A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease

There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (4489 samples). Within most studies, microbiome-based machine learning models accurately classify PD patients (average AUC 71.9%). However, these models are study-specific and do not generalise well across other studies (average AUC 61%). Training models on multiple datasets improves their generalizability (average LOSO AUC 68%) and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Moreover, meta-analysis of shotgun metagenomes delineates PD-associated microbial pathways potentially contributing to gut health deterioration and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, microbial pathways for solvent and pesticide biotransformation are enriched in PD. These results align with epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbes modulate their toxicity. Here, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.

Association between red blood cell distribution width-to-albumin ratio and depression: a cross-sectional analysis among US adults, 2011-2018

BACKGROUND

Red blood cell distribution width (RDW)-to-albumin ratio (RAR) is a novel index. Its relationship with depression, a common and complex psychiatric disorder, remains unclear. This study utilized the National Health and Nutrition Examination Survey (NHANES) database to investigate this relationship.

METHODS

Multivariate logistic regression, restricted cubic spline (RCS) regression, receiver operating characteristic (ROC) analysis, and sensitivity analyses were used to examine the relationship between RAR and depression based on NHANES data from 2011-2018. The study also used subgroup analyses and interaction tests to explore whether the relationship was stable across populations.

RESULTS

RAR was positively associated with depression in 18,150 participants aged ≥ 20 years. In fully adjusted models, each one-unit increase in RAR was associated with a 22% increase in the likelihood of depression [1.22 (1.05, 1.41)]. Participants in the highest quartile of RAR had a 30% higher risk of depression than those in the lowest quartile of RAR [1.30 (1.04, 1.63)]. Subgroup analyses revealed that the association between RAR and depression was significantly stronger among men, alcohol-drinking and high-income groups.

CONCLUSIONS

Higher baseline RAR was associated with an increased risk of depression in US adults and was more informative than RDW, albumin, and hemoglobin-to-RDW ratio (HRR). Further large-scale prospective studies are needed to analyze the role of RAR in depression. These findings emphasize that RAR can be a simple, reliable and cost-effective predictor of depression in clinical practice.

Chronic Exposure to Fluxapyroxad Exacerbated Susceptibility to Colitis in Mice via a Gut Microbiota-Indole Derivatives-Th17/Treg Cell Balance Axis

Fluxapyroxad is the most commonly used succinate dehydrogenase inhibitor fungicide. This work investigated its adverse effects on colitis susceptibility and explored the underlying mechanisms based on a mouse model. After 13 weeks of exposure at the acceptable daily intake (ADI) level, fluxapyroxad exacerbated the susceptibility to colitis, impaired the intestinal barrier, and elevated proinflammatory cytokines and chemokines of the colon in mice. It was found that this toxic effect was caused by the disruption of the gut microbiome. Specifically, the abundance of Lachnospiraceae and Muribaculaceae decreased, while Desulfovibrionaceae and Eggerthellaceae increased. Altered microbiota reduced fecal indole derivatives, including indole-3-lactic acid (ILA), indole-3-acetic acid (IAA), and indole-3-acrylic acid (IArA), inhibiting aryl hydrocarbon receptor (AHR) activation, disrupting immune homeostasis by overactivating Th17 cells and insufficient Treg cell differentiation, and causing mild colonic inflammation. Oral antibiotic-treated mice and fecal transfer experiments validated the pathway. Susceptibility to colitis induced by fluxapyroxad was not detected in the oral antibiotic-treated mice. Fecal transfer of the disordered gut microbiota caused by fluxapyroxad could aggravate the severity of colitis in recipient oral antibiotic-treated mice that did not receive fluxapyroxad exposure. In conclusion, chronic fluxapyroxad exposure at the ADI level exacerbated colitis via a gut microbiota-indole derivatives-Treg/Th17 cell balance axis, offering a new risk assessment perspective of fluxapyroxad.

Effect of different fermentation substrates on rumen microorganisms and microbe-derived extracellular vesicles (EVs)

Diet composition and microbiota play a crucial role in animal health and productivity. The study aimed to explore the effects of different fermentation substrates on rumen microbiota and their extracellular vesicles (EVs). Straw (fiber), corn starch (starch), and casein (protein) were used as substrates for in vitro fermentation. After 24 h of fermentation, samples were collected and subjected to 16 S rRNA gene sequencing to analyze rumen microbiota. Microbe-derived EVs were extracted and their morphology and particle size were determined. Results showed that fiber increased the diversity of rumen microorganisms, protein increased richness, and starch decreased both diversity and richness of the microbes. Rumen microbiota was dominated by Firmicutes in the protein group, Bacteroidota in the fiber group and Prevotella in the starch group. Principal co-ordinates analysis (PCoA) revealed significant differences in microbial community structure among the three groups. LEfSe analysis at the genus level identified that Prevotella, Succinivibrio, Clostridia_UCG_014 were enriched in the starch group, whereas Acidaminococcus, Muribaculaceae, Pyramidobacter were enriched in the protein group. For the fiber group, the enriched genera included F082 and Rikenellaceae_RC9_gut_group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis showed that the top ten microbial functions were mainly involved in signaling and cellular processes (K06142, K03310, K02030, K06147, K01990, K02004, K01992, K02014) and genetic information processing (K06180, K03088), with the fiber group showing better performance in these processes compared to other two groups. Additionally, the particle sizes of extracellular vesicles ranged from 20 to 400 nm, with an average particle distribution coefficients (PDI) close to 0.3 in each group, indicating uniform particle size. Overall, different fermentation substrates significantly affected the diversity of rumen microbes, without affecting the morphology and particle size of microbial EVs.

Artificial intelligence in autoimmune diseases: a bibliometric exploration of the past two decades

Objective

Autoimmune diseases have long been recognized for their intricate nature and elusive mechanisms, presenting significant challenges in both diagnosis and treatment. The advent of artificial intelligence technology has opened up new possibilities for understanding, diagnosing, predicting, and managing autoimmune disorders. This study aims to explore the current state and emerging trends in the field through bibliometric analysis, providing guidance for future research directions.

Methods

The study employed the Web of Science Core Collection database for data acquisition and performed bibliometric analysis using CiteSpace, HistCite Pro, and VOSviewer.

Results

Over the past two decades, 1,695 publications emerged in this research field, including 1,409 research articles and 286 reviews. This investigation unveils the global development landscape predominantly led by the United States and China. The research identifies key institutions, such as Brigham & Women's Hospital, influential journals like the Annals of the Rheumatic Diseases, distinguished authors including Katherine P. Liao, and pivotal articles. It visually maps out the research clusters' evolutionary path over time and explores their applications in patient identification, risk factors, prognosis assessment, diagnosis, classification of disease subtypes, monitoring and decision support, and drug discovery.

Conclusion

AI is increasingly recognized for its potential in the field of autoimmune diseases, yet it continues to face numerous challenges, including insufficient model validation and difficulties in data integration and computational power. Significant advancements have been demanded to enhance diagnostic precision, improve treatment methodologies, and establish robust frameworks for data protection, thereby facilitating more effective management of these complex conditions.

Microbial imbalance in the gut: a new frontier in Rheumatoid arthritis research

A chronic autoimmune illness that causes joint destruction and inflammation, rheumatoid arthritis (RA) often results in disability. Genetic, environmental, and immune system variables all have a role in the pathophysiology of RA. The complex community of bacteria that live in the gastrointestinal system, known as the gut microbiota, has been implicated in the onset and progression of RA in recent years, according to mounting data. An imbalance in the gut microbiota's composition, known as dysbiosis, has been noted in RA patients. This imbalance may impact inflammatory pathways and immunological responses, which in turn may contribute to the development and severity of the illness. Research has shown that some bacterial species, including Firmicutes, Bacteroidetes, and Proteobacteria, are either more abundant or less prevalent in RA patients than in healthy people. The gut-immune system axis may be modulated, immunological tolerance may be affected, and pro-inflammatory cytokine production may be enhanced by these microbial changes, all of which may lead to systemic inflammation linked to RA. Moreover, changes in intestinal permeability and a rise in microbial metabolite translocation may make autoimmune reactions worse. Probiotics, antibiotics, and dietary changes have also been investigated as possible treatment approaches to help RA patients regain the balance of their gut microbiota. Still up for debate, however, are the precise ways in which the gut microbiome affects RA. Comprehending the complex connection between gut microbiota and RA may give new perspectives on managing and preventing the condition, as well as future prospects for medicines that target the microbiome.

Roles of the gut microbiota in hepatocellular carcinoma: from the gut dysbiosis to the intratumoral microbiota

Hepatocellular carcinoma (HCC) is closely linked to alterations in the gut microbiota. This dysbiosis is characterized by significant changes in the microbial population, which correlate with the progression of HCC. Gut dysbiosis ultimately promotes HCC development in several ways: it damages the integrity of the gut-vascular barrier (GVB), alters the tumor microenvironment (TME), and even affects the intratumoral microbiota. Subsequently, intratumoral microbiota present a characteristic profile and play an essential role in HCC progression mainly by causing DNA damage, mediating tumor-related signaling pathways, altering the TME, promoting HCC metastasis, or through other mechanisms. Both gut microbiota and intratumoral microbiota have dual effects on HCC progression; a comprehensive understanding of their complex biological roles will provide a theoretical foundation for potential clinical applications in HCC treatment.

Gut microbiota, inflammatory proteins and bone mineral density in different age groups: A Mendelian randomization study

Several studies have indicated a potential association between gut microbiota and bone density. However, the causal relationship between gut microbiota and bone mineral density across different age groups, as well as the potential role of inflammatory proteins as mediators, remains unclear. Gut microbiota, inflammatory proteins, and bone mineral density (BMD) were identified in various age groups using summary data from large-scale genome-wide association studies. Mendelian randomization was employed to examine the causal connections between gut microbiota, inflammatory proteins, and BMD in different age groups, primarily utilizing inverse variance weighted as the statistical method. Furthermore, the potential role of inflammatory proteins as mediators in the pathway from gut microbiota to BMD was investigated. Eight positive and 19 negative causal relationships between gut microbiota and BMD were observed across various age groups. We also identified 14 positive and 8 negative causal relationships between inflammatory proteins and BMD in different age groups. Inflammatory proteins did not appear to function as mediators in the pathway from gut microbiota to BMD. Gut microbiota and inflammatory proteins were causally linked to BMD; however, inflammatory proteins did not seem to function as mediators in the pathway from gut microbiota to BMD because the effects of intestinal flora on bone density and the effects of inflammatory factors on bone density were in different directions.

Vitamin E ameliorates blood cholesterol level and alters gut microbiota composition: A randomized controlled trial

BACKGROUND AND AIMS

Antioxidants, including vitamin E (VE) and grape seed extract (GSE), as anti-aging supplementation have been widely used to improve human health. The gut microbiota plays a crucial role in health and affects the treatment effect of various interventions. However, the role of gut microbiota in VE remains unclear. This study aimed to assess the longitudinal impact of VE treatment on body health and the gut microbiota.

METHODS AND RESULTS

A randomized controlled trial was conducted with 90 healthy individuals. The participants were randomly assigned to three groups: a treatment group receiving VE, another antioxidant treatment group receiving GSE, and a control group receiving a placebo. We found that VE ameliorated blood cholesterol levels by reducing the levels of low-density lipoprotein cholesterol (LDL-C) in healthy volunteers. After the intervention, there was an increase in the relative abundance of short-chain fatty acid (SCFA)-producing bacteria and bile acid metabolizers. Specifically, the abundances of Lachnospira sp. and Faecalibacterium spp. increased in the VE. Interestingly, the gut microbiota of poor responders harbored a greater proportion of disease-associated bacterial species.

CONCLUSIONS

VE could promote health by lowering LDL-C, partly and indirectly by affecting gut bacteria with the ability to produce SCFAs or metabolize bile acids.

REGISTRATION NUMBER FOR CLINICAL TRIALS

The clinical trial was registered on August 28, 2021. Registration number was ChiCTR2100050567 (https://www.chictr.org.cn).

Perturbations in gut microbiota composition in patients with autoimmune neurological diseases: a systematic review and meta-analysis

Studies suggest that gut dysbiosis occurs in autoimmune neurological diseases, but a comprehensive synthesis of the evidence is lacking. Our aim was to systematically review and meta-analyze the correlation between the gut microbiota and autoimmune neurological disorders to inform clinical diagnosis and therapeutic intervention. We searched the databases of PubMed, Embase, Web of Science, and the Cochrane Library until 1 March 2024 for research on the correlation between gut microbiota and autoimmune neurological disorders. A total of 62 studies provided data and were included in the analysis (n = 3,126 patients, n = 2,843 healthy individuals). Among the included studies, 42 studies provided data on α-diversity. Regarding α-diversity, except for Chao1, which showed a consistent small decrease (SMD = -0.26, 95% CI = -0.45 to -0.07, p < 0.01), other indices demonstrated no significant changes. While most studies reported significant differences in β-diversity, consistent differences were only observed in neuromyelitis optica spectrum disorders. A decrease in short-chain fatty acid (SCFA)-producing bacteria, including Faecalibacterium and Roseburia, was observed in individuals with autoimmune encephalitis, neuromyelitis optica spectrum disorders, myasthenia gravis, and multiple sclerosis. Conversely, an increase in pathogenic or opportunistic pathogens, including Streptococcus and Escherichia-Shigella, was observed in these patients. Subgroup analyses assessed the confounding effects of geography and immunotherapy use. These findings suggest that disturbances of the gut flora are associated with autoimmune neurological diseases, primarily manifesting as non-specific and shared microbial alterations, including a reduction in SCFA-producing bacteria and an increase in pathogenic or opportunistic pathogens.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42023410215.

Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people

The gut microbiome is amenable to dietary interventions, and polyphenol-rich diets have been shown to enhance abundances of bacteria associated with short-chain fatty acid (SCFA) production. We examined the effects of a strawberry-based intervention on the gut microbiome of 69 healthy elderly German adults. Participants in five groups consumed varying amounts of strawberries, freeze-dried strawberries, and capers in olive oil over 10 weeks as part of a randomized controlled trial. 16S rRNA sequencing was used to analyze differences in microbial composition, diversity, phenotypes, differential abundance, and functional pathways. The intervention group featuring the highest amounts of fresh and freeze-dried strawberries without capers in olive oil (group 4) showed changes in gut microbial diversity and differential abundance that could be linked to improved health. Beta diversity, based on weighted UniFrac distances, increased significantly (P = 0.0035), potentially pathogenic bacteria decreased (P = 0.04), and abundances of SCFA-producing genera Faecalibacterium and Prevotella increased significantly. Other findings included a significant reduction of CAG-352, Preveotellaceae_NK3B31-group, and Eubacterium coprostanoligenes (group 2), and a trend of lowered Firmicutes-to-Bacteroidetes ratio (P = 0.067) and a reduction in Ruminococcaceae (group 3). Our findings suggest that a dietary intervention based on strawberries can positively alter the gut microbiota of healthy elderly people as seen in an enrichment of SCFA-producing genera, increased diversity, and a reduction in potentially pathogenic bacteria.IMPORTANCEAging is often associated with changes in the gut microbiome, including a decline in beneficial bacteria and an increase in potentially pathogenic species. Addressing these changes through lifestyle interventions is of significant interest. Our study demonstrates that a 10-week dietary intervention with strawberries can beneficially modulate gut microbial composition and diversity in healthy elderly individuals. Notably, the group consuming the highest amount of strawberries (without capers in olive oil) initially had higher abundances of potentially pathogenic bacteria. Here, the intervention led to increased abundances of the beneficial genera Faecalibacterium and Prevotella, which are linked to health benefits including reduced inflammation and improved lipid metabolism. These findings suggest that strawberry consumption can positively influence gut microbial composition, thereby contributing to overall health and disease prevention in older adults.

The role of the gastrointestinal microbiome on rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis and reactive arthritis: A systematic review

BACKGROUND

There is an increasing body of literature observing a state of dysbiosis in the gut microbiome in different autoimmune conditions including inflammatory arthritis. It is unknown whether the microbiome can be a biomarker for prognostication purposes or for stratification of treatment strategies. This review aims to evaluate the existing evidence on the association between the microbiome and inflammatory arthritis, including rheumatoid arthritis (RA), psoriatic arthritis (PsA) and ankylosing spondylitis (AS) and reactive arthritis (ReA) population groups.

METHODS

This systematic review was performed based on methods from the Cochrane guidelines and reported based on PRISMA criteria. Studies exploring the microbiome of patients with RA, AS, PsA or ReA compared with controls via 16s rRNA or shotgun sequencing were evaluated. The outcomes of interest include alpha and beta diversity, abundance or depletion of organisms and functional analysis. Literature up to August 2024 was retrieved searching the databases PubMed, Medline, ScienceDirect, Scopus, Web of Science, Cochrane, EMBASE and CINAHL. All references were systematically evaluated by two reviewers. Quality of the studies were evaluated by the Newcastle-Ottawa Scale.

FINDINGS

The review yielded 25,794 search results, of which 53 studies were included for the RA group, 34 studies for the AS group, 6 studies for the PsA group and 2 studies for the ReA group. Reduced diversity has been observed in disease groups and in patients with higher disease activity.

INTERPRETATION

There are limited longitudinal studies on the role of the microbiome in inflammatory arthritis, in particular PsA. Existing cross-sectional studies suggest altered microbiome in disease states compared with controls. Further studies are required to understand the utility of the microbiome as a biomarker to better understand prognosis and tailor treatments.

Exploring precision treatments in immune-mediated inflammatory diseases: Harnessing the infinite potential of nucleic acid delivery

Immune-mediated inflammatory diseases (IMIDs) impose an immeasurable burden on individuals and society. While the conventional use of immunosuppressants and disease-modifying drugs has provided partial relief and control, their inevitable side effects and limited efficacy cast a shadow over finding a cure. Promising nucleic acid drugs have shown the potential to exert precise effects at the molecular level, with different classes of nucleic acids having regulatory functions through varying mechanisms. For the better delivery of nucleic acids, safe and effective viral vectors and non-viral delivery systems (including liposomes, polymers, etc.) have been intensively explored. Herein, after describing a range of nucleic acid categories and vectors, we focus on the application of therapeutic nucleic acid delivery in various IMIDs, including rheumatoid arthritis, inflammatory bowel disease, psoriasis, multiple sclerosis, asthma, ankylosing spondylitis, systemic lupus erythematosus, and uveitis. Molecules implicated in inflammation and immune dysregulation are abnormally expressed in a series of IMIDs, and their meticulous modulation through nucleic acid therapy results in varying degrees of remission and improvement of these diseases. By synthesizing findings centered on specific molecular targets, this review delivers a systematic elucidation and perspective towards advancing and utilization of nucleic acid therapeutics for managing IMIDs.

Impact of commercial gut health interventions on caecal metagenome and broiler performance

BACKGROUND

Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.

RESULTS

Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.

CONCLUSIONS

All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.

The Role of Gut Microbiota Dysbiosis in Erectile Dysfunction: From Pathophysiology to Treatment Strategies

Erectile dysfunction (ED) is a prevalent male sexual disorder characterized by the persistent inability to achieve or maintain an erection sufficient for satisfactory sexual performance. While its etiology is multifactorial, encompassing vascular, neurological, hormonal, and psychological components, emerging evidence suggests a significant role for gut microbiota dysbiosis in its development. The gut microbiota influences various metabolic, inflammatory, and neuropsychological processes critical to erectile function. Dysbiosis can lead to systemic inflammation, endothelial dysfunction, hormonal imbalances, and altered neurotransmitter production, all of which are key factors in ED pathogenesis. This narrative review synthesizes current research on the association between gut microbiota alterations and ED, highlighting specific bacterial taxa implicated in ED through mechanisms involving inflammation, metabolic disturbances, and hormonal regulation. This review explores potential mechanisms linking gut microbiota and ED, including pro-inflammatory cytokines, gut barrier integrity disruption, metabolic disorders, psychological factors via the gut-brain axis, and hormonal regulation. Furthermore, the gut microbiota offers promising avenues for developing non-invasive biomarkers and therapeutic interventions such as probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation. Future research should focus on longitudinal studies, mechanistic explorations, and clinical trials to validate these findings and translate them into clinical practice. Understanding the interplay between the gut microbiota and erectile function could unveil novel diagnostic biomarkers and pave the way for innovative treatments targeting the microbiota, ultimately improving men's sexual and overall health.

Inflammatory disease microbiomes share a functional pathogenicity predicted by C-reactive protein

We examine disease-specific and cross-disease functions of the human gut microbiome by colonizing germ-free mice, at risk for inflammatory arthritis, colitis, or neuroinflammation, with over 100 human fecal microbiomes from subjects with rheumatoid arthritis, ankylosing spondylitis, multiple sclerosis, ulcerative colitis, Crohn's disease, or colorectal cancer. We find common inflammatory phenotypes driven by microbiomes from individuals with intestinal inflammation or inflammatory arthritis, as well as distinct functions specific to microbiomes from multiple sclerosis patients. Inflammatory disease in mice colonized with human microbiomes correlated with systemic inflammation, measured by C-reactive protein, in the human donors. These cross-disease patterns of human microbiome pathogenicity mirror features of the inflammatory diseases, including therapeutic targets and the presence or absence of systemic inflammation, suggesting shared and disease-specific mechanisms by which the microbiome is shaped and drives pathogenic inflammatory responses.

Lactobacillus acidophilus alleviate Salmonella enterica Serovar Typhimurium-induced murine inflammatory/oxidative responses via the p62-Keap1-Nrf2 signaling pathway and cecal microbiota

Background

Salmonella enterica Serovar Typhimurium (S. Typhimurium) infection can cause inflammation and oxidative stress in the body, leading to gastroenteritis, fever and other diseases in humans and animals. More and more studies have emphasized the broad prospects of probiotics in improving inflammation and oxidative stress, but the ability and mechanism of Lactobacillus acidophilus (LA) to alleviate the inflammatory/oxidative reaction caused by pathogens are still unclear.

Methods and results

In this study, we treated the mice with LA for 14 days, infected them with S. Typhimurium for 24 h, and sacrificed the mice to collect samples. We found that the early intervention of LA alleviated the pathological injury and reversed the down-regulation of the duodenal and hepatic tight junction protein mRNA levels caused by S. Typhimurium infection. Compared with S. Typhimurium group, LA early intervention increased the expression of antioxidant enzymes, but decreased the levels of serum malondialdehyde (MDA), interleukin-8 and tumor necrosis factor-α (TNF-α). Additionally, LA early intervention significantly increased Nrf2 mRNA expression in the liver and decreased Keap1 mRNA expression in the duodenum compared to the S. Typhimurium group. Furthermore, early LA treatment reduced the abundance of Bacteroides acidificiens, increased the abundance of Akkermansia, and alleviated the decrease in SCFAs levels in the cecum of S. Typhimurium-infected mice. Spearman correlation analysis showed that there was a certain correlation between cecal flora and serum indicators and short chain fatty acids.

Conclusion

Taken together, the results indicate that LA early intervention may alleviates S. Typhimurium-induced inflammation and oxidative responses in mice by activating the p62-Keap1-Nrf2 signaling pathway and regulating the gut microbial community.

Significance and impact of the study

Exploring the ability of LA to resist animal oxidative stress and microflora regulation caused by pathogenic microbes, so as to provide more options for developing healthy disease-resistant feed additives.

Roseburia intestinalis-derived butyrate alleviates neuropathic pain

Approximately 20% of patients with shingles develop postherpetic neuralgia (PHN). We investigated the role of gut microbiota in shingle- and PHN-related pain. Patients with shingles or PHN exhibited significant alterations in their gut microbiota with microbial markers predicting PHN development among patients with shingles. Functionally, fecal microbiota transplantation from patients with PHN to mice heightened pain sensitivity. Administration of Roseburia intestinalis, a bacterium both depleted in patients with shingles and PHN, alleviated peripheral nerve injury-induced pain in mice. R. intestinalis enhanced vagal neurotransmission to the nucleus tractus solitarius (NTS) to suppress the central amygdala (CeA), a brain region involved in pain perception. R. intestinalis-generated butyrate activated vagal neurons through the receptor, G protein-coupled receptor 41 (GPR41). Vagal knockout of Gpr41 abolished the effects of R. intestinalis on the NTS-CeA circuit and reduced pain behaviors. Overall, we established a microbiota-based model for PHN risk assessment and identified R. intestinalis as a potential pain-alleviating probiotic.

Gut microbiota strain richness is species specific and affects engraftment

Despite the fundamental role of bacterial strain variation in gut microbiota function1-6, the number of unique strains of a species that can stably colonize the human intestine is still unknown for almost all species. Here we determine the strain richness (SR) of common gut species using thousands of sequenced bacterial isolates with paired metagenomes. We show that SR varies across species, is transferable by faecal microbiota transplantation, and is uniquely low in the gut compared with soil and lake environments. Active therapeutic administration of supraphysiologic numbers of strains per species increases recipient SR, which then converges back to the population average after dosing is ceased. Stratifying engraftment outcomes by high or low SR shows that SR predicts microbial addition or replacement in faecal transplants. Together, these results indicate that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and thereby influence strain addition and replacement in faecal microbiota transplantation and defined live biotherapeutic products.

Exploring the gut microbiota landscape in cow milk protein allergy: Clinical insights and diagnostic implications in pediatric patients

Cow milk protein allergy (CMPA) is a significant health concern characterized by adverse immune reactions to cow milk proteins. Biomarkers for the accurate diagnosis and prognosis of CMPA are lacking. This study analyzed the clinical features of CMPA, and 16S RNA sequencing was used to investigate potential biomarkers through fecal microbiota profiling. Children with CMPA exhibit a range of clinical symptoms, including gastrointestinal (83% of patients), skin (53% of patients), and respiratory manifestations (26% of patients), highlighting the complexity of this condition. Laboratory analysis revealed significant differences in red cell distribution width and inflammatory markers between the CMPA and control groups, suggesting immune activation and inflammatory responses in CMPA. Microbial diversity analysis revealed higher specific diversity indices in the CMPA group compared with those in control group, with significant differences at the genus and species levels. Bacteroides were more abundant in the CMPA group, whereas Bifidobacterium, Ruminococcus, Faecalibacterium, and Parabacteroides were less abundant. The control group exhibited a balanced microbial profile, with a predominant presence of Bifidobacterium bifidum and Akkermansia muciniphila. The significant abundance of Bifidobacterium in the control group (23.19% vs. 9.89% in CMPA) was associated with improved growth metrics such as height and weight, suggesting its potential as a probiotic to prevent CMPA and enhance gut health. Correlation analysis linked specific microbial taxa such as Coprococcus and Bifidobacterium to clinical parameters such as family allergy history, weight, and height, providing insights into CMPA pathogenesis. Significant differences in bacterial abundance suggested diagnostic potential, with a panel of 6 bacteria achieving high predictive accuracy (area under curve = 0.8708). This study emphasizes the complex relationship between the gut microbiota and CMPA, offering valuable insights into disease mechanisms and diagnostic strategies.

The influence of alterations in the composition of intestinal microbiota on neurovascular coupling and cognitive dysfunction in individuals afflicted with CSVD

INTRODUCTION

An expanding body of research has explored the crucial role of gut microbiota in cerebral small vessel disease (CSVD). The objective of this study is to investigate alterations in the gut microbiota structure among CSVD patients, to explore the correlation between differential taxonomic levels and the neurovascular coupling index as well as cognitive function and to elucidate the imaging and biomarkers of mild cognitive impairment (MCI) in CSVD.

METHODS

We enrolled 104 patients with CSVD and 40 healthy controls (HC). Based on cognitive test scores, CSVD patients were categorized into a cognitively normal group (CSVD-NCI, n=61) and a mild cognitive impairment group (CSVD-MCI, n=43). Performing magnetic resonance imaging (MRI) scans, gut microbiota analysis, as well as clinical and neuropsychological assessments for all participants. Based on arterial spin labeling (ASL) and blood oxygen level-dependent (BOLD) imaging data, cerebral blood flow (CBF) and neural activity indices are computed. The coupling indices of CBF/mReHo, CBF/mfALFF, CBF/mALFF, and CBF/mDC are calculated to assess the whole-brain neurovascular coupling changes in patients with CSVD.

RESULTS

Species annotation revealed differences in the composition at the phylum and genus levels among the HC, CSVD-NCI, and CSVD-MCI groups. Additionally, differential analysis using the Kruskal-Wallis test demonstrated specific dominant microbial communities in all three groups. The relative abundance of certain dominant microbial communities in CSVD patients exhibited correlations with neurovascular coupling and cognitive function. The combined assessment of Bacteroides genus and CBF/mDC proved effective in distinguishing between CSVD-NCI and CSVD-MCI, providing a novel non-invasive approach for the diagnosis of MCI in CSVD.

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.

Patterns of antibiotic resistance genes and virulence factor genes in the gut microbiome of patients with osteoarthritis and rheumatoid arthritis

Background

The gut microbiome compositions of osteoarthritis (OA) and rheumatoid arthritis (RA) patients have been revealed; however, the functional genomics, particularly antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), have not yet been explored.

Methods

We used gut metagenomic data to elucidate the distribution of ARGs and VFGs. Building on these differences in gut microbiome, we developed a diagnostic model using a random forest classifier based on ARG and VFG abundances.

Results

Our results indicated that both OA and RA patients exhibit significantly higher alpha diversity in ARGs, as measured by observed genes, the Shannon index, and the Simpson index, compared to healthy controls. However, this increased diversity is not significantly different between OA and RA patients. In contrast, VFGs showed higher diversity in RA patients than in healthy individuals, which was not as pronounced in OA patients. An analysis of the top 20 ARGs and VFGs revealed a largely similar composition between the three groups, with notable exceptions of certain genes that were uniquely enriched in either OA or RA patients. This suggests unique microbial patterns associated with each condition. Our beta diversity analysis further demonstrated distinct distributions of ARG and VFG profiles across the three groups, with several genes significantly enriched in both OA and RA patients, indicating potential markers for these diseases. The model achieved high accuracy (74.7-83.6%) when distinguishing both OA and RA from healthy controls using ARG profiles and substantial accuracy using VFG profiles.

Conclusion

These results support the potential of ARGs and VFGs as reliable biomarkers for diagnosing OA and RA.

Dynamics of the gut microbiome in individuals at risk of rheumatoid arthritis: a cross-sectional and longitudinal observational study

OBJECTIVES

This work aimed to resolve the conflicting reports on Prevotellaceae abundance in the development of rheumatoid arthritis (RA) and to observe structural, functional and temporal changes in the gut microbiome in RA progressors versus non-progressors.

METHODS

Individuals at risk of RA were defined by the presence of anticyclic citrullinated protein (anti-CCP) antibodies and new musculoskeletal symptoms without clinical synovitis. Baseline sampling included 124 participants (30 progressed to RA), with longitudinal sampling of 19 participants (5 progressed to RA) over 15 months at five timepoints. Gut microbiome taxonomic alterations were investigated using 16S rRNA amplicon sequencing and confirmed with shotgun metagenomic DNA sequencing on 49 samples.

RESULTS

At baseline, CCP+ at risk progressors showed significant differences in Prevotellaceae abundance compared with non-progressors, contingent on intrinsic RA risk factors and time to progression. Longitudinal sampling revealed gut microbiome instability in progressors 10 months before RA onset, a phenomenon absent in non-progressors. This may indicate a late microbial shift before RA onset, with Prevotellaceae contributing but not dominating these changes. Structural changes in the gut microbiome during arthritis development were associated with increased amino acid metabolism.

CONCLUSION

These data suggest conflicting reports on Prevotellaceae overabundance are likely due to sampling within a heterogeneous population along a dynamic disease spectrum, with certain Prevotellaceae strains/clades possibly contributing to the establishment and/or progression of RA. Gut microbiome changes in RA may appear at the transition to clinical arthritis as a late manifestation, and it remains unclear whether they represent a primary or secondary phenomenon.

The interplay between diet and the gut microbiome: implications for health and disease

Diet has a pivotal role in shaping the composition, function and diversity of the gut microbiome, with various diets having a profound impact on the stability, functionality and diversity of the microbial community within our gut. Understanding the profound impact of varied diets on the microbiome is crucial, as it will enable us not only to make well-informed dietary decisions for better metabolic and intestinal health, but also to prevent and slow the onset of specific diet-related diseases that stem from suboptimal diets. In this Review, we explore how geographical location affects the gut microbiome and how different diets shape its composition and function. We examine the mechanisms by which whole dietary regimes, such as the Mediterranean diet, high-fibre diet, plant-based diet, high-protein diet, ketogenic diet and Western diet, influence the gut microbiome. Furthermore, we underscore the need for exhaustive studies to better understand the causal relationship between diet, host and microorganisms for the development of precision nutrition and microbiome-based therapies.

Alterations of the microbiome across body sites in systemic lupus erythematosus: A systematic review and meta-analysis

BACKGROUND

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear etiology. Growing evidence suggests the microbiome plays a role in SLE pathogenesis. However, findings are inconsistent across studies due to factors like small sample sizes and geographical variations. A comprehensive meta-analysis is needed to elucidate microbiome alterations in SLE.

OBJECTIVE

This study aimed to provide a systematic overview of microbiota dysbiosis across body sites in SLE through a meta-analysis of alpha diversity indices, beta diversity indices, and abundance taxa of microbiome.

METHODS

A literature search was conducted across four databases to identify relevant studies comparing SLE patients and healthy controls. Extracted data encompassed alpha and beta diversity metrics, as well as bacterial, fungal, and viral abundance across gut, oral, skin, and other microbiota. Study quality was assessed using the Newcastle-Ottawa Scale. Standardized mean differences and pooled effect sizes were calculated through meta-analytical methods.

RESULTS

The analysis showed reduced alpha diversity and distinct beta diversity in SLE, particularly in the gut microbiota. Taxonomic analysis revealed compositional variations in bacteria from the gut and oral cavity. However, results for fungi, viruses, and bacteria from other sites were inconsistent due to limited studies.

CONCLUSIONS

This meta-analysis offers a comprehensive perspective on microbiome dysbiosis in SLE patients across diverse body sites and taxa. The observed variations underscore the microbiome's potential role in SLE pathogenesis. Future research should address geographical variations, employ longitudinal designs, and integrate multi-omics approaches.

Immune-Mediated Inflammatory Diseases and Cancer - a dangerous liaison

Patients with Immune-Mediated Inflammatory Diseases (IMIDs) are known to have an elevated risk of developing cancer, but the exact causative factors remain subject to ongoing debate. This narrative review aims to present the available evidence concerning the intricate relationship between these two conditions. Environmental influences and genetic predisposition lead to a dysregulated immune response resulting in chronic inflammation, which is crucial in the pathogenesis of IMIDs and oncogenic processes. Mechanisms such as the inflammatory microenvironment, aberrant intercellular communication due to abnormal cytokine levels, excessive reparative responses, and pathological angiogenesis are involved. The chronic immunosuppression resulting from IMIDs treatments further adds to the complexity of the pathogenic scenario. In conclusion, this review highlights critical gaps in the current literature, suggesting potential avenues for future research. The intricate interplay between IMIDs and cancer necessitates more investigation to deepen our understanding and improve patient management.

Association of lipid-lowering drugs with gut microbiota: A Mendelian randomization study

BACKGROUND

The gut microbiota can be influenced by lipid metabolism. We aimed to evaluate the impact of lipid-lowering medications, such as proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibitors, Niemann-Pick C1-Like 1 protein (NPC1L1) inhibitors, and 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) inhibitors, on gut microbiota through drug target Mendelian randomization (MR) investigation.

METHODS

We used genetic variants that were associated with low-density lipoprotein cholesterol (LDL-C) in genome-wide association studies and located within or near drug target genes as proxies for lipid-lowering drug exposure. In addition, expression trait loci in drug target genes were used as complementary genetic tools. We used effect estimates calculated using inverse variance weighted MR (IVW-MR) and summary data-based MR (SMR). Multiple sensitivity analyses were performed.

RESULTS

Genetic proxies for lipid-lowering drugs broadly affected the abundance of gut microbiota. High expression of NPC1L1 was significantly associated with an increase in the genus Eggerthella (β = 1.357, SE = 0.337, P = 5.615 × 10-5). An HMGCR-mediated increase in LDL-C was significantly associated with the order Pasteurellales (β = 0.489, SE = 0.123, P = 6.955 × 10-5) and the genus Haemophilus (β = 0.491, SE = 0.125, P = 8.379 × 10-5), whereas a PCSK9-mediated increase in LDL-C was associated with the genus Terrisporobacter (β = 0.666, SE = 0.127, P = 1.649 × 10-5). No pleiotropy was detected.

CONCLUSIONS

This drug target MR highlighted the potential interventional effects of lipid-lowering drugs on the gut microbiota and separately revealed the possible effects of different types of lipid-lowering drugs on specific gut microbiota.

Risk factors and clinical outcomes associated with multiple as opposed to single pathogens detected on the gastrointestinal disease polymerase chain reaction assay

BACKGROUND

The use of gastrointestinal disease multiplex polymerase chain reaction (GI PCR) testing has become common for suspected gastrointestinal infection. Patients often test positive for multiple pathogens simultaneously through GI PCR, although the clinical significance of this is uncertain.

METHODS

This retrospective cohort study investigated risk factors and clinical outcomes associated with detection of multiple (as opposed to single) pathogens on GI PCR. We included adult patients who underwent GI PCR testing from 2020 to 2023 and had one or more pathogens detected. We compared patients with multiple versus those with single pathogens and hypothesized that immunosuppression would be a risk factor for detection of multiple pathogens. We further hypothesized that, during the 90 days after GI PCR testing, patients with multiple pathogens would have worse clinical outcomes such as increased rates of emergency department (ED) visits, death, hospitalization, or ambulatory care visits.

RESULTS

GI PCR was positive in 1341 (29%) of tested patients; 356 patients had multiple pathogens and 985 had one pathogen. The most common pathogens included Enteropathogenic Escherichia coli (EPEC, 27%), norovirus (17%), and Enteroaggregative E. coli (EAEC, 14%) in both multi- and singly positive patients. Immunosuppression was not associated with multiple pathogens (adjusted odds ratio [aOR] 1.35, 95% CI 0.96, 1.86). The factors most associated with multiple pathogens were Hispanic ethnicity (OR 1.86, 95% CI 1.42, 2.45) and chronic kidney disease (OR 1.69, 95% CI 1.13, 2.49). Patients with multiple pathogens were more likely to have ED visits during the 90 days after GI PCR testing (40% vs. 32%, p < 0.01), but they were not more likely to die, be hospitalized, or to have ambulatory medical visits.

CONCLUSIONS

Immunosuppression was not associated with detection of multiple as opposed to single pathogens on GI PCR testing. There were worse clinical outcomes associated with detection of multiple pathogens, although these effects were modest.

A Comprehensive Review of the Triangular Relationship among Diet-Gut Microbiota-Inflammation

The human gastrointestinal tract hosts a complex and dynamic community of microorganisms known as the gut microbiota, which play a pivotal role in numerous physiological processes, including digestion, metabolism, and immune function. Recent research has highlighted the significant impact of diet on the gut microbiota composition and functionality, and the consequential effects on host health. Concurrently, there is growing evidence linking the gut microbiota to inflammation, a key factor in many chronic diseases such as inflammatory bowel disease (IBD), obesity, diabetes, and cardiovascular diseases (CVDs). This review explores how dietary components influence the gut microbiota composition, how these microbial changes affect inflammatory pathways, and the therapeutic implications of modulating this axis for chronic inflammatory disease prevention and management. Beneficial dietary patterns, such as the Mediterranean diet (MD) and plant-based diets, promote a diverse and balanced gut microbiota composition, supporting anti-inflammatory pathways. Conversely, the Western diet (WD), high in saturated fats and refined sugars, is associated with dysbiosis and increased inflammation. With all the links between the three variables considered, this review attempts to offer a thorough examination of the triangle formed by inflammation, the gut microbiota, and food.

Gut microbiome diversity within Clostridia is negatively associated with human obesity

Clostridia are abundant in the human gut and comprise families associated with host health such as Oscillospiraceae, which has been correlated with leanness. However, culturing bacteria within this family is challenging, leading to their detection primarily through 16S rRNA amplicon sequencing, which has a limited ability to unravel diversity at low taxonomic levels, or by shotgun metagenomics, which is hindered by its high costs and complexity. In this cross-sectional study involving 114 Colombian adults, we used an amplicon-based sequencing strategy with alternative markers-gyrase subunit B (gyrB) and DNA K chaperone heat protein 70 (dnaK)-that evolve faster than the 16S rRNA gene. Comparing the diversity and abundance observed with the three markers in our cohort, we found a reduction in the diversity of Clostridia, particularly within Lachnospiraceae and Oscillospiraceae among obese individuals [as measured by the body mass index (BMI)]. Within Lachnospiraceae, the diversity of Ruminococcus_A negatively correlated with BMI. Within Oscillospiraceae, the genera CAG-170 and Vescimonas also exhibited this negative correlation. In addition, the abundance of Vescimonas was negatively correlated with BMI. Leveraging shotgun metagenomic data, we conducted a phylogenetic and genomic characterization of 120 metagenome-assembled genomes from Vescimonas obtained from a larger sample of the same cohort. We identified 17 of the 72 reported species. The functional annotation of these genomes showed the presence of multiple carbohydrate-active enzymes, particularly glycosyl transferases and glycoside hydrolases, suggesting potential beneficial roles in fiber degradation, carbohydrate metabolism, and butyrate production.

IMPORTANCE

The gut microbiota is diverse across various taxonomic levels. At the intra-species level, it comprises multiple strains, some of which may be host-specific. However, our understanding of fine-grained diversity has been hindered by the use of the conserved 16S rRNA gene. While shotgun metagenomics offers higher resolution, it remains costly, may fail to identify specific microbes in complex samples, and requires extensive computational resources and expertise. To address this, we employed a simple and cost-effective analysis of alternative genetic markers to explore diversity within Clostridia, a crucial group within the human gut microbiota whose diversity may be underestimated. We found high intra-species diversity for certain groups and associations with obesity. Notably, we identified Vescimonas, an understudied group. Making use of metagenomic data, we inferred functionality, uncovering potential beneficial roles in dietary fiber and carbohydrate degradation, as well as in short-chain fatty acid production.

Unraveling the association between gut microbiota and chemotherapy efficacy: a two-sample Mendelian randomization study

Emerging evidence has underscored the complex link between gut microbiota and chemotherapy efficacy; however, establishing causality remains elusive due to confounding factors. This study, leveraging bidirectional two-sample Mendelian randomization (MR) analyses, explores the casual relationship between gut microbiota and chemotherapy efficacy. Utilizing genome-wide association study (GWAS) data from the MiBioGen consortium for gut microbiota and IEU Open GWAS for chemotherapy efficacy, we employed genetic variants as instrumental variables (IVs). The inverse variance weighted (IVW) method, weighted median estimator (WME), and MR-Egger regression method were applied, with sensitivity analyses ensuring robustness. Furthermore, we conducted reverse MR analyses between chemotherapy efficacy and identified significant gut microbial taxa. The results indicated that genus Butyricicoccus (OR = 3.7908, 95% CI: 1.4464-9.9350, P = 0.01), Dorea (OR = 3.3295, 95% CI: 1.2794-8.6643, P = 0.01), Hungatella (OR = 2.6284, 95% CI: 1.0548-6.5498, P = 0.04), and Turicibacter (OR = 2.5694, 95% CI: 1.0392-6.3526, P = 0.04) were positively associated with chemotherapy efficacy using the IVW method. Conversely, family Porphyromonadaceae (OR = 0.2283, 95% CI: 0.0699-0.7461, P = 0.01) and genus Eggerthella (OR = 0.4953, 95% CI: 0.2443-1.0043, P = 0.05) exhibited negative associations. WME demonstrated consistent results with IVW method only for genus Eggerthella (OR = 0.3343, 95% CI: 0.1298-0.8610, P = 0.02). No significant heterogeneity or horizontal pleiotropy was observed. Reverse MR analyses revealed no significant causal effect of chemotherapy on identified gut microbiota. This study sheds light on the intricate relationship between gut microbiota, with a particular emphasis on the genus Eggerthella, and chemotherapy efficacy, offering valuable insights for refining cancer treatment strategies.IMPORTANCEGlobal advancements in cancer treatment, particularly in chemotherapy, have notably decreased mortality rates in recent years. However, the correlation between gut microbiota and chemotherapy efficacy remains elusive. Our study, emphasizing the role of genus Eggerthella, represented a crucial advance in elucidating this intricate interplay. The identified associations offer potential therapeutic targets, contributing to global efforts for enhanced treatment precision and improved patient outcomes. Furthermore, our findings hold promise for personalized therapeutic interventions, shaping improved strategies in the ever-evolving landscape of cancer treatment.

Healing from Within: How Gut Microbiota Predicts IBD Treatment Success-A Systematic Review

Recent research indicates that the microbiome has a significant impact on the progression of inflammatory bowel disease (IBD) and that creating therapies that change its composition could positively impact the outcomes of IBD treatment. This review summarizes the results of extensive studies that examined IBD patients undergoing several therapies, including anti-TNF medication, vedolizumab, ustekinumab, probiotics, and fecal microbiota transplantation (FMT), and the alterations in their gut microbiota's composition and function. The objective was to investigate the variety and effectiveness of microbial species in order to discover new biomarkers or therapeutic targets that could improve the outcome of treatment for these patients. This research aimed to offer useful insights into personalized medicine techniques for managing IBD. Beneficial bacteria such as Faecalibacterium prausnitzii and Roseburia have been consistently linked to favorable clinical outcomes, whereas pathogenic bacteria such as Escherichia coli and Clostridioides difficile are associated with worsening disease conditions. Although many studies have examined the role of gut microbiota in IBD, there is still a need for more targeted research on the connection between specific microbial communities and treatment outcomes. This study sought to address this gap by exploring the intricate relationship between the gut microbiota composition and the effectiveness of IBD medications.

Gut microbiota composition links to variation in functional domains across psychiatric disorders

OBJECTIVE

Changes in microbial composition are observed in various psychiatric disorders, but their specificity to certain symptoms or processes remains unclear. This study explores the associations between the gut microbiota composition and the Research Domain Criteria (RDoC) domains of functioning, representing symptom domains, specifically focusing on stress-related and neurodevelopmental disorders in patients with and without psychiatric comorbidity.

METHODS

The gut microbiota was analyzed in 369 participants, comprising 272 individuals diagnosed with a mood disorder, anxiety disorder, attention deficit/hyperactivity disorder, autism spectrum disorder, and/or substance use disorder, as well as 97 psychiatrically unaffected individuals. The RDoC domains were estimated using principal component analysis (PCA) with oblique rotation on a range of psychiatric, psychological, and personality measures. Associations between the gut microbiota and the functional domains were assessed using multiple linear regression and permanova, adjusted for age, sex, diet, smoking, medication use and comorbidity status.

RESULTS

Four functional domains, aligning with RDoC's negative valence, social processes, cognitive systems, and arousal/regulatory systems domains, were identified. Significant associations were found between these domains and eight microbial genera, including associations of negative valence with the abundance of the genera Sellimonas, CHKCI001, Clostridium sensu stricto 1, Oscillibacter, and Flavonifractor; social processes with Sellimonas; cognitive systems with Sporobacter and Hungatella; and arousal/regulatory systems with Ruminococcus torques (all pFDR < 0.05).

CONCLUSION

Our findings demonstrate associations between the gut microbiota and the domains of functioning across patients and unaffected individuals, potentially mediated by immune-related processes. These results open avenues for microbiota-focused personalized interventions, considering psychiatric comorbidity. However, further research is warranted to establish causality and elucidate mechanistic pathways.

Meta-analysis identifies common gut microbiota associated with multiple sclerosis

BACKGROUND

Previous studies have identified a diverse group of microbial taxa that differ between patients with multiple sclerosis (MS) and the healthy population. However, interpreting findings on MS-associated microbiota is challenging, as there is no true consensus. It is unclear whether there is gut microbiota commonly altered in MS across studies.

METHODS

To answer this, we performed a meta-analysis based on the 16S rRNA gene sequencing data from seven geographically and technically diverse studies comprising a total of 524 adult subjects (257 MS and 267 healthy controls). Analysis was conducted for each individual study after reprocessing the data and also by combining all data together. The blocked Wilcoxon rank-sum test and linear mixed-effects regression were used to identify differences in microbial composition and diversity between MS and healthy controls. Network analysis was conducted to identify bacterial correlations. A leave-one-out sensitivity analysis was performed to ensure the robustness of the findings.

RESULTS

The microbiome community structure was significantly different between studies. Re-analysis of data from individual studies revealed a lower relative abundance of Prevotella in MS across studies, compared to controls. Meta-analysis found that although alpha and beta diversity did not differ between MS and controls, a higher abundance of Actinomyces and a lower abundance of Faecalibacterium were reproducibly associated with MS. Additionally, network analysis revealed that the recognized negative Bacteroides-Prevotella correlation in controls was disrupted in patients with MS.

CONCLUSIONS

Our meta-analysis identified common gut microbiota associated with MS across geographically and technically diverse studies.

Mediterranean diet and associations with the gut microbiota and pediatric-onset multiple sclerosis using trivariate analysis

BACKGROUND

The interplay between diet and the gut microbiota in multiple sclerosis (MS) is poorly understood. We aimed to assess the interrelationship between diet, the gut microbiota, and MS.

METHODS

We conducted a case-control study including 95 participants (44 pediatric-onset MS cases, 51 unaffected controls) enrolled from the Canadian Pediatric Demyelinating Disease Network study. All had completed a food frequency questionnaire ≤21-years of age, and 59 also provided a stool sample.

RESULTS

Here we show that a 1-point increase in a Mediterranean diet score is associated with 37% reduced MS odds (95%CI: 10%-53%). Higher fiber and iron intakes are also associated with reduced MS odds. Diet, not MS, explains inter-individual gut microbiota variation. Several gut microbes abundances are associated with both the Mediterranean diet score and having MS, and these microbes are potential mediators of the protective associations of a healthier diet.

CONCLUSIONS

Our findings suggest that the potential interaction between diet and the gut microbiota is relevant in MS.

The Biomolecular Basis of Gut Microbiome on Neurological Diseases

The human gastrointestinal (GI) tract harbors many microorganisms, including viruses, protozoa, archaea, fungi, and bacteria. Altogether, these microbes constitute what we know as the gut microbiome (GM). These commensal communities have important implications for human health. They influence physiological processes through different mechanisms, including synthesizing neurotransmitters, regulating enzymatic pathways, and releasing molecules responsible for different signal pathways. The interaction between GM and brain function has been associated with the development and pathogenesis of neuropsychiatric diseases. This review discusses current studies targeting the regulation and modulation of GM in nerve, neuroendocrine, and immune pathways. Thus, we analyze current evidence on transcription, changes in composition, and specific interactions between the gut and brain from a biomolecular perspective. Special attention is paid to mood disorders and neurodegenerative diseases.

Bifidobacterium animalis subsp. lactis LPL-RH improves postoperative gastrointestinal symptoms and nutrition indexes by regulating the gut microbiota in patients with valvular heart disease: a randomized controlled trial

Gastrointestinal symptoms constitute a frequent complication in postoperative patients with valvular heart disease (VHD), impacting their postoperative recovery. Probiotics contribute to regulating human gut microbiota balance and alleviating postoperative gastrointestinal symptoms. Our objective involved assessing the potential of Bifidobacterium animalis subsp. lactis LPL-RH to alleviate postoperative gastrointestinal symptoms and expedite patient recovery. Adult patients diagnosed with VHD scheduled for valve surgery were enrolled. 110 patients were randomly divided into two groups and received LPL-RH or a placebo for 14 days. Gastrointestinal symptoms were evaluated using the Gastrointestinal Symptoms Questionnaire. An analysis of the time to recovery of bowel function and various postoperative variables was conducted in both study groups. Variations in the intestinal microbiota were detected via 16S rRNA sequencing. The study was completed by 105 participants, with 53 in the probiotic group and 52 in the placebo group. Compared to the placebo group, LPL-RH significantly reduced the total gastrointestinal symptom score after surgery (p = 0.004). Additionally, LPL-RH was found to significantly reduce abdominal pain (p = 0.001), bloating (p = 0.018), and constipation (p = 0.022) symptom scores. Furthermore, LPL-RH dramatically shortened the time to recovery of bowel function (p = 0.017). Moreover, LPL-RH administration significantly enhanced patients' postoperative nutrition indexes (red blood cell counts, hemoglobin level, p < 0.05). Microbiome analysis showed that the composition and diversity of the postoperative intestinal microbiota differed between the probiotic and placebo groups. No adverse incidents associated with probiotics were documented, emphasizing their safety. This study initially discovered that oral B. animalis subsp. lactis LPL-RH can assist in regulating intestinal microbiota balance, alleviating gastrointestinal symptoms, promoting intestinal function recovery, and enhancing nutrition indexes in patients with VHD after surgery. Regulating the intestinal microbiota may represent a potential mechanism for LPL-RH to exert clinical benefits.

Alcohol consumption during pregnancy differentially affects the fecal microbiota of dams and offspring

Microbiota imbalances are linked to inflammation and disease, as well as neurodevelopmental conditions where they may contribute to behavioral, physiological, and central nervous system dysfunction. By contrast, the role of the microbiota in Fetal Alcohol Spectrum Disorder (FASD), the group of neurodevelopmental conditions that can occur following prenatal alcohol exposure (PAE), has not received similar attention. Here we utilized a rodent model of alcohol consumption during pregnancy to characterize the impact of alcohol on the microbiota of dam-offspring dyads. Overall, bacterial diversity decreased in alcohol-consuming dams and community composition differed from that of controls in alcohol-consuming dams and their offspring. Bacterial taxa and predicted biochemical pathway composition were also altered with alcohol consumption/exposure; however, there was minimal overlap between the changes in dams and offspring. These findings illuminate the potential importance of the microbiota in the pathophysiology of FASD and support investigation into novel microbiota-based interventions.

Exploring the Role of the Microbiome in Rheumatoid Arthritis-A Critical Review

Rheumatoid arthritis (RA) is a chronic, autoimmune rheumatic disease characterized by synovial joint inflammation with subsequent destruction as well as systemic manifestation, leading to impaired mobility and impaired quality of life. The etiopathogenesis of RA is still unknown, with genetic, epigenetic and environmental factors (incl. tobacco smoking) contributing to disease susceptibility. The link between genetic factors like "shared epitope alleles" and the development of RA is well known. However, why only some carriers have a break in self-tolerance and develop autoimmunity still needs to be clarified. The presence of autoantibodies in patients' serum months to years prior to the onset of clinical manifestations of RA has moved the focus to possible epigenetic factors, including environmental triggers that could contribute to the initiation and perpetuation of the inflammatory reaction in RA. Over the past several years, the role of microorganisms at mucosal sites (i.e., microbiome) has emerged as an essential mediator of inflammation in RA. An increasing number of studies have revealed the microbial role in the immunopathogenesis of autoimmune rheumatic diseases. Interaction between the host immune system and microbiota initiates loss of immunological tolerance and autoimmunity. The alteration in microbiome composition, the so-called dysbiosis, is associated with an increasing number of diseases. Immune dysfunction caused by dysbiosis triggers and sustains chronic inflammation. This review aims to provide a critical summary of the literature findings related to the hypothesis of a reciprocal relation between the microbiome and the immune system. Available data from studies reveal the pivotal role of the microbiome in RA pathogenesis.

Changes in Gut Microbiota in Patients with Multiple Sclerosis Based on 16s rRNA Gene Sequencing Technology: A Review and Meta-Analysis

BACKGROUND

This meta-analysis explores alterations in the gut microbiota of patients with Multiple Sclerosis (MS) using 16S ribosomal RNA (rRNA) gene sequencing.

METHODS

Adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, our comprehensive review spanned major databases, including PubMed, Web of Science, Embase, Cochrane, and Ovid, targeting observational studies that implemented 16S rRNA gene sequencing on fecal specimens. The quality of these studies was meticulously evaluated using the Newcastle-Ottawa scale.

RESULTS

Our search yielded 26 relevant studies conducted between 2015-2022, encompassing 2885 participants. No significant differences were observed in alpha diversity indices (Shannon, Chao1, Operational Taxonomic Units (OTU), and Simpson) between MS patients and controls in general. Nonetheless, subgroup analyses according to disease activity using the Shannon index highlighted a significant decrease in microbial diversity during MS's active phase. Similarly, an evaluation focusing on MS phenotype revealed diminished diversity in individuals with relapsing-remitting MS (RRMS). Microbial composition analysis revealed no consistent increase in pro-inflammatory Bacteroidetes or decrease in anti-inflammatory Firmicutes within the MS cohort.

CONCLUSION

The gut microbiome's role in MS presents a complex panorama, where alterations in microbial composition might hold greater significance to disease mechanisms than diversity changes. The impact of clinical factors such as disease activity and phenotype are moderately significant, underscoring the need for further research to elucidate these relationships. Prospective research should employ longitudinal methodologies to elucidate the chronological interplay among gut microbiota, disease evolution, and therapeutic strategies.

Current and future microbiome-based therapies in inflammatory bowel disease

PURPOSE OF REVIEW

The role of the microbiome and dysbiosis is increasingly recognized in the pathogenesis of inflammatory bowel disease (IBD). Intestinal microbiota transplant (IMT), previously termed fecal microbiota transplant has demonstrated efficacy in restoring a healthy microbiome and promoting gut health in recurrent Clostridioides difficile infection. Several randomized trials (RCTs) highlighted IMT's potential in treating ulcerative colitis, while smaller studies reported on its application in managing Crohn's disease and pouchitis.

RECENT FINDINGS

This review delves into the current understanding of dysbiosis in IBD, highlighting the distinctions in the microbiota of patients with IBD compared to healthy controls. It explores the mechanisms by which IMT can restore a healthy microbiome and provides a focused analysis of recent RCTs using IMT for inducing and maintaining remission in IBD. Lastly, we discuss the current knowledge gaps that limit its widespread use.

SUMMARY

The body of evidence supporting the use of IMT in IBD is growing. The lack of a standardized protocol impedes its application beyond clinical trials. Further research is needed to identify patient profile and disease phenotypes that benefit from IMT, to delineate key donor characteristics, optimize the delivery route, dosage, and frequency.

The Role of Gut Microbiota in Thromboangiitis Obliterans: Cohort and Mendelian Randomization Study

BACKGROUND AND AIMS

Thromboangiitis obliterans (TAO), also known as Buerger's disease, is a rare vasculitis. Observational epidemiology studies have suggested a relationship between the gut microbiota and TAO. However, due to confounding factors and reverse causality, the causal relationship remains unclear. Based on the assumption of their association, this study sought specific gut microbiota causally linked to TAO.

METHODS

The case-control study was conducted at the Xiangya Hospital of Central South University from November 2022 to January 2023 including twelve TAO patients and nine healthy controls. We conducted a Mendelian randomization (MR) study using summary statistics from a genome-wide association study (GWAS) of gut microbiota and TAO. Considering the scale and accessibility of the data, the MiBioGen consortium served as the exposure, whereas the FinnGen consortium GWAS study served as the outcome. Finally, we compared the results of the MR with those of the case-control studies.

RESULTS

The inverse variance weighted (IVW) (OR = 0.119, 95% CI: 0.021-0.688, p = 0.017) and maximum likelihood (ML) (OR = 0.121, 95% CI: 0.020-0.742, p = 0.022) estimates suggest that Ruminiclostridium 5 has a suggestive protective effect on TAO while the IVW (OR = 5.383, 95% CI: 1.128-25.693, p = 0.035) and ML (OR = 5.658, 95% CI: 1.142-28.021, p = 0.034) estimates suggest that Eubacterium (xylanophilum group) has a suggestive risk effect on TAO, and the ML (OR = 0.055, 95% CI: 0.004-0.755, p = 0.030) estimates suggest that Lachnospira has a suggestive protective effect on TAO. No significant heterogeneity of instrumental variables or horizontal pleiotropy was found. The results of the case-control study showed that the TAO had a lower relative abundance of Ruminiclostridium 5 (p = 0.015) and Lachnospira (p = 0.048), and a higher relative abundance of Eubacterium (xylanophilum group) (p = 0.029) than the healthy controls. These results were consistent with the MR analysis.

CONCLUSIONS

Our study demonstrates that Ruminiclostridium 5, Lachnospira, and Eubacterium (xylanophilum group) are causally related to TAO, suggesting their potential significance for the prevention and treatment of TAO.

An Isofibrous Diet with Fiber Konjac Glucomannan Ameliorates Salmonella typhimurium-Induced Colonic Injury by Regulating TLR2-NF-κB Signaling and Intestinal Microbiota in Mice

This study aimed to investigate the hypothesis that dietary konjac glucomannan (KGM) could alleviate Salmonella typhimurium-induced colitis by modulating intestinal microbiota. Mice were fed an isocaloric and isofibrous diet supplemented with either 7% KGM or cellulose and were treated with 5 × 108 CFU of S. typhimurium. The results showed that KGM had an average molecular weight of 936 kDa and predominantly consisted of mannose and glucose at a molar ratio of 1:1.22. In vivo studies demonstrated that dietary KGM effectively mitigated colonic lesions, oxidative stress, disruption of tight junction protein 2 and occludin, and the inflammatory response induced by S. typhimurium. Moreover, KGM administration alleviated the dramatic upregulation of toll-like receptor 2 (TLR2) and phosphonuclear factor κB (NF-κB) protein abundance, induced by Salmonella treatment. Notably, dietary KGM restored the reduced Muribaculaceae and Lactobacillus abundance and increased the abundance of Blautia and Salmonella in S. typhimurium-infected mice. Spearman correlation analysis revealed that the gut microbiota improved by KGM contribute to inhibit inflammation and oxidative stress. These results demonstrated the protective effects of dietary KGM against colitis by modulating the gut microbiota and the TLR2-NF-κB signaling pathway in response to Salmonella infection.

Elevated fecal calprotectin is associated with gut microbial dysbiosis, altered serum markers and clinical outcomes in older individuals

Fecal calprotectin is an established marker of gut inflammation in inflammatory bowel disease (IBD). Elevated levels of fecal calprotectin as well as gut microbial dysbiosis have also been observed in other clinical conditions. However, systemic and multi-omics alterations linked to elevated fecal calprotectin in older individuals remain unclear. This study comprehensively investigated the relationship between fecal calprotectin levels, gut microbiome composition, serum inflammation and targeted metabolomics markers, and relevant lifestyle and medical data in a large sample of older individuals (n = 735; mean age ± SD: 68.7 ± 6.3) from the TREND cohort study. Low (0-50 μg/g; n = 602), moderate (> 50-100 μg/g; n = 64) and high (> 100 μg/g; n = 62) fecal calprotectin groups were stratified. Several pro-inflammatory gut microbial genera were significantly increased and short-chain fatty acid producing genera were decreased in high vs. low calprotectin groups. In serum, IL-17C, CCL19 and the toxic metabolite indoxyl sulfate were increased in high vs. low fecal calprotectin groups. These changes were partially mediated by the gut microbiota. Moreover, the high fecal calprotectin group showed increased BMI and a higher disease prevalence of heart attack and obesity. Our findings contribute to the understanding of fecal calprotectin as a marker of gut dysbiosis and its broader systemic and clinical implications in older individuals.

A Comprehensive Pilot Study to Elucidate the Distinct Gut Microbial Composition and Its Functional Significance in Cardio-Metabolic Disease

Cardio-metabolic disease is a significant global health challenge with increasing prevalence. Recent research underscores the disruption of gut microbial balance as a key factor in disease susceptibility. We aimed to characterize the gut microbiota composition and function in cardio-metabolic disease and healthy controls. For this purpose, we collected stool samples of 18 subjects (12 diseased, 6 healthy) and we performed metagenomics analysis and functional prediction using QIIME2 and PICRUSt. Furthermore, we carried out assessments of microbe-gene interactions, gene ontology, and microbe-disease associations. Our findings revealed distinct microbial patterns in the diseased group, particularly evident in lower taxonomic levels with significant variations in 14 microbial features. The diseased cohort exhibited an enrichment of Lachnospiraceae family, correlating with obesity, insulin resistance, and metabolic disturbances. Conversely, reduced levels of Clostridium, Gemmiger, and Ruminococcus genera indicated a potential inflammatory state, linked to compromised butyrate production and gut permeability. Functional analyses highlighted dysregulated pathways in amino acid metabolism and energy equilibrium, with perturbations correlating with elevated branch-chain amino acid levels-a known contributor to insulin resistance and type 2 diabetes. These findings were consistent across biomarker assessments, microbe-gene associations, and gene ontology analyses, emphasizing the intricate interplay between gut microbial dysbiosis and cardio-metabolic disease progression. In conclusion, our study unveils significant shifts in gut microbial composition and function in cardio-metabolic disease, emphasizing the broader implications of microbial dysregulation. Addressing gut microbial balance emerges as a crucial therapeutic target in managing cardio-metabolic disease burden.

Exploration of gut microbiome and inflammation: A review on key signalling pathways

The gut microbiome, a crucial component of the human system, is a diverse collection of microbes that belong to the gut of human beings as well as other animals. These microbial communities continue to coexist harmoniously with their host organisms and perform various functions that affect the host's general health. Each person's gut microbiota has a unique makeup. The gut microbiota is well acknowledged to have a part in the local as well as systemic inflammation that underlies a number of inflammatory disorders (e.g., atherosclerosis, diabetes mellitus, obesity, and inflammatory bowel disease).The gut microbiota's metabolic products, such as short-chain fatty acids (butyrate, propionate, and acetate) inhibit inflammation by preventing immune system cells like macrophages and neutrophils from producing pro-inflammatory factors, which are triggered by the structural elements of bacteria (like lipopolysaccharide). The review's primary goal is to provide comprehensive and compiled data regarding the contribution of gut microbiota to inflammation and the associated signalling pathways.

Microbiota and IBD: Current knowledge and future perspectives

Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.

Advances in the mechanism of metformin with wide-ranging effects on regulation of the intestinal microbiota

Metformin is of great focus because of its high safety, low side effects, and various effects other than lowering blood sugar, such as anti-inflammation, anti-tumor, and anti-aging. Studies have shown that metformin has a modulating effect on the composition and function of the intestinal microbiota other than acting on the liver. However, the composition of microbiota is complex and varies to some extent between species and individuals, and the experimental design of each study is also different. Multiple factors present a major obstacle to better comprehending the effects of metformin on the gut microbiota. This paper reviews the regulatory effects of metformin on the gut microbiota, such as increasing the abundance of genus Akkermansia, enriching short-chain fatty acids (SCFAs)-producing bacterial genus, and regulating gene expression of certain genera. The intestinal microbiota is a large and vital ecosystem in the human body and is considered to be the equivalent of an "organ" of the human body, which is highly relevant to human health and disease status. There are a lot of evidences that the gut microbiota is responsible for metformin's widespread effects. However, there are only a few systematic studies on this mechanism, and the specific mechanism is still unclear. This paper aims to summarize the possible mechanism of metformin in relation to gut microbiota.

In vitro digestion and fermentation behaviors of polysaccharides from Choerospondias axillaris fruit and its effect on human gut microbiota

Choerospondias axillaris fruit has attracted more and more attention due to its various pharmacological activities, which are rich in polysaccharides. This study investigated the in vitro saliva-gastrointestinal digestion and fecal fermentation behaviors of polysaccharides from Choerospondias axillaris fruit (CAP), as well as its impact on human gut microbiota. The results showed that CAP could be partially degraded during the gastrointestinal digestion. The FT-IR spectra of the digested CAP didn't change significantly, however, the morphological feature of SEM changed to disordered flocculent and rod-like structures. 16S rRNA sequencing analysis found that after in vitro fermentation, CAP could increase the relative abundances of beneficial bacteria including Megasphaera, Megamonas and Bifidobacterium to produce short-chain fatty acids (SCFAs), while it can also reduce the abundances of harmful bacteria of Collinsella, Gemmiger, Klebsiella and Citrobacter, suggesting that CAP could modulate the composition and abundance of gut microbiota. These results implied that CAP can be developed as a potential prebiotic in the future.