The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases

Gut Microbiota Modulation in IBD: From the Old Paradigm to Revolutionary Tools

Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders primarily comprising two main conditions: ulcerative colitis and Crohn's disease. The gut microbiota's role in driving inflammation in IBD has garnered significant attention, yet the precise mechanisms through which the microbiota influences IBD pathogenesis remain largely unclear. Given the limited therapeutic options for IBD, alternative microbiota-targeted therapies-including prebiotics, probiotics, postbiotics, and symbiotics-have been proposed. While these approaches have shown promising results, microbiota modulation is still mainly considered an adjunct therapy to conventional treatments, with a demonstrated impact on patients' quality of life. Fecal microbiota transplantation (FMT), already approved for treating Clostridioides difficile infection, represents the first in a series of innovative microbiota-based therapies under investigation. Microbial biotherapeutics are emerging as personalized and cutting-edge tools for IBD management, encompassing next-generation probiotics, bacterial consortia, bacteriophages, engineered probiotics, direct metabolic pathway modulation, and nanotherapeutics. This review explores microbial modulation as a therapeutic strategy for IBDs, highlighting current approaches and examining promising tools under development to better understand their potential clinical applications in managing intestinal inflammatory disorders.

Dietary Fatty Acid Composition Alters Gut Microbiome in Mice with Obesity-Induced Peripheral Neuropathy

BACKGROUND

Peripheral neuropathy (PN), a complication of diabetes and obesity, progresses through a complex pathophysiology. Lifestyle interventions to manage systemic metabolism are recommended to prevent or slow PN, given the multifactorial risks of diabetes and obesity. A high-fat diet rich in saturated fatty acids (SFAs) induces PN, which a diet rich in monounsaturated fatty acids (MUFAs) rescues, independent of weight loss, suggesting factors beyond systemic metabolism impact nerve health. Interest has grown in gut microbiome mechanisms in PN, which is characterized by a distinct microbiota signature that correlates with sciatic nerve lipidome.

METHODS

Herein, we postulated that SFA- versus MUFA-rich diet would impact gut microbiome composition and correlate with PN development. To assess causality, we performed fecal microbiota transplantation (FMT) from donor mice fed SFA- versus MUFA-rich diet to lean recipient mice and assessed metabolic and PN phenotypes.

RESULTS

We found that the SFA-rich diet altered the microbiome community structure, which the MUFA-rich diet partially reversed. PN metrics correlated with several microbial families, some containing genera with feasible mechanisms of action for microbiome-mediated effects on PN. SFA and MUFA FMT did not impact metabolic phenotypes in recipient mice although SFA FMT marginally induced motor PN.

CONCLUSIONS

The involvement of diet-mediated changes in the microbiome on PN and gut-nerve axis may warrant further study.

Integrative Roles of Functional Foods, Microbiotics, Nutrigenetics, and Nutrigenomics in Managing Type 2 Diabetes and Obesity

Diabetes and obesity are globally prevalent metabolic disorders posing significant public health challenges. The effective management of these conditions requires integrated and personalized strategies. This study conducted a systematic literature review, identifying 335 relevant papers, with 129 core articles selected after screening for duplicates and irrelevant studies. The focus of the study is on the synergistic roles of functional foods, microbiotics, and nutrigenomics. Functional foods, including phytochemicals (e.g., polyphenols and dietary fibers), zoochemicals (e.g., essential fatty acids), and bioactive compounds from macrofungi, exhibit significant potential in enhancing insulin sensitivity, regulating lipid metabolism, reducing inflammatory responses, and improving antioxidant capacity. Additionally, the critical role of gut microbiota in metabolic health is highlighted, as its interaction with functional foods facilitates the modulation of metabolic pathways. Nutrigenomics, encompassing nutrigenetics and genomics, reveals how genetic variations (e.g., single-nucleotide polymorphisms (SNPs)) influence dietary responses and gene expression, forming a feedback loop between dietary habits, genetic variations, gut microbiota, and metabolic health. This review integrates functional foods, gut microbiota, and genetic insights to propose comprehensive and sustainable personalized nutrition interventions, offering novel perspectives for preventing and managing type 2 diabetes and obesity. Future clinical studies are warranted to validate the long-term efficacy and safety of these strategies.

Lactiplantibacillus plantarum BXM2 Treatment Alleviates Disorders Induced by a High-Fat Diet in Mice by Improving Intestinal Health and Modulating the Gut Microbiota

Objective:Lactiplantibacillus plantarum BXM2 is a novel probiotic derived from fermented passion fruit (Passiflora edulis) juice that possesses promising probiotic potential. The aim of this study was to evaluate the beneficial effects of L. plantarum BXM2 supplementation in mice. Methods:L. plantarum BXM2 was orally administered to male SPF C57BL/6J mice fed a high-fat diet (HFD) to evaluate its anti-obesity potential, as well as the effects on intestinal health and microbiota. Results: Our results demonstrated that L. plantarum BXM2 significantly decreased the perirenal adipose index and improved intestinal health by increasing the ratio of villus height to crypt depth and the goblet cell number in the intestine. Furthermore, L. plantarum BXM2 treatment exhibited regulatory effects on intestinal chronic inflammation in mice by normalizing the mRNA expression of TNF-α and IL-6. Of note, L. plantarum BXM2 reversed HFD-induced gut dysbiosis, as evidenced by the decreased ratio of Bacillota (Firmicutes) to Bacteroidota, the decreased abundance of obesity-related genera Dubosiella, Romboutsia, and Lachnospiraceae_UCG006, and the increased abundance of beneficial genera Akkermansia and Lactobacillus. Conclusions: Our findings support the beneficial role of L. plantarum BXM2 supplementation in interventions targeting gut dysbiosis and obesity-related disorders.

Ten computational challenges in human virome studies

In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent, primarily hindered by the lack of effective methods, particularly in the domain of computational tools. This perspective systematically outlines ten computational challenges spanning various types of virome studies. These challenges arise due to the vast diversity of viromes, the absence of a universal marker gene in viral genomes, the low abundance of virus populations, the remote or minimal homology of viral proteins to known proteins, and the highly dynamic and heterogeneous nature of viromes. For each computational challenge, we discuss the underlying reasons, current research progress, and potential solutions. The resolution of these challenges necessitates ongoing collaboration among computational scientists, virologists, and multidisciplinary experts. In essence, this perspective serves as a comprehensive guide for directing computational efforts in human virome studies.

A Novel Dhillonvirus Phage against Escherichia coli Bearing a Unique Gene of Intergeneric Origin

Antibiotics resistance is expanding amongst pathogenic bacteria. Phage therapy is a revived concept for targeting bacteria with multiple antibiotics resistances. In the present study, we isolated and characterized a novel phage from hospital treatment plant input, using Escherichia coli (E. coli) as host bacterium. Phage lytic activity was detected by using soft agar assay. Whole-genome sequencing of the phage was performed by using Next-Generation Sequencing (NGS). Host range was determined using other species of bacteria and representative genogroups of E. coli. Whole-genome sequencing of the phage revealed that Escherichia phage Ioannina is a novel phage within the Dhillonvirus genus, but significantly diverged from other Dhillonviruses. Its genome is a 45,270 bp linear double-stranded DNA molecule that encodes 61 coding sequences (CDSs). The coding sequence of CDS28, a putative tail fiber protein, presented higher similarity to representatives of other phage families, signifying a possible recombination event. Escherichia phage Ioannina lytic activity was broad amongst the E. coli genogroups of clinical and environmental origin with multiple resistances. This phage may present in the future an important therapeutic tool against bacterial strains with multiple antibiotic resistances.

Viral metagenomics combined with non-targeted serum metabolomics reveals the role of enteroviruses in a mouse model of coronary heart disease

BACKGROUND

Coronary heart disease (CHD) is a common cardiovascular disease that is associated with altered gut microbiota. Enteroviruses, an essential component of the gut microbiome, may play an important role in disease progression. However, the relationship between enteroviruses and CHD remains unclear. The development of high-throughput sequencing technologies has facilitated research on the interconnections between viruses and disease-related metabolites.

METHODS AND RESULTS

Mice were fed a high-fat diet (CHD group) or chow diet (Sham group) for 12 weeks, and ligation of the left anterior descending coronary artery was performed at the end of week 8. After 4 weeks, all animals were euthanised. Subsequently, the animals were evaluated for basic haemato-biochemical parameters and cardiac function, and aorta staining was performed. Based on enteroviral metagenomics and serum UPLC-MS/MS metabolomics analyses, we evaluated the association between enteroviral groups and serum metabolites of CHD mouse model. A high-fat diet and coronary ligation enabled the establishment of the CHD mouse model. Notably, the enterovirus spectrum of the sham group was significantly different from that of the CHD group, with 24 viral communities of different family and species classification, such as Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus, exhibiting significant differences. In addition, 731 Differential metabolites were detected in the serum of both groups of mice. Correlation network analysis revealed a close relationship between various metabolites related to lipid metabolism and different viruses, including Tsarbombavirus, Mingyongvirus, Claudivirus, and Firehammervirus.

CONCLUSIONS

An animal model of CHD, characterised by lipid disturbance and myocardial ischaemia, was established using a high-fat diet and ligation of the left anterior descending branch of the coronary artery. Tsarbombavirus, Firehammervirus, Mingyongvirus, and Claudivirus were associated with metabolites in the lipid metabolism pathway. The results indicate that Tsarbombavirus may be the main genus interacting with CHD-related metabolites in mice. Conclusively, the findings of our study provide novel insights into the potential relationship enterovirus groups and metabolites associated with CHD.

Distinct characteristics of the gut virome in patients with osteoarthritis and gouty arthritis

BACKGROUND/PURPOSE(S)

The gut microbiota and its metabolites play crucial roles in pathogenesis of arthritis, highlighting gut microbiota as a promising avenue for modulating autoimmunity. However, the characterization of the gut virome in arthritis patients, including osteoarthritis (OA) and gouty arthritis (GA), requires further investigation.

METHODS

We employed virus-like particle (VLP)-based metagenomic sequencing to analyze gut viral community in 20 OA patients, 26 GA patients, and 31 healthy controls, encompassing a total of 77 fecal samples.

RESULTS

Our analysis generated 6819 vOTUs, with a considerable proportion of viral genomes differing from existing catalogs. The gut virome in OA and GA patients differed significantly from healthy controls, showing variations in diversity and viral family abundances. We identified 157 OA-associated and 94 GA-associated vOTUs, achieving high accuracy in patient-control discrimination with random forest models. OA-associated viruses were predicted to infect pro-inflammatory bacteria or bacteria associated with immunoglobulin A production, while GA-associated viruses were linked to Bacteroidaceae or Lachnospiraceae phages. Furthermore, several viral functional orthologs displayed significant differences in frequency between OA-enriched and GA-enriched vOTUs, suggesting potential functional roles of these viruses. Additionally, we trained classification models based on gut viral signatures to effectively discriminate OA or GA patients from healthy controls, yielding AUC values up to 0.97, indicating the clinical utility of the gut virome in diagnosing OA or GA.

CONCLUSION

Our study highlights distinctive alterations in viral diversity and taxonomy within gut virome of OA and GA patients, offering insights into arthritis etiology and potential treatment and prevention strategies.

Causal effects of gut microbiota on the prognosis of ischemic stroke: evidence from a bidirectional two-sample Mendelian randomization study

Background

Increasing research has implicated the possible effect of gut microbiota (GM) on the prognosis of ischemic stroke (IS). However, the precise causal relationship between GM and functional outcomes after IS remains unestablished.

Methods

Data on 211 GM taxa from the MiBioGen consortium and data on prognosis of IS from the Genetics of Ischemic Stroke Functional Outcome (GISCOME) network were utilized as summary-level data of exposure and outcome. Four kinds of Mendelian randomization (MR) methods were carried out to ascertain the causal effect of GM on functional outcomes following IS. A reverse MR analysis was performed on the positive taxa identified in the forward MR analysis to determine the direction of causation. In addition, we conducted a comparative MR analysis without adjusting the baseline National Institute of Health Stroke Scale (NIHSS) of post-stroke functional outcomes to enhance confidence of the results obtained in the main analysis.

Results

Four taxa were identified to be related to stroke prognosis in both main and comparative analyses. Specifically, genus Ruminococcaceae UCG005 and the Eubacterium oxidoreducens group showed significantly negative effects on stroke prognosis, while the genus Lachnospiraceae NK4A136 group and Lachnospiraceae UCG004 showed protective effects against stroke prognosis. The reverse MR analysis did not support a causal role of stroke prognosis in GM. No evidence of heterogeneity, horizontal pleiotropy, and outliers was found.

Conclusion

This MR study provided evidence that genetically predicted GM had a causal link with post-stroke outcomes. Specific gut microbiota taxa associated with IS prognosis were identified, which may be helpful to clarify the pathogenesis of ischemic stroke and making treatment strategies.

Effect of the gut microbiome, plasma metabolome, peripheral cells, and inflammatory cytokines on obesity: a bidirectional two-sample Mendelian randomization study and mediation analysis

Background

Obesity is a metabolic and chronic inflammatory disease involving genetic and environmental factors. This study aimed to investigate the causal relationship among gut microbiota abundance, plasma metabolomics, peripheral cell (blood and immune cell) counts, inflammatory cytokines, and obesity.

Methods

Summary statistics of 191 gut microbiota traits (N = 18,340), 1,400 plasma metabolite traits (N = 8,299), 128 peripheral cell counts (blood cells, N = 408,112; immune cells, N = 3,757), 41 inflammatory cytokine traits (N = 8,293), and 6 obesity traits were obtained from publicly available genome-wide association studies. Two-sample Mendelian randomization (MR) analysis was applied to infer the causal links using inverse variance-weighted, maximum likelihood, MR-Egger, weighted median, weighted mode, and Wald ratio methods. Several sensitivity analyses were also utilized to ensure reliable MR results. Finally, we used mediation analysis to identify the pathway from gut microbiota to obesity mediated by plasma metabolites, peripheral cells, and inflammatory cytokines.

Results

MR revealed a causal effect of 44 gut microbiota taxa, 281 plasma metabolites, 27 peripheral cells, and 8 inflammatory cytokines on obesity. Among them, five shared causal gut microbiota taxa belonged to the phylum Actinobacteria, order Bifidobacteriales, family Bifidobacteriaceae, genus Lachnospiraceae UCG008, and species Eubacterium nodatum group. Furthermore, we screened 42 shared causal metabolites, 7 shared causal peripheral cells, and 1 shared causal inflammatory cytokine. Based on known causal metabolites, we observed that the metabolic pathways of D-arginine, D-ornithine, linoleic acid, and glycerophospholipid metabolism were closely related to obesity. Finally, mediation analysis revealed 20 mediation relationships, including the causal pathway from gut microbiota to obesity, mediated by 17 metabolites, 2 peripheral cells, and 1 inflammatory cytokine. Sensitivity analysis represented no heterogeneity or pleiotropy in this study.

Conclusion

Our findings support a causal relationship among gut microbiota, plasma metabolites, peripheral cells, inflammatory cytokines, and obesity. These biomarkers provide new insights into the mechanisms underlying obesity and contribute to its prevention, diagnosis, and treatment.

Gut microbiota and risk of endocarditis: a bidirectional Mendelian randomization study

Background

The associations between gut microbiota and cardiovascular disease have been reported in previous studies. However, the relationship between gut microbiota and endocarditis remains unclear.

Methods

A bidirectional Mendelian randomization (MR) study was performed to detect the association between gut microbiota and endocarditis. Inverse variance weighted (IVW) method was considered the main result. Simultaneously, heterogeneity and pleiotropy tests were conducted.

Results

Our study suggests that family Victivallaceae (p = 0.020), genus Eubacterium fissicatena group (p = 0.047), genus Escherichia Shigella (p = 0.024), genus Peptococcus (p = 0.028) and genus Sellimonas (p = 0.005) play protective roles in endocarditis. Two microbial taxa, including genus Blautia (p = 0.006) and genus Ruminococcus2 (p = 0.024) increase the risk of endocarditis. At the same time, endocarditis has a negative effect on genus Eubacterium fissicatena group (p = 0.048). Besides, no heterogeneity or pleiotropy was found in this study.

Conclusion

Our study emphasized the certain role of specific gut microbiota in patients with endocarditis and clarified the negative effect of endocarditis on gut microbiota.

Does the Human Gut Virome Contribute to Host Health or Disease?

The human gastrointestinal (GI) tract harbors eukaryotic and prokaryotic viruses and their genomes, metabolites, and proteins, collectively known as the "gut virome". This complex community of viruses colonizing the enteric mucosa is pivotal in regulating host immunity. The mechanisms involved in cross communication between mucosal immunity and the gut virome, as well as their relationship in health and disease, remain largely unknown. Herein, we review the literature on the human gut virome's composition and evolution and the interplay between the gut virome and enteric mucosal immunity and their molecular mechanisms. Our review suggests that future research efforts should focus on unraveling the mechanisms of gut viruses in human homeostasis and pathophysiology and on developing virus-prompted precision therapies.