. This disease can lead to substantial morbidity and mortality and is a major global health concern. Managing ETEC infections is challenging owing to the increasing prevalence of antibiotic resistance. Berberine, categorized as a substance with similarities in "medicine and food," has been used in China for hundreds of years to treat gastrointestinal disorders and bacteria-induced diarrhea. This study investigated the preventive effect of dietary berberine on the intestinal mucosal barrier induced by ETEC and the microbial community within the intestines of weaned piglets.

Methods

Twenty-four piglets were randomly divided into four groups. Piglets were administered either a standard diet or a standard diet supplemented with berberine at concentrations of 0.05 and 0.1%. and orally administered ETEC or saline.

Results

Dietary supplementation with berberine reduced diamine oxidase, d-lactate, and endotoxin levels in piglets infected with ETEC (P < 0.05). Berberine increased jejunal villus height, villus/crypt ratio, mucosal thickness (P < 0.05), and goblet cell numbers in the villi and crypts (P < 0.05). Furthermore, berberine increased the optical density of mucin 2 and the mucin 2, P-glycoprotein, and CYP3A4 mRNA expression levels (P < 0.05). Berberine increased the expressions of zonula occludins-1 (ZO-1), zonula occludins-2 (ZO-2), Claudin-1, Occludin, and E-cadherin in the ileum (P < 0.05). Moreover, berberine increased the expression of BCL2, reduced intestinal epithelial cell apoptosis (P < 0.05) and decreased the expression of BAX and BAK in the duodenum and jejunum, as well as that of CASP3 and CASP9 in the duodenum and ileum (P < 0.05). Berberine decreased the expression of IL-1β, IL-6, IL-8, TNF-α, and IFN-γ (P < 0.05) and elevated total volatile fatty acids, acetic acid, propionic acid, valeric acid, and isovaleric acid concentrations (P < 0.05). Notably, berberine enhanced the abundance of beneficial bacteria including Enterococcus, Holdemanella, Weissella, Pediococcus, Muribaculum, Colidextribacter, Agathobacter, Roseburia, Clostridium, Fusicatenibacter, and Bifidobacterium. Simultaneously, the relative abundance of harmful and pathogenic bacteria, such as Prevotella, Paraprevotella, Corynebacterium, Catenisphaera, Streptococcus, Enterobacter, and Collinsella, decreased (P < 0.05).

Discussion

Berberine alleviated ETEC-induced intestinal mucosal barrier damage in weaned piglets models. This is associated with enhancement of the physical, chemical, and immune barrier functions of piglets by enhancing intestinal microbiota homeostasis.

Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum

Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. The genes encoding an electron bifurcating, tungsten-containing oxidoreductase (WOR1) and a tungsten-containing formate dehydrogenase (FDH), along with an electron bifurcating lactate dehydrogenase (LCT), lactate permease, and enzymes of the propanediol pathway, are all up-regulated on lactate compared to growth on glucose. Lactate metabolism is controlled by a GntR-family repressor (LctR) and two global regulators, Rex and CcpA, where Rex in part controls W storage and tungstopyranopterin (Tuco) biosynthesis. Tuco-dependent riboswitches, along with CcpA, also control two iron transporters, consistent with the increased iron demand for many iron-containing enzymes, including WOR1 and FDH, involved in SCFA production. From intracellular aldehyde concentrations and the substrate specificity of WOR1, we propose that WOR1 is involved in detoxifying acetaldehyde produced during lactate degradation. Lactate to SCFA conversion by E. limosum is clearly highly tungstocentric and tungsten might be an overlooked micronutrient in the human microbiome and in overall human health.

EGCG protects intestines of mice and pelvic cancer patients against radiation injury via the gut microbiota/D-tagatose/AMPK axis

BACKGROUND AND PURPOSE

Radiation-induced intestinal injury (RIII) compromises the clinical utility of pelvic radiotherapy (RT). We aimed to explore the protective effect and underlying mechanism of (-)-epigallocatechin-3-gallate (EGCG) on RIII.

MATERIALS AND METHODS

We evaluated the protective effect of EGCG on intestine in RIII mouse model and pelvic cancer patients, while explored the underlying mechanism through (1) 16S rRNA sequencing, (2) metabolomic profiles, (3) fresh sterile fecal filtrate (SFF) transplantation, and (4) transcriptome sequencing.

RESULTS

EGCG efficiently prevented RIII in mouse, as reflected by improved survival, alleviated intestinal structure damage, promoted intestinal regeneration, and ameliorated gut microbiota dysbiosis. Prophylactic EGCG intervention reduced the severity of RIII in patients receiving pelvic RT. Mechanistically, the protective effect of EGCG could be transferred to other mice by SFF transplantation. EGCG enriched gut microbiota-derived metabolite D-tagatose, and oral administration of D-tagatose reproduced the radio-protective effect of EGCG via activating AMPK.

CONCLUSION

Oral EGCG may be a promising strategy for preventing RIII clinically, and warrant further investigation in prospective randomized phase III trials.

Role of Gut-Liver Axis in Non-Alcoholic Fatty Liver Disease

Non-alcoholic fatty liver disease (NAFLD) has emerged as a significant global health problem, mainly due to the increasing prevalence of obesity and metabolic syndrome. The gut microbiota plays an essential role in the development of NAFLD through the gut-liver axis. Dysbiosis of. the gut microbiota (GM) is associated with the pathogenesis of NAFLD. Dietary choices and other lifestyle factors influence the composition of the GM and contribute to the development of NAFLD. At the phylum level, individuals with NAFLD show an increased level in Actinobacteria and Firmicutes, while Verrucomicrobia, Thermus, Proteobacteria, Lentiphaerae, and Fusobacteria are found to be decreased. Several genera, including Faecalibacterium and Akkermansia, exhibit alterations in NAFLD and are linked to disease progression. Modulating the GM through prebiotics, probiotics, or fecal microbiota transplantation represents a promising therapeutic strategy for NAFLD. This review summarizes the current understanding of GM changes in NAFLD, focusing on findings from both human and animal studies.

Beneficial microbiome and diet interplay in early-onset colorectal cancer

Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related deaths worldwide. Although the risk of developing CRC increases with age, approximately 10% of newly diagnosed cases occur in individuals under the age of 50. Significant changes in dietary habits in young adults since industrialization create a favorable microenvironment for colorectal carcinogenesis. We aim here to shed light on the complex interplay between diet and gut microbiome in the pathogenesis and prevention of early-onset CRC (EO-CRC). We provide an overview of dietary risk factors associated with EO-CRC and contrast them with the general trends for CRC. We delve into gut bacteria, fungi, and phages with potential benefits against CRC and discuss the underlying molecular mechanisms. Furthermore, based on recent findings from human studies, we offer insights into how dietary modifications could potentially enhance gut microbiome composition to mitigate CRC risk. All together, we outline the current research landscape in this area and propose directions for future investigations that could pave the way for novel preventive and therapeutic strategies.

Effects of prebiotics from diverse sources on dysbiotic gut microbiota associated to western diet: Insights from the human Mucosal ARtificial COLon (M-ARCOL)

Associated to various illnesses, Western Diet (WD) is acknowledged to have deleterious effects on human gut microbiota, decreasing bacterial diversity, lowering gut bacteria associated to health (such as Akkermansia muciniphila), while increasing those linked to diseases (e.g., Proteobacteria). In this study, we evaluated the potential of two new prebiotics to counteract the negative effect of WD on gut microbiota, namely raffinose family oligosaccharides (RFO) from chickpeas and laminarin (LAM) from algae, when compared to the well-known inulin (INU). The effects of prebiotics on gut microbiota composition and metabolic activities were investigated in the Mucosal-Artificial Colon, set-up to reproduce WD condition, as compared to healthy control (n = 3). None of the prebiotics was able to efficiently offset the shift in microbiota induced by WD. Nevertheless, when compared to non-supplemented WD, all prebiotics showed significant impacts on microbiota composition, that were both prebiotic and donor-dependant. RFO was the only prebiotic to enhance α-diversity, while it led to an increase in Blautia and Butyricicoccaceae, associated with higher amounts of gas and butyrate. LAM and INU did not strongly impact microbial metabolic activities but were associated with a rise in Prevotella_9/Agathobacter and Faecalibacterium, respectively. To conclude, this study showed that all tested prebiotics had different impacts on human gut microbiota structure and activities, which was further donor-dependent. M-ARCOL appears as a suitable in vitro tool to better understand the mechanisms of action of prebiotic compounds in relation to gut microbes and define responders and non-responders to prebiotic supplementation, opening the possibility of customized nutritional strategies.

The Role of Gut Microbiome in Irritable Bowel Syndrome: Implications for Clinical Therapeutics

Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder (FGID) characterized by chronic or recurrent gastrointestinal symptoms without organic changes, and it is also a common disorder of gut-brain interaction (DGBIs).. The symptoms of IBS not only affect the quality of life for individual patients but also place a significant burden on global healthcare systems. The lack of established and universally applicable biomarkers for IBS, along with the substantial variability in symptoms and progression, presents challenges in developing effective clinical treatments. In recent years, preclinical and clinical studies have linked the pathogenesis of IBS to alterations in the composition and function of the intestinal microbiota. Within the complex microbial community of the gut, intricate metabolic and spatial interactions occur among its members and between microbes and their hosts. Amid the multifaceted pathophysiology of IBS, the role of intestinal microenvironment factors in symptom development has become more apparent. This review aims to delve into the changes in the composition and structure of the gut microbiome in individuals with IBS. It explores how diet-mediated alterations in intestinal microbes and their byproducts play a role in regulating the pathogenesis of IBS by influencing the "brain-gut" axis, intestinal barrier function, immune responses, and more. By doing so, this review seeks to lay a theoretical foundation for advancing the development of clinical therapeutics for IBS.

A Meta-Analysis of the Human Gut Mycobiome Using Internal Transcribed Spacer Data

The intestinal mycobiome is closely related to human health. There have been several reports investigating the association between the gut fungi and disease, but there is still a lack of overall assessment of the human gut mycobiome. Here, we performed a meta-analysis based on 2372 ITS (Internal Transcribed Spacer) data collected publicly online. We found that the mycobiome diversity of human gut fungi varies significantly across diseases by using EasyAmplicon, and these fungi are mainly composed of three genera, Saccharomyces, Candida, and Aspergillus. In addition, we performed the construction of disease prediction models based on ITS data by using the random forest model and verified the generalization ability of the models. We hope that our results will provide strong support for subsequent studies of the intestinal mycobiome.

Development of Saccharomyces cerevisiae accumulating excessive amount of glycogen and its effects on gut microbiota in a mouse model

Saccharomyces cerevisiae accumulates glycogen, a hyperbranched glucose polymer with multiple bio-functionalities. In this study, mutants of S. cerevisiae that accumulate excessive amounts of glycogen were developed through UV mutagenesis. From over 30,000 mutants, the mutant strain CEY1, which exhibited the highest glycogen production, was selected using iodine vapor screening. The glycogen structures of wild type (WT) and CEY1 were analyzed and found to be relatively similar in molecular weight, hydrodynamic diameter, and side-chain distribution. The glycogen from CEY1 contained long branches (DP >12) 23.6 % greater than those in Escherichia coli TBP38. In addition, WT and CEY1 glycogen showed 32 %-34 % digestibility, which is significantly lower than E. coli glycogen. The glycogen content in dried CEY1 cells was increased to 21.7 % during laboratory-scale fed-batch fermentation. Glycogen with a homogeneous structure was accumulated to 17.5 % (w/w dried cell), and the total glucan content was increased by 33.2 % during large-scale fed-batch fermentation. In a mouse model, a diet containing 30 % CEY1 increased the production of butyrate and populations of beneficial bacteria, including Bacteroides and Parabacteroides. Therefore, glycogen from CEY1 exhibits a distinct structure from other polysaccharides, with notably slow and low digestibility, thereby indicating its potential application as a dietary supplement.

Systematic Review and Meta-Analysis: Taurine and Its Association With Colorectal Carcinoma

BACKGROUND

Colorectal cancer (CRC) is one of the most common cancers. Various options are available for treatment, but prognosis is still poor in the more advanced stages. Current screening methods are not as accurate for distinguishing between benign and malignant growths, resulting in unnecessary invasive procedures. Recently a focus has been placed on identifying metabolites. Of these, taurine has frequently been detected, and this particular compound has a multifactorial role in human physiology.

METHODS

We conducted a systematic review of studies up till November 2023. Searches were done in three databases- MEDLINE, CINAHL-Ebsco, and PubMed. Three independent reviewers filter titles, abstracts, and full-texts according to selection criteria. Ten studies (samples = 1714) were identified showing a differential level of taurine in CRC patient samples. Quality assessment accounted for the risk of bias of each study using the 'robvis' tool. Where meaningful comparisons could be made, meta-analyses were carried out using the 'R' program for precalculated effect sizes with 'metagen' in R. The 'meta' package was utilised for creation of forest plots.

FINDINGS

Taurine was shown to significantly increase odds of CRC. It was also significantly associated with being a discriminator for CRC as a diagnostic metabolite. This was maintained at various stages of CRC. Taurine had increased expression in CRC patients, especially when the matrix utilised was blood. Nevertheless, there was significant heterogeneity for some outcomes.

INTERPRETATION

In conclusion, these findings highlight the potential of using taurine as well as other bile acid metabolites (lithocholic and ursodeoxycholic acid) to diagnose CRC and illustrate the link with microbiome interactions. Overall increased taurine concentration are associated with significantly increased odds for CRC. There was mostly an increase in relative expression of taurine in CRC samples, excluding results from Wang et al.

Bile's Hidden Weapon: Modulating the Microbiome and Tumor Microenvironment

The human gut microbiome is a dynamic and intricate ecosystem, composed of trillions of microorganisms that play a pivotal role in maintaining overall health and well-being. However, the gut microbiome is constantly exposed to various environmental factors, including the bile produced by the liver, which can significantly impact its composition and function. Bile acids, secreted by the liver and stored in the gallbladder, modulate the gut microbiome, influencing its composition and function. This altered microbiome profile can, in turn, impact the tumor microenvironment (TME), promoting an immunosuppressive environment that favors tumor growth and metastasis. Furthermore, changes in the gut microbiome can also influence the production of bile acids and other metabolites that directly affect cancer cells and their behavior. Moreover, bile acids have been shown to shape the microbiome and increase antibiotic resistance, underscoring the need for targeted interventions. This review provides a comprehensive overview of the intricate relationships between bile, the gut microbiome, and the TME, highlighting the mechanisms by which this interplay drives cancer progression and resistance to therapy. Understanding these complex interactions is crucial for developing novel therapeutic strategies that target the gut-bile-TME axis and improve patient outcomes.

Gut microbiota and Parkinson's disease: potential links and the role of fecal microbiota transplantation

Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide and seriously affects the quality of life of elderly patients. PD is characterized by the loss of dopaminergic neurons in the substantia nigra as well as abnormal accumulation of α-synuclein in neurons. Recent research has deepened our understanding of the gut microbiota, revealing that it participates in the pathological process of PD through the gut-brain axis, suggesting that the gut may be the source of PD. Therefore, studying the relationship between gut microbiota and PD is crucial for improving our understanding of the disease's prevention, diagnosis, and treatment. In this review, we first describe the bidirectional regulation of the gut-brain axis by the gut microbiota and the mechanisms underlying the involvement of gut microbiota and their metabolites in PD. We then summarize the different species of gut microbiota found in patients with PD and their correlations with clinical symptoms. Finally, we review the most comprehensive animal and human studies on treating PD through fecal microbiota transplantation (FMT), discussing the challenges and considerations associated with this treatment approach.

Association of Gut Microbiome and Dipeptidyl Peptidase 4 in Immune-Mediated Inflammatory Bowel Disease: A Rapid Literature Review

Immune-mediated inflammatory diseases (IMIDs) are characterized by dysregulated immune responses and chronic tissue inflammation. In the setting of inflammatory bowel disease (IBD), dipeptidyl peptidase 4 (DPP4) and gut microorganisms have been proved to interplay, potentially influenced by dietary factors. This rapid review aimed to study the DPP4-gut microbiome link in IBD. A search across five databases and two gray literature sources identified seven relevant studies reporting data on DPP4 and gut microbiome in patients with IBD-related IMIDs or in vitro or in vivo models: one cross-sectional, one in vitro, and five in vivo studies. The findings revealed a significant impact of DPP4 and its substrates, i.e., glucagon-like peptide-1/2 (GLP-1/2), on the composition of gut microbiome and on the development of dysbiosis. Increased DPP4 activity is associated with decreased GLP-1/2; increased pathogenic bacterial phyla such as Actinobacteria, Bacteroidetes, Deferribacteres, Firmicutes, Fusobacteriota, Proteobacteria, and Verrucomicrobia; and decreased alpha diversity of beneficial gut microbes, including Clostridiaceae, Lachnospiraceae, and Ruminococcaceae families and short-chain fatty acid-producing bacteria like Odoribacter and Butryvibrio spp., with exacerbation of intestinal inflammation. This overview revealed that understanding the DPP4-gut microbiome association is critical for the development of DPP4-targeted therapeutic strategies to guarantee gut microbiome balance and modulation of immune response in IBD.

Optimizing microbiome reference databases with PacBio full-length 16S rRNA sequencing for enhanced taxonomic classification and biomarker discovery

Background

The study of the human microbiome is crucial for understanding disease mechanisms, identifying biomarkers, and guiding preventive measures. Advances in sequencing platforms, particularly 16S rRNA sequencing, have revolutionized microbiome research. Despite the benefits, large microbiome reference databases (DBs) pose challenges, including computational demands and potential inaccuracies. This study aimed to determine if full-length 16S rRNA sequencing data produced by PacBio could be used to optimize reference DBs and be applied to Illumina V3-V4 targeted sequencing data for microbial study.

Methods

Oral and gut microbiome data (PRJNA1049979) were retrieved from NCBI. DADA2 was applied to full-length 16S rRNA PacBio data to obtain amplicon sequencing variants (ASVs). The RDP reference DB was used to assign the ASVs, which were then used as a reference DB to train the classifier. QIIME2 was used for V3-V4 targeted Illumina data analysis. BLAST was used to analyze alignment statistics. Linear discriminant analysis Effect Size (LEfSe) was employed for discriminant analysis.

Results

ASVs produced by PacBio showed coverage of the oral microbiome similar to the Human Oral Microbiome Database. A phylogenetic tree was trimmed at various thresholds to obtain an optimized reference DB. This established method was then applied to gut microbiome data, and the optimized gut microbiome reference DB provided improved taxa classification and biomarker discovery efficiency.

Conclusion

Full-length 16S rRNA sequencing data produced by PacBio can be used to construct a microbiome reference DB. Utilizing an optimized reference DB can increase the accuracy of microbiome classification and enhance biomarker discovery.

Changes in the Composition and Diversity of the Intestinal Microbiota Associated with Carbohydrate Consumption in Type 2 Diabetes Mellitus Patients

Type 2 diabetes mellitus (T2DM) is a multifactorial disease, influenced by dietary and environmental factors that can modify the intestinal microbiota. The aim of this study was to evaluate changes in the composition and diversity of the intestinal microbiota associated with carbohydrate (CHO) consumption in T2DM patients. Forty patients participated, with and without T2DM. Fecal samples were collected for the characterization of microbial diversity from the massive sequencing of the 16S rRNA gene. Carbohydrate consumption was quantified using the Frequency Consumption Foods questionnaire (FCF), the groups were categorized according to Body Mass Index (BMI) and BMI + CHO consumption. The group without T2DM showed normal biochemical and anthropometric parameters, although they had a high carbohydrate consumption compared to the group with T2DM. At the phylum level, there were differences in relative abundance; the control overweight group (CL-OW > CHO) and T2DM-Normal Weight > CHO patients had increased Bacteroides and decreased Firmicutes. In contrast, the CL-OW > CHO and T2DM-OW < CHO patients, showed reduced Bacteroidetes and an elevated amount of Firmicutes. At the genus level, the differences were in the relative abundance of Roseburia, Clostridium_IV, Prevotella, and Sporobacter, associated with the consumption of carbohydrates. The groups that consumed high amounts of carbohydrates, regardless of whether they had diabetes mellitus or were overweight, had a significantly reduced proportion of Faecalibacterium, an altered proportion of Bacteroides. The high consumption of carbohydrates showed considerable modifications in the composition and diversity of the bacterial communities.

Unraveling the Role of the Human Gut Microbiome in Health and Diseases

The human gut is a complex ecosystem that supports billions of living species, including bacteria, viruses, archaea, phages, fungi, and unicellular eukaryotes. Bacteria give genes and enzymes for microbial and host-produced compounds, establishing a symbiotic link between the external environment and the host at both the gut and systemic levels. The gut microbiome, which is primarily made up of commensal bacteria, is critical for maintaining the healthy host's immune system, aiding digestion, synthesizing essential nutrients, and protecting against pathogenic bacteria, as well as influencing endocrine, neural, humoral, and immunological functions and metabolic pathways. Qualitative, quantitative, and/or topographic shifts can alter the gut microbiome, resulting in dysbiosis and microbial dysfunction, which can contribute to a variety of noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, cancer, and irritable bowel syndrome. While most evidence to date is observational and does not establish direct causation, ongoing clinical trials and advanced genomic techniques are steadily enhancing our understanding of these intricate interactions. This review will explore key aspects of the relationship between gut microbiota, eubiosis, and dysbiosis in human health and disease, highlighting emerging strategies for microbiome engineering as potential therapeutic approaches for various conditions.

Agar oligosaccharides improve the intestinal health of induced-aging mice by maintaining intestinal homeostasis via balancing the ISCs proliferation and differentiation

PURPOSE

Aging is a process that accompanies a decline in the function of various tissues and organs, especially affecting intestinal health. Agarose oligosaccharide (AOS) can prolong the lifespan of organisms and protect the intestine in the previous study. It was examined to evaluate the effects of AOS on intestinal health, and the potential associations between intestinal homeostasis and health status were further validated.

METHODS

D-galactose-induced aging mice were used to investigate the role of AOS in promoting intestinal health by determining intestinal physiology, microbiota and stem cells.

RESULTS

AOS supplementation decreased the clinical frailty index of aging mice with increasing intestinal length and crypt depth; moreover, it decreased the average flatulence index and PCNA protein content in the intestine. Besides, AOS contributed to the diversity of the gut microbiota by increasing the relative abundance of Bacteroidetes and other bacteria that could produce short-chain fatty acids. Furthermore, AOS affected the expression of proinflammatory factors in aging mice, promoting the proliferative equilibrium of intestinal stem cells.

CONCLUSION

These findings confirmed that AOS could improve intestinal health in aging mice by maintaining intestinal homeostasis, which provides new insights into the potential application of AOS as a prebiotic.

Impacts of polyhydroxybutyrate (PHB) microplastic exposure on physiology and metabolic profiles of Litopenaeus vannamei

In light of increasing concerns about microplastic pollution, it is crucial to understand the biological impacts of biodegradable PHB microplastics on marine organisms. This study included a 96-h exposure experiment to assess acute toxicity at PHB concentrations of 0 mg/L, 100 mg/L, 500 mg/L and 1000 mg/L. Additionally, a 60-day feeding trial was conducted with PHB concentrations of 0, 0.5, 1.0 and 2.0 g/kg to evaluate the long-term effects on growth, physiological health and metabolic responses of Litopenaeus vannamei. Results from the exposure experiment indicated that PHB microplastics up to 100 mg/L were non-toxic to shrimp. However, the 60-day feeding trial revealed that higher concentrations led to slight reductions in survival rates and growth performance, indicating a concentration-dependent response. Analysis of antioxidant and immune enzymes showed minimal changes across most parameters. However, increases in malondialdehyde content and lysozyme activity at higher PHB levels suggested a stress response. Microbial analysis indicated higher species richness and greater community diversity in the PHB group compared to controls, as evidenced by Chao1, ACE, Shannon and Simpson indices. Linear discriminant analysis revealed that Enterobacteriales and related taxa were more prevalent in the PHB group, while Rhodobacteraceae and associated taxa dominated the control group. Pathway analysis highlighted enhanced signal transduction, cell mobility and metabolic resource reallocation in response to PHB-induced stress. Integrated transcriptomic and metabolomic analyses revealed significant regulatory changes, especially in lipid metabolism pathways. These findings suggest that while PHB microplastics trigger adaptive metabolic responses in shrimp, they do not cause acute toxicity. Significant variations in intestinal microbiome composition reflect potential shifts in gut health dynamics due to PHB ingestion. This study enhances our understanding of the ecological impacts of microplastics and underscores the necessity for further research into the environmental safety of biodegradable alternatives.

Pristimerin Alleviates DSS-Induced Colitis in Mice by Modulating Intestinal Barrier Function, Gut Microbiota Balance and Host Metabolism

Pristimerin is a pentacyclic triterpenoid mainly derived from Celastraceae plants such as Maytenus ilicifolia, which has been traditionally used for the treatment of gastrointestinal disorders. Pharmacological studies have shown that pristimerin exhibited anti-inflammatory, antioxidant, anticancer and antibacterial activities. However, the potential mechanism of pristimerin for the treatment of ulcerative colitis (UC) remains elusive. In the present study, pristimerin could effectively inhibit the NO generation induced by LPS in RAW 264.7 cells and upregulate the decreased expression of tight junction proteins such as occludin and claudin-1. In vivo, oral administration of pristimerin (0.5 mg/kg and 1 mg/kg) could significantly relieve UC symptoms such as body weight loss, disease activity index, shortened colon length and colonic pathological damage. Meanwhile, pristimerin decreased the TNF-α, MPO and MDA levels and increased the levels of IL-10, IL-22, SOD activity, occludin and claudin-1 in colon tissues. Gut microbiota analysis of cecum contents revealed that pristimerin treatment effectively alleviated gut microbiota dysbiosis. Additionally, serum metabolomics showed that 33 potential biomarkers involving lipid and tryptophan metabolism were identified, which may account for the therapeutic effects of pristimerin on UC mice. In conclusion, our findings indicate that pristimerin attenuates UC symptoms in DSS-induced mice through modulating intestinal barrier integrity, gut microbiota composition, lipid and tryptophan metabolism.

Advances in the study of oral microbiota and metabolism associated fatty liver disease: a systematic review

Objective

The oral microbiota is the second largest microbiota in the human body and has a significant impact on human health. Recent evidence suggests that dysbiosis of the oral microbiota may be associated with the development of metabolism-associated fatty liver disease (MAFLD). This review aimed to validate the relationship between oral microbial diversity and the development of MAFLD.

Methods

A systematic evaluation was performed based on PRISMA guidelines. Three independent reviewers searched for relevant literature in several databases, including PubMed/Medline, Web of Science, and Scopus, with a search date ranging from the establishment of the databases to June 2024.

Results

A total of 1278 publications were initially screened, including five cross-sectional studies, seven case-control studies, one cohort study, and one retrospective study. These studies included a total of 3335 patients with MAFLD, 254 patients with MASH, and 105 patients with liver cirrhosis. All 14 included studies concluded that there was a correlation or potential correlation between oral microbiota and MAFLD. Seven studies found that the composition of the oral microbiota in MAFLD patients differed from that of healthy controls, and specific oral bacteria may be associated with an increased incidence of MAFLD. At the phylum level, several studies found differences in the abundance of the phyla Firmicutes, Proteobacteria, and Clostridia compared to healthy controls. Additionally, a study on oral fungi found significant differences in the phyla Proteobacteria and in the genus Staphylococcus between patients with MAFLD and healthy controls. At the genus level, Porphyromonas was studied most frequently, with all 8 studies identifying infection with Porphyromonas as a significant risk factor for pathological progression in MAFLD. Furthermore, a dysbiosis in the ratio of Porphyromonas gingivalis./Porphyromonas anomalies may be an important marker of MAFLD progression.

Conclusion

There is an important association between the diversity of oral microbiota composition and MAFLD. This finding suggests the importance of oral health assessment and monitoring for the prevention or intervention of MAFLD.

Extensive genomic characterization, pre-clinical probiotic evaluation, and safety analysis of Bifidobacterium longum subsp. longum BL21 isolated from infant feces

OBJECTIVE

This study aimed to evaluate the safety and probiotic properties of Bifidobacterium longum subsp. longum BL21 isolated from infant feces for use as a commercial probiotic strain.

METHODS

Whole-genome sequencing; physiological and biochemical assessments; enzymatic assays; metabolite, antibiotic sensitivity, cell adhesion and cytotoxicity, and tolerance tests; and a 14-day oral toxicity study were conducted.

RESULTS

BL21 exhibited genetic integrity, and its genome lacked genes related to antibiotic resistance or virulence. It was found to be non-pathogenic, had efficient carbohydrate metabolism and mucin degradation ability, and was free from biogenic amines. It also showed susceptibility to antibiotics, strong cell adhesion, and resilience to adverse conditions. The aforementioned results confirm that BL21 is a functional probiotic strain with genetic stability, enzymatic capabilities, and non-pathogenic properties that mean it is safe for oral consumption, demonstrating that it is a promising candidate for probiotic applications.

CONCLUSION

The study demonstrates that BL21 is a genetically stable, non-pathogenic probiotic strain with metabolic potential. The strain lacks virulence and antibiotic resistance genes, and its resilience to gastrointestinal conditions, as well as the results of the 14-day oral toxicity study, suggest that BL21 is safe for oral consumption. However, further long-term studies and clinical trials are needed to confirm its safety and efficacy for therapeutic use.

Rationale and design of a randomized placebo-controlled nutritional trial embracing a citizen science approach

Modulation of the gut microbiota through specific dietary interventions shows potential for maintenance and optimization of health. A dietary fiber diet and fermented foods diet appear to alter the gut microbiota, but evidence is limited. Therefore, we designed the Gut Health Enhancement by Eating Favorable Food study, a 21-week randomized controlled trial studying effects of dietary fibers and fermented foods on gut microbiota diversity and composition, while also stimulating dietary behavior changes through a citizen science (CS) approach. We hypothesized that a high-fermented food diet would increase microbial diversity, whereas a high-dietary fiber diet would stimulate the growth of specific fiber-degrading bacteria. The following elements of CS were adopted: education on the gut microbiota, tailored dietary intervention, remote data collection by participants, sharing of personal gut microbiota outcomes with participants, and vlogs by participants for dissemination of results. Here we describe the study protocol and report the flow of participants, baseline characteristics, and compliance rates. Completed in March 2024, the trial included 147 healthy adults randomized to a high-dietary fiber intervention, high-fermented food intervention, or control group. Each group received an additional study product after 2 weeks: dried chicory root, a fermented beverage, or maltodextrin (placebo). A 3-month follow-up assessed the participants' ability to sustain dietary changes. The recruitment of participants was successful, reflected by 1448 applications. The compliance with the dietary guidelines and study products was >90%. This study shows that including elements of CS in an randomized controlled trial is feasible and may help recruitment and compliance.