Enterotypes of the human gut microbiome

Novel insights into carbohydrate utilisation, antimicrobial resistance, and sporulation potential in Roseburia intestinalis isolates across diverse geographical locations

Roseburia intestinalis is one of the most abundant and important butyrate-producing human gut anaerobic bacteria that plays an important role in maintaining health and is a potential next-generation probiotic. We investigated the pangenome of 16 distinct strains, isolated over several decades, identifying local and time-specific adaptations. More than 50% of the genes in each individual strain were assigned to the core genome, and 77% of the cloud genes were unique to individual strains, revealing the high level of genome conservation. Co-carriage of the same enzymes involved in carbohydrate binding and degradation in all strains highlighted major pathways in carbohydrate utilization and reveal the importance of xylan, starch and mannose as key growth substrates. A single strain had adapted to use rhamnose as a sole growth substrate, the first time this has been reported. The ubiquitous presence of motility and sporulation gene clusters demonstrates the importance of these phenotypes for gut survival and acquisition of this bacterium. More than half the strains contained functional, potentially transferable, tetracycline resistance genes. This study advances our understanding of the importance of R. intestinalis within the gut ecosystem by elucidating conserved metabolic characteristics among different strains, isolated from different locations. This information will help to devise dietary strategies to increase the abundance of this species providing health benefits.

Fecal microbiota transplantation in allergic diseases

Microorganisms such as bacteria, fungi, viruses, parasites living in the human intestine constitute the human intestinal microbiota. Dysbiosis refers to compositional and quantitative changes that negatively affect healthy gut microbiota. In recent years, with the demonstration that many diseases are associated with dysbiosis, treatment strategies targeting the correction of dysbiosis in the treatment of these diseases have begun to be investigated. Faecal microbiota transplantation (FMT) is the process of transferring faeces from a healthy donor to another recipient in order to restore the gut microbiota and provide a therapeutic benefit. FMT studies have gained popularity after probiotic, prebiotic, symbiotic studies in the treatment of dysbiosis and related diseases. FMT has emerged as a potential new therapy in the treatment of allergic diseases as it is associated with the maintenance of intestinal microbiota and immunological balance (T helper 1/T helper 2 cells) and thus suppression of allergic responses. In this article, the definition, application, safety and use of FMT in allergic diseases will be discussed with current data.

Impact of dietary carbohydrate, fat or protein restriction on the human gut microbiome: a systematic review

Restriction of dietary carbohydrates, fat and/or protein is often used to reduce body weight and/or treat (metabolic) diseases. Since diet is a key modulator of the human gut microbiome, which plays an important role in health and disease, this review aims to provide an overview of current knowledge of the effects of macronutrient-restricted diets on gut microbial composition and metabolites. A structured search strategy was performed in several databases. After screening for inclusion and exclusion criteria, thirty-six articles could be included. Data are included in the results only when supported by at least three independent studies to enhance the reliability of our conclusions. Low-carbohydrate (<30 energy%) diets tended to induce a decrease in the relative abundance of several health-promoting bacteria, including Bifidobacterium, as well as a reduction in short-chain fatty acid (SCFA) levels in faeces. In contrast, low-fat diets (<30 energy%) increased alpha diversity, faecal SCFA levels and abundance of some beneficial bacteria, including Faecalibacterium prausnitzii. There were insufficient data to draw conclusions concerning the effects of low-protein (<10 energy%) diets on gut microbiota. Although the data of included studies unveil possible benefits of low-fat and potential drawbacks of low-carbohydrate diets for human gut microbiota, the diversity in study designs made it difficult to draw firm conclusions. Using a more uniform methodology in design, sample processing and sharing raw sequence data could foster our understanding of the effects of macronutrient restriction on gut microbiota composition and metabolic dynamics relevant to health. This systematic review was registered at https://www.crd.york.ac.uk/prospero as CRD42020156929.

Differences in anti-obesity effects between raw and ripened Pu-erh tea polyphenols: impact on gut microbiota enterotypes

BACKGROUND

Pu-erh tea, a dark tea from China, is classified into raw and ripened types. Both have significant anti-obesity effects. Polyphenols are among their major bioactive components. This study aimed to explore the anti-obesity properties and mechanisms of raw (R-TP) and ripened (F-TP) Pu-erh tea polyphenols.

RESULTS

The results showed that R-TP and F-TP significantly reduced body weight, improved insulin resistance, and enhanced glucose and lipid metabolism in high-fat-diet (HFD)-induced obese mice. Mild differences were observed in their impact on fat metabolism, carbohydrate metabolism, and inflammation levels. Both R-TP and F-TP were able to restore the disrupted intestinal flora caused by HFD treatment, returning them to a composition and levels similar to those of normal mice. Interestingly, the gut microbiota of all the mice could be reclassified into three enterotypes (enterotype Type-1, Type-2, and Type-HFD). Lactobacillaceae predominated in Type-1. Lactobacillaceae, Muribaculaceae, and Lachnospiraceae were the most common in Type-2. Type-HFD was primarily composed of Atopobiaceae, Lachnospiraceae, Lactobacillaceae, Ruminococcaceae, and Erysipelotrichaceae. The small differences in the effects of R-TP and F-TP may be due to variations in enterotypes.

CONCLUSION

These findings indicate that R-TP and F-TP can alleviate obesity by regulating the enterotype of gut microbiota, suggesting that they possess the potential for application in the treatment of obesity and the development of anti-obesity agents. © 2025 Society of Chemical Industry.

Dietary Relationships between Obesity and Inflammatory Bowel Diseases: A Narrative Review of Diets Which May Promote Both Diseases

PURPOSE OF REVIEW

The pandemic of obesity preceded global spread of Inflammatory Bowel diseases by almost 2 decades. A pathogenic relationship has been described between obesity and inflammatory bowel diseases, but Crohn`s disease may be selectively impacted. The role of diet in pathogenesis has also gained significant support in the last few decades. This review explores dietary relationships to account for epidemiological observations. Quantifiable indices for diets have been described including a glycemic index, inflammatory indices and levels of food processing. Meta-analyses have been published which examine each for effects on obesity and co-morbidities as well as Crohn's disease and ulcerative colitis. This review suggests that ultra-processed foods provide the best link between obesity and Crohn's disease explaining epidemiological observations. However, the other 2 types of dietary indices likely contribute to ulcerative colitis as well as to co-morbidities related to both obesity and inflammatory bowel diseases. The term ultra-processed foods cover a large number of additives and extensive work is needed to define individual or combined harmful effects. Furthermore, the interactions among the 3 main indices need clarification in order to precisely apply therapeutic diets to both diseases (obesity and inflammatory bowel disease).

Human milk oligosaccharides modulating inflammation in infants, adults and older individuals - from concepts to applications

The increasing global prevalence of inflammatory diseases such as ulcerative colitis and irritable bowel syndrome, represents a challenging task for healthcare systems. Several approaches to disease management target the intestinal microbiome, which plays a key role in health and disease. One promising approach is modulating the microbiome using human milk oligosaccharides (HMOs). Originating from human milk, HMOs are indigestible carbohydrates which act in a host-optimized prebiotic fashion by providing an energy source for health-promoting intestinal bacteria and exhibiting systemic effects. Commercial products supporting infant health and development have been the primary fields of HMO application. Advancements in the large-scale production of HMOs through bioengineering and precision fermentation have led to evaluating their potential for managing inflammatory diseases. Several in vitro studies and observations on model systems have been clinically validated in infants, resulting in a large body of evidence supporting the safety and efficacy of HMOs in inflammatory disorders. While novel approaches seek to explore interventions in adults, the primary goal for the future is to provide cost-efficient, safe, and reliable healthcare compounds across all age groups.

Investigating the impact of fecal contamination on antibiotic resistance genes in urban environments using host-associated molecular indicators

Antibiotic resistome of gut microbiota can be transmitted into the urban ecosystems via fecal pollution, potentially leading to a public health crisis. It is essential to determine the primary sources of fecal contamination and accurately evaluate the health risks for the propagation of antibiotic resistance genes (ARGs) from the intestinal microbiota. In this research, the occurrence, sources and potential hosts of ARGs in urban environmental samples collected from a wastewater treatment plant (WWTP), natural water bodies, tap water and farmland soil were comprehensively investigated. Host-associated fecal indicators for general warm-blooded animals (BacGeneral), humans (crAssphage), and other animals (bovines and swine) were employed for reliable microbial source tracking (MST). Results showed that the fecal indicator BacGeneral was detected in 84.00 % of collected environmental samples, indicating the widespread fecal contamination in local water and farmland. The WWTP was the reservoir and main source of fecal contamination in local environment, harboring the highest total abundances of ARGs (3.85 ± 2.72 ARGs/16S rRNA) and mobile genetic elements (MGEs) (0.32 ± 0.12 MGEs/16S rRNA) from multiple animals and humans. Although the swine-associated indicator was undetected, fecal contamination from both bovines and humans was prevalent in collected samples, with detection rates of pollution indicators at 52.00 % for bovine and 28.00 % for human sources. The co-occurrence of ARGs, fecal indicators and MGEs was analyzed, and significant correlation (P < 0.01) between total ARG abundance and fecal indicator (BacGeneral) in contaminated environments demonstrated that fecal pollution exhibited a great influence on overall resistome in local environment. This research offers a comprehensive understanding of the sources and dissemination of ARGs in feces-polluted urban environments, providing data for the monitoring and prevention of ARG pollution.

Atypical gut microbial ecosystem from athletes with very high exercise capacity improves insulin sensitivity and muscle glycogen store in mice

Although the gut microbiota is known to act as a bridge between dietary nutrients and the body's energy needs, the interactions between the gut microbiota, host energy metabolism, and exercise capacity remain uncertain. Here, we characterized the gut microbiota ecosystem in a cohort of healthy normo-weight humans with highly heterogeneous aerobic exercise capacities and closely related body composition and food habits. While our data support the idea that the bacterial ecosystem appears to be modestly altered between individuals with low-to-high exercise capacities and close food habits, we report that gut bacterial α diversity, density, and functional richness are significantly reduced in athletes with very high exercise capacity. By using fecal microbiota transplantation, we report that the engraftment of gut microbiota from athletes with very high exercise capacity improves insulin sensitivity and muscle glycogen stores into transplanted mice, which highlights promising therapeutic perspectives in fecal transplantation from human donors selected based on exercise capacity traits.

TEAL-Seq: targeted expression analysis sequencing

Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.

Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice

BACKGROUND

Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

RESULTS

We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

CONCLUSIONS

This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.

Bacteroides maternus sp. nov., a novel species isolated from human faeces

A novel bacterial strain, MSB163, was isolated from the stool sample of a healthy mother, 4 weeks after giving birth via vaginal delivery. Taxonomic identification tools revealed that MSB163 belongs to the genus Bacteroides, but it is distinct from any currently known species. The closest related species is Bacteroides cellulosilyticus strain BFG- 250, with an average nucleotide identity (fastANI) of 94.51%. The genome length of MSB163 is 6,440,948 bp and the GC content 42.95%. Two plasmids were identified in the whole genome sequence. MSB163 is a Gram-negative, rod-shaped, non-motile anaerobic bacterium. The optimum growth conditions were at 37 °C, pH 7 and 0% (w/v) NaCl. The respiratory quinones were the menaquinones MK- 10 and MK- 11 and C15:0 ANTEISO was the major fatty acid. The predominant polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phospholipid. According to the taxonomic results and physiological analysis, strain MSB163 represents a novel species of the genus Bacteroides, for which we propose the name Bacteroides maternus, since the type strain was isolated from the stool sample of a mother. B. maternus type strain (MSB163) sequencing can be accessed under the biosample ID SAMN3953129 on NCBI. The strain was deposited on BCCM/LMG Bacteria Collection under the accession number LMG 33,374 and Leibniz Institut DSMZ GMBH under the accession number DSM 117,047.

Optimizing anti-PD-1/PD-L1 therapy efficacy and fecal microbiota transplantation donor selection through gut mycobiome-based enterotype

Immunotherapy has revolutionized cancer treatment, but response variability remains a challenge. The gut microbiome's role in therapeutic efficacy is well established, but the impact of the gut mycobiome is less understood. Using unsupervised clustering, we identify two gut mycobiome-based enterotypes, favorable type and unfavorable type, characterized by distinct microbial compositions linked to immunotherapy outcomes. Favorable-type enterotypes exhibit higher fungal and bacterial alpha diversity, enriched butyrate-producing bacteria, and metabolic pathways related to butyric acid and sugar/starch metabolism. External validation confirms their predictive value in assessing immunotherapy efficacy. Multi-omics analysis reveals increased CD8+ T cell infiltration in the tumor microenvironment of favorable-type patients. Fecal microbiota transplantation (FMT) from favorable-type donors enhances anti-PD-1 sensitivity, promotes CD8+ T cell infiltration, and boosts butyrate production in vivo. These findings highlight the gut mycobiome's role in immunotherapy response and support FMT from favorable-type donors as a potential strategy for improving treatment outcomes and patient stratification.

Relationship Between Dietary Habits and Stress Responses Exerted by Different Gut Microbiota

BACKGROUND/OBJECTIVES

A number of studies have reported on the improvement in physical and psychological diseases through diet; however, the findings for these ameliorative effects have differed. Such differences may be due to the varying metabolism of the nutrient content in food among subjects. It has been reported that differences in the enterotypes of gut microbiota are associated with metabolic differences, and enterotypes vary between countries and regions. This study investigated whether differences in gut microbiota affect the relationship between dietary habits and stress responses.

METHODS

We administered a questionnaire to 810 subjects who participated in the "Sukoyaka Health Survey" regarding their dietary habits and stress reactions. We also performed an analysis of the gut microbiota from fecal samples.

RESULTS

The gut microbiota was grouped into four clusters based on the abundance of genus strains. The relationship between dietary habits and stress responses revealed two patterns of eating: one where more frequent intakes were associated with a lower stress response, and another with a higher stress response. We investigated the relationship between dietary habits and stress responses for each gut microbiota cluster. The results showed that the relationship between dietary habits and stress responses differed for each cluster.

CONCLUSIONS

Our analysis showed that dietary habits affect stress responses, but the relationship varies depending on the gut microbiota. This finding suggests that one of the factors for the difference in the ameliorative efficacy of physical and psychological diseases through diet is the difference in the abundance ratio of the gut microbiota (enterotype).

Commensalism and pathogenesis of Candida albicans at the mucosal interface

Fungi are important and often underestimated human pathogens. Infections with fungi mostly originate from the environment, from soil or airborne spores. By contrast, Candida albicans, one of the most common and clinically important fungal pathogens, permanently exists in the vast majority of healthy individuals as a member of the human mucosal microbiota. Only under certain circumstances will these commensals cause infections. However, although the pathogenic behaviour and disease manifestation of C. albicans have been at the centre of research for many years, its asymptomatic colonization of mucosal surfaces remains surprisingly understudied. In this Review, we discuss the interplay of the fungus, the host and the microbiome on the dualism of commensal and pathogenic life of C. albicans, and how commensal growth is controlled and permitted. We explore hypotheses that could explain how the mucosal environment shapes C. albicans adaptations to its commensal lifestyle, while still maintaining or even increasing its pathogenic potential.

Use of consensus clustering to identify subtypes of clinical early-stage non-small cell lung cancer and its association with lymph node metastasis

Limited studies have investigated the metabolic heterogeneity of patients with clinical early-stage non-small cell lung cancer (NSCLC). Consensus clustering analysis has the potential to reveal distinct metabolic subgroups within clinical early-stage NSCLC patients. A total of 3324 clinical early-stage NSCLC patients who underwent surgery were included in this comprehensive evaluation. The evaluation encompassed 26 serum assessments related to metabolism and histopathological examination of the lymph nodes. By utilizing consensus clustering analysis, three clusters were identified based on various measurements, including blood glucose levels, blood uric acid, blood lipids, renal and liver function, and tumor markers. The differences in characteristics and lymph node metastasis (LNM) prevalence between the clusters were investigated and compared. The patients were classified into three distinct clusters that exhibited different patterns defined by the highest or lowest levels of metabolic feature variables. NSCLC cluster 1 had the lowest rates of LNM, while cluster 3 showed a significantly higher prevalence of LNM (1.6-fold increase, 95% CI: 1.21, 2.13) compared to cluster 1. Moreover, cluster 2 had the highest odds ratio (OR) of 1.78 (95% CI: 1.37, 2.33) for LNM prevalence. In subsequent sensitivity analysis, metabolic heterogeneity was observed among patients with a tumor measuring less than 2 cm in the long axis, along with similar differences in the prevalence of lymph node metastasis. This present study successfully categorized clinical early-stage NSCLC into three distinct subgroups, each with unique characteristics that reflect metabolic heterogeneity and significant disparities in the prevalence of LNM. Such an approach holds potential implications for clinical early-stage interventions targeting risk factors.

Artificial Sweeteners: A Double-Edged Sword for Gut Microbiome

Background and Aim: The human gut microbiome plays a crucial role in maintaining health. Artificial sweeteners, also known as non-nutritive sweeteners (NNS), have garnered attention for their potential to disrupt the balance of the gut microbiome. This review explores the complex relationship between NNS and the gut microbiome, highlighting their potential benefits and risks. By synthesizing current evidence, we aim to provide a balanced perspective on the role of AS in dietary practices and health outcomes, emphasizing the need for targeted research to guide their safe and effective use. Methods: A comprehensive literature review was conducted through searches in PubMed and Google Scholar, focusing on the effects of artificial sweeteners on gut microbiota. The search utilized key terms including "Gut Microbiome", "gut microbiota", "Eubiosis", "Dysbiosis", "Artificial Sweeteners", and "Nonnutritive Sweeteners". Results: NNS may alter the gut microbiome, but findings remain inconsistent. Animal studies often report a decrease in beneficial bacteria like Bifidobacterium and Lactobacillus, and an increase in harmful strains such as Clostridium difficile and E. coli, potentially leading to inflammation and gut imbalance. Disruptions in short-chain fatty acid (SCFA) production and gut hormone signaling have also been observed. However, human studies generally show milder or no significant changes, highlighting the limitations in translating animal model findings directly to humans. Differences in study design, dosage, exposure time, and sweetener type likely contribute to these varied outcomes. Conclusions: While NNS offer certain benefits, including reduced caloric intake and improved blood sugar regulation, their impact on gut microbiome health raises important concerns. The observed reduction in beneficial bacteria and the rise in pathogenic strains underscore the need for caution in NNS consumption. Furthermore, the disruption of SCFA production and metabolic pathways illustrates the intricate relationship between diet and gut health.

Recent Advances in Gut Microbiota in Psoriatic Arthritis

Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.

Two-year follow-up of gut microbiota alterations in patients after COVID-19: from the perspective of gut enterotype

Gut microbiota dysbiosis plays a role in the pathogenesis of post-acute coronavirus disease (COVID-19); however, the long-term recovery of the gut microbiota following SARS-CoV-2 infection remains insufficiently understood. In this study, 239 fecal samples were collected from 87 COVID-19 patients during the acute phase, and at 6 months, 1 year, and 2 years post-discharge. An additional 48 fecal samples from non-COVID-19 controls were also analyzed. Gut enterotypes were determined through 16S rRNA sequencing, and dynamic changes from the acute phase through recovery were assessed. Correlations between enterotypes and clinical characteristics were also examined. Two distinct enterotypes were identified: a Blautia-dominated enterotype (Enterotype-B) and a Streptococcus-dominated enterotype (Enterotype-S). Species diversity and richness were significantly higher in Enterotype-B. Enterotype-S, associated with inflammation, was more prevalent during the acute phase. Six months post-discharge, the ratio of Enterotype-B to Enterotype-S approached normal levels. Patients with Enterotype-S at admission had a higher incidence of severe cases during hospitalization and a longer duration of nasopharyngeal viral shedding compared with those with Enterotype-B. Furthermore, at 6 months post-discharge, residual pulmonary Computed Tomography (CT) abnormalities were more common in patients with Enterotype-S (55%) than in those with Enterotype-B (20%, P = 0.046). An index, B/S, representing the ratio of Blautia and Bifidobacterium to Streptococcus, was introduced and found to correlate closely with clinical characteristics. The Streptococcus-dominated enterotype is associated with inflammation and appears to influence both the severity of illness during the acute phase and cardiopulmonary recovery.

IMPORTANCE

This study sheds new light on the intricate process of rehabilitating the gut microbiota following disruptions caused by COVID-19. Our approach, which examines the dynamics from the vantage point of enterotypes, reveals a more rapid recovery than previously reported, with the majority of the microbiota rebounding within a 6-month timeframe. Furthermore, our findings underscore the importance of the Blautia-dominated enterotype as a marker of gut health, which plays a pivotal role in mitigating the risk of severe progression and lingering effects post-SARS-CoV-2 infection. By scrutinizing these enterotypes, we can now foresee the potential severity and aftermath of COVID-19, offering a valuable tool for prognosis and intervention.

Thiamine, gastrointestinal beriberi and acetylcholine signaling

Research has highlighted numerous detrimental consequences of thiamine deficiency on digestive function. These range from impaired gastric and intestinal motility to aberrant changes in pancreatic exocrine function, gastric acidity and disturbances in gut barrier integrity and inflammation. Thiamine and its pharmacological forms, as a primary or adjunctive therapy, have been shown to improve symptoms such as nausea, constipation, dysphagia and intestinal dysmotility, in both humans and animals. This review aims to explore molecular mechanisms underlying the therapeutic action of thiamine in gastrointestinal dysfunction. Our analysis demonstrates that thiamine insufficiency restricted to the gastrointestinal system, i.e., lacking well-known symptoms of dry and wet beriberi, may arise through (i) a disbalance between the nutrient influx and efflux in the gastrointestinal system due to increased demands of thiamine by the organism; (ii) direct exposure of the gastrointestinal system to oral drugs and gut microbiome, targeting thiamine-dependent metabolism in the gastrointestinal system in the first line; (iii) the involvement of thiamine in acetylcholine (ACh) signaling and cholinergic activity in the enteric nervous system and non-neuronal cells of the gut and pancreas, employing both the coenzyme and non-coenzyme actions of thiamine. The coenzyme action relies on the requirement of the thiamine coenzyme form - thiamine diphosphate - for the production of energy and acetylcholine (ACh). The non-coenzyme action involves participation of thiamine and/or derivatives, including thiamine triphosphate, in the regulation of ACh synaptic function, consistent with the early data on thiamine as a co-mediator of ACh in neuromuscular synapses, and in allosteric action on metabolic enzymes. By examining the available evidence with a focus on the gastrointestinal system, we deepen the understanding of thiamine's contribution to overall gastrointestinal health, highlighting important implications of thiamine-dependent mechanisms in functional gastrointestinal disorders.

Nanoparticle-based antifungal therapies innovations mechanisms and future prospects

Fungal infections present an increasing global health challenge, with a substantial annual mortality rate of 1.6 million deaths each year in certain situations. The emergence of antifungal resistance has further complicated treatment strategies, underscoring the urgent need for novel therapeutic approaches. This review explores recent advances in nanoparticle-based therapies targeting fungal infections, emphasizing their unique potential to enhance drug solubility, bioavailability, and targeted delivery. Nanoparticles offer the ability to penetrate biological barriers, improve drug stability, and act as direct antifungal agents by disrupting fungal cell walls and generating reactive oxygen species. Despite their promising applications, challenges such as potential toxicity, scalability of production, and the need for controlled drug release remain. Future research should focus on optimizing nanoparticle properties, evaluating long-term safety profiles, developing environmentally sustainable synthesis methods, and exploring synergistic approaches with existing antifungal drugs. Nanotechnology offers a transformative opportunity in the management of fungal diseases, paving the way for more effective and targeted treatments.

Role of Gut Microbiota and Metabolomics in Predicting Response to Vedolizumab in Inflammatory Bowel Disease: A Systematic Review

Background: This review explores the impact of gut microbiota profiles in predicting the response to anti-integrin biologic therapy, particularly vedolizumab, in inflammatory bowel disease (IBD) patients. IBD, encompassing Crohn's disease and ulcerative colitis, is a chronic inflammatory condition with a growing prevalence linked to industrialization and lifestyle changes. Disruption in the gut microbiota balance, characterized by reduced diversity and altered short-chain fatty acid (SCFA) production, is associated with IBD and its symptoms. Current pharmacological treatments target healing and remission, with vedolizumab offering a gut-selective treatment approach. Methods: A search of the literature was performed on the relationship between anti-integrin treatment and the microbiome profile in IBD. Articles were examined from the PubMed, Medline, Cochrane, and Web of Science databases. Results: This review identified five human studies investigating the relationship between gut microbiome composition, SCFAs, and response to vedolizumab, revealing an increased abundance of beneficial bacteria and levels of SCFAs like butyrate in remission cases. Despite promising findings, the small sample sizes and limited scope of the existing studies highlight the need for larger, comprehensive research. Conclusions: This review underscores the potential of gut microbiome and metabolite profiling as non-invasive biomarkers for IBD severity and treatment outcomes, advocating for personalized therapeutic strategies to enhance efficacy. The insights gained could lead to novel diagnostic and treatment modalities, although further validation is necessary to fully understand the intricate connections between gut microbiota and IBD prognosis.

Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota

Breast cancer is the most commonly diagnosed cancer in women and the second leading cause of female death. Altered interactions between the host and the gut microbiota appear to play an influential role in carcinogenesis. Several studies have shown different signatures of the gut microbiota in patients with breast cancer compared to healthy women. Currently, there is disagreement regarding the different DNA isolation and sequencing methodologies for studies on the human microbiota, given that they can influence the interpretation of the results obtained. The goal of this work was to compare (1) three different DNA extraction strategies to minimize the impact of human DNA, and (2) two sequencing strategies (16S rRNA and shotgun) to identify discrepancies in microbiome results. We made use of breast tissue and fecal samples from both healthy women and breast cancer patients who participated in the MICROMA study (reference NCT03885648). DNA was isolated by means of mechanical lysis, trypsin, or saponin. The amount of eukaryotic DNA isolated using the trypsin and saponin methods was lower compared to the mechanical lysis method (mechanical lysis, 89.11 ± 2.32%; trypsin method, 82.63 ± 1.23%; saponin method, 80.53 ± 4.09%). In samples with a predominance of prokaryotic cells, such as feces, 16S rRNA sequencing was the most advantageous approach. For other tissues, which are expected to have a more complex microbial composition, the need for an in-depth evaluation of the multifactorial interaction between the various components of the microbiota makes shotgun sequencing the most appropriate method. As for the three extraction methods evaluated, when sequencing samples other than stool, the trypsin method is the most convenient. For fecal samples, where contamination by host DNA is low, no prior treatment is necessary.

Nasal microbiome in relation to olfactory dysfunction and cognitive decline in older adults

Emerging evidence has highlighted that olfactory dysfunction, a common feature of aging, is increasingly linked to cognitive decline in older adults. However, research on the underlying mechanism, particularly the role of nasal microbiome, remains limited. In this study, we investigated the associations between olfactory function, the nasal microbiome, and cognition among 510 older adults with an average age of 77.9 years. Olfactory function was assessed using the brief Chinese Smell Identification Test, and cognitive assessments were conducted via the Mini-Mental State Examination and the Revised Hasegawa Dementia Scale. Nasal microbiome profiles were generated through 16S RNA gene sequencing. We observed that olfactory dysfunction (i.e., hyposmia) was associated with a higher richness of nasal bacteria, and such observation was replicated in an external dataset. A total of 18 nasal bacterial genera were identified to be associated with olfactory function, with eight genera such as Acidovorax and Morganella being enriched in the hyposmic group. A composite microbial index of nasal olfactory function significantly improved the reclassification accuracy of traditional risk model in distinguishing hyposmic from normosmic participants (P = 0.008). Furthermore, participants with a nasal biotype dominated by Corynebacterium had a lower prevalence of mild cognitive impairment compared to those dominated by Dolosigranulum or Moraxella. Our findings suggested that the nasal microbiome may play a role in the association of olfactory function with cognition in older adults, providing new insights into the microbial mechanisms underlying hyposmia and cognitive decline.

Body mass index matters: morbid obese patients have different microorganism profiles in the setting of periprosthetic hip joint infections

PURPOSE

This study investigated the relationship between BMI and microorganism profiles, with a particular focus on gut microorganisms in patients with PJI following total hip arthroplasty (THA). It also explored comorbidities, that may contribute to these variations.

METHODS

This study included all patients treated at our institution for a PJI of a THA between 1996 and 2021. Patients were categorized into four distinct BMI groups: <30; 30-34.9; 35-39.9; ≥ 40. Bivariate and logistic regression analysis were conducted, with presentation of odds ratio (OR) and 95% confidence interval (CI).

RESULTS

A total of 3645 hip PJI cases were recruited for the final analysis. Patients with a BMI ≥ 40 had approximately a ten fold higher risk for Streptococcus dysgalactiae (p < 0.001; OR = 9.92; 95% CI 3.87-25.44) and a seven fold higher risk for Proteus mirabilis (p < 0.001; OR = 7.43; 95% CI 3.13-17.67) and Klebsiella pneumoniae (p < 0.001; OR = 6.9; 95% CI 2.47-19.31). Furthermore, polymicrobial infections (p < 0.001; OR = 2.17; 95% CI 1.50-3.15) were found to be significantly more prevalent in patients with a BMI ≥ 40.

CONCLUSION

Obese patients (BMI ≥ 30) displayed a distinct microorganism profile in hip PJIs, mainly dominated by Firmicutes and Proteobacteria. Comorbidities such as diabetes, hypertension, and hyperlipidaemia may contribute to a leaky gut syndrome, increasing PJI risk caused by gut microorganisms. Optimizing comorbidities may help reduce the risk of hip PJI. Further research is needed to clarify the relationship between obesity, gut microbiome alterations and hip PJI development.

Functional diversification of dietary plant small molecules by the gut microbiome

Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the Bacteroides, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This Bacteroides metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen Clostridioides difficile via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone "effector" functions by a distinct gut-microbiome-encoded PSM-processing system.

Therapeutic potential of faecal microbiota transplantation for alcohol use disorder, a narrative synthesis

BACKGROUND

Faecal microbiota transplantation is proposed as an alternative therapy to treat alcohol use disorder and has completed a Phase 1 clinical trial, with a Phase 2 clinical trial underway. Alcohol, a modifiable risk factor for noncommunicable diseases, resulted in approximately 3 million global deaths (5 %) in 2016 according to the World Health Organization.

AIMS

A narrative synthesis examines the effects of alcohol and faecal microbiota transplantation on gut microbiota and how gut microbiota impacts the gut-brain axis, leading to certain behavioural symptoms of alcohol use disorder. These behavioural symptoms are alcohol craving and relapse in humans; and preference for alcohol, anxiety and depression in rodents.

SEARCH METHODS AND RESULTS

Electronic databases PubMed, Embase, and Scopus were searched in January 2024 using the terms: faecal microbiota trans* AND alcohol AND microbio*. Ten studies out of 964 met the inclusion criteria of published primary studies with faecal microbiota transplantation as an intervention to study the gut-brain axis in alcohol use disorder.

RESULTS

The gut microbiota is altered in alcohol use disorder, which can be modified with faecal microbiota transplantation. Behavioural symptoms such as alcohol craving and relapse are associated with inflammation due to a loss of intestinal barrier function. Beneficial microbiota produce short-chain fatty acids that maintain intestinal barrier function and reduce inflammation. Studies also reported anxiety and depression-like behaviours, in addition to a preference for alcohol in alcohol-naïve rodents after faecal microbiota transplantation from patients with alcohol use disorder.

CONCLUSIONS

Faecal microbiota transplantation may moderate the behavioural symptoms of alcohol use disorder by altering gut microbiota, affecting intestinal permeability and inflammation, however, specific gut microbiota composition and long-term treatment outcomes require further clinical studies.

Supplementation With Human Foods Affects the Gut Microbiota of Wild Howler Monkeys

Wild primates face a wide range of anthropogenic influences globally that impact their health, fitness, and survival. One area of potential impact that has been particularly understudied is the supplementation of wild primate diets with human foods. Although the consumption of human foods represents a substantial dietary change for wild primates, knowledge of how it impacts their physiology and behavior is limited. Here we explore how human food supplementation impacts wild primates by comparing the gut microbiomes of free-ranging brown howler monkeys (Alouatta guariba) in periurban Brazil that do or do not have access to human foods. We found that howler monkeys consuming human foods had reduced gut microbial diversity and reduced relative abundances of fiber degrading microbial taxa, which has been associated with negative health consequences in other animals, including humans. However, the effect size of these differences was relatively small and varied over time. Additionally, the composition of the gut microbiome varied significantly across months, regardless of the access to human foods. We suggest that the biology of this howler monkey population is minimally impacted by human foods. Further empirical research will help clarify the relationship between human food supplementation and health across primate populations, facilitating conservation applications.

Gestational diabetes mellitus - more than the eye can see - a warning sign for future maternal health with transgenerational impact

Gestational diabetes mellitus (GDM) is regarded by many as maternal maladaptation to physiological insulin resistance during the second half of pregnancy. However, recent evidence indicates that alterations in carbohydrate metabolism can already be detected in early pregnancy. This observation, the increasing prevalence of GDM, and the significant short and long-term implications for the mother and offspring call for reevaluation of the conceptual paradigm of GDM as a syndrome. This review will present evidence for the syndromic nature of GDM and the controversies regarding screening, diagnosis, management, and treatment.

Iron Fortification and Inulin Supplementation in Early Infancy: Evaluating the Impact on Gut Microbiome in a Piglet Model

Background

Prophylactic iron fortification in infant formula effectively prevents iron deficiency anemia. However, the low absorption rate results in excess unabsorbed iron accumulates in colon, where it has been linked to harmful microbiota changes and increased diarrheal incidence. Prebiotic oligosaccharides have shown promise in mitigating these adverse effects, but the role of inulin or synbiotic supplementation with inulin-fermenting lactic acid bacteria in modulating early gut microbiome under iron fortification remains understudied.

Objectives

This study used a neonatal pig model to investigate the effects of iron fortification and inulin supplementation, with or without Ligilactobacillus agilis YZ050 (L. agilis), on gut microbiome.

Methods

Twenty-four piglets were stratified and randomly assigned into 1 of the 4 dietary treatments from postnatal day (PD) 2: iron-adequate milk (AI), high-iron milk (HI), high-iron milk with 5% inulin (HIP), or HIP milk with oral gavage of L . agilis every third day (HIS). Piglets were individually housed and fed milk in proportion to body weight in 14 meals daily, simulating formula feeding in infants. Fecal and colonic microbiome were analyzed via 16S rRNA sequencing, with microbial diversity and relative abundance analyzed using QIIME2 and R.

Results

Iron fortification, regardless of inulin supplementation, decreased α-diversity compared with AI. β-Diversity showed clustering of HIP and HIS samples, which were distinct from AI and HI. Although iron fortification had minor impact on microbial composition, inulin supplementation significantly modified microbiome diversity, increasing Prevotella, Megasphaera, and Lachnospiraceae_NK3A20_group species, while reducing Bacteroides and Ruminococcus. Colonic microbiome shifted from Bacteroides-dominant enterotype in AI and HI groups to Prevotella-dominant enterotype in HIP and HIS groups, indicating enhanced fiber degrading capacity. Despite its inulin-fermenting property, L . agilis showed limited colonization and minimal microbiome impact.

Conclusions

Inulin supplementation significantly influenced gut microbiome, shifting enterotype from Bacteroides to Prevotella. dominance and overriding the effect of high-iron fortification in a milk-fed piglet model.

The gut microbiome as a potential therapeutic target in IgA nephropathy

Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis and a leading cause of kidney failure, with limited treatment options available. The pathophysiology of IgAN remains unclear; however, recent studies suggest that genetic, epigenetic and environmental factors play significant roles. There is also strong evidence linking the gut microbiome to the development of IgAN. In this review, we will examine the relationship between the microbiome and the pathogenesis of IgAN, as well as its potential as a target for future therapeutic interventions.

Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses

Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.

Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance

BACKGROUND & AIMS

Cirrhosis complications are often triggered by bacterial infections with multidrug-resistant organisms. Alterations in the gut and oral microbiome in decompensated cirrhosis (DC) influence clinical outcomes. We interrogated: (i) gut and oral microbiome community structures, (ii) virulence factors (VFs) and antimicrobial resistance genes (ARGs) and (iii) oral-gut microbial overlap in patients with differing cirrhosis severity.

METHODS

Fifteen healthy controls (HCs), as well as 26 patients with stable cirrhosis (SC), 46 with DC, 14 with acute-on-chronic liver failure (ACLF) and 14 with severe infection without cirrhosis participated. Metagenomic sequencing was undertaken on paired saliva and faecal samples. 'Salivatypes' and 'enterotypes' based on genera clustering were assessed against cirrhosis severity and clinical parameters. VFs and ARGs were evaluated in oral and gut niches, and distinct resistotypes identified.

RESULTS

Salivatypes and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity and hyperammonaemia. Increasing overlap between oral and gut microbiome communities was observed in DC and ACLF vs. SC and HCs, independent of antimicrobial, beta-blocker and gastric acid-suppressing therapies. Two distinct gut microbiome clusters harboured genes encoding for the PTS (phosphoenolpyruvate:sugar phosphotransferase system) and other VFs in DC and ACLF. Substantial ARGs (oral: 1,218 and gut: 672) were detected (575 common to both sites). The cirrhosis resistome was distinct, with three oral and four gut resistotypes identified, respectively.

CONCLUSIONS

The degree of oral-gut microbial community overlap, frequency of VFs and ARGs all increase significantly with cirrhosis severity, with progressive dominance of pathobionts and loss of commensals. Despite similar antimicrobial exposure, patients with DC and ACLF have reduced microbial richness compared to patients with severe infection without cirrhosis, supporting the additive pathobiological effect of cirrhosis.

IMPACT AND IMPLICATIONS

This research underscores the crucial role of microbiome alterations in the progression of cirrhosis in an era of escalating multidrug resistant infections, highlighting the association and potential impact of increased oral-gut microbial overlap, virulence factors, and antimicrobial resistance genes on clinical outcomes. These findings are particularly significant for patients with decompensated cirrhosis and acute-on-chronic liver failure, as they reveal the intricate relationship between microbiome alterations and cirrhosis complications. This is relevant in the context of multidrug-resistant organisms and reduced oral-gut microbial diversity that exacerbate cirrhosis severity, drive hepatic decompensation and complicate treatment. For practical applications, these insights could guide the development of targeted microbiome-based therapeutics and personalised antimicrobial regimens for patients with cirrhosis to mitigate infectious complications and improve clinical outcomes.

Gut Microbiota and Their Metabolites: The Hidden Driver of Diabetic Nephropathy? Unveiling Gut Microbe's Role in DN

BACKGROUND

Diabetic nephropathy (DN) is a severe microvascular complication of diabetes with a complex pathogenesis.

METHODS

Recent studies were reviewed to explore the role of gut microbiota and its metabolites in DN development.

RESULTS

Dysbiosis of gut bacteria contributes to pathological changes such as glomerular sclerosis and renal tubule injury. Microbial metabolites are involved in DN through immune and inflammatory pathways.

CONCLUSIONS

Understanding the relationship between gut microbiota, its metabolites, and DN may offer potential implications for DN diagnosis, prevention, and treatment. Translating this knowledge into clinical practice presents challenges and opportunities.

Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices

We assessed the analytical performance of metagenomic workflows using NIST Reference Material (RM) 8376 DNA from bacterial pathogens spiked into two simulated clinical samples: cerebrospinal fluid (CSF) and stool. Sequencing and taxonomic classification were used to generate signals for each sample and taxa of interest and to estimate the limit of detection (LOD), the linearity of response, and linear dynamic range. We found that the LODs for taxa spiked into CSF ranged from approximately 100 to 300 copy/mL, with a linearity of 0.96 to 0.99. For stool, the LODs ranged from 10 to 221 kcopy/mL, with a linearity of 0.99 to 1.01. Furthermore, discriminating different E. coli strains proved to be workflow-dependent as only one classifier:database combination of the three tested showed the ability to differentiate the two pathogenic and commensal strains. Surprisingly, when we compared the linear response of the same taxa in the two different sample types, we found those functions to be the same, despite large differences in LODs. This suggests that the "agnostic diagnostic" theory for metagenomics (i.e., any organism can be identified because DNA is the measurand) may apply to different target organisms and different sample types. Because we are using RMs, we were able to generate quantitative analytical performance metrics for each workflow and sample set, enabling relatively rapid workflow screening before employing clinical samples. This makes these RMs a useful tool that will generate data needed to support the translation of metagenomics into regulated use.IMPORTANCEAssessing the analytical performance of metagenomic workflows, especially when developing clinical diagnostics, is foundational for ensuring that the measurements underlying a diagnosis are supported by rigorous characterization. To facilitate the translation of metagenomics into clinical practice, workflows must be tested using control samples designed to probe the analytical limitations (e.g., limit of detection). Spike-ins allow developers to generate fit-for-purpose control samples for initial workflow assessments and inform decisions about further development. However, clinical sample types include a wide range of compositions and concentrations, each presenting different detection challenges. In this work, we demonstrate how spike-ins elucidate workflow performance in two highly dissimilar sample types (stool and CSF), and we provide evidence that detection of individual organisms is unaffected by background sample composition, making detection sample-agnostic within a workflow. These demonstrations and performance insights will facilitate the translation of the technology to the clinic.

Dynamic changes in the gut microbiota play a critical role in age-associated cognitive dysfunction via SCFAs and LPS synthesis metabolic pathways during brain aging

BACKGROUND

Gut microbiota plays an essential role in cognitive dysfunction during aging. The aim of this study was to investigate the dynamic alterations in the gut microbiota and screen for key gut bacterial taxa correlated with age-associated cognitive dysfunction during natural aging.

METHODS

16S rRNA gene sequencing was performed to determine the composition of the gut microbiota in faecal samples from SAMR1 and SAMP8 mice, cognitively normal controls (NC), and patients with amnestic mild cognitive impairment (aMCI). Faecal microbiota transplantation (FMT) and GMrepo database were used to screen key gut microbiota associated with cognitive decline in aging mice and humans.

RESULTS

The composition of the gut microbiota dynamically changed during natural aging in SAMR1 and SAMP8 mice, as well as in healthy subjects of different ages extracted from the GMrepo database. FMT from SAMR1 to SAMP8 mice altered the gut microbiota composition and improved the cognitive impairment in SAMP8 mice. Key gut bacterial taxa, including Lactobacillus, Akkermansia, Clostridium, Oscillospira and Dorea, were screened and validated to correlate with aging-associated cognitive decline. The function of the key gut bacterial taxa predicted by PICRUSt2 indicated that the metabolic pathways related to short-chain fatty acids (SCFAs) and lipopolysaccharide (LPS) synthesis were involved in age-associated cognitive dysfunction during natural aging.

CONCLUSION

These results demonstrate that the composition of the gut microbiota changes dynamically during brain aging, with some key gut bacterial taxa playing critical roles in age-associated cognitive dysfunction through SCFAs and LPS synthesis metabolic pathways.

The Role of Intestinal Fungi in the Pathogenesis and Treatment of Ulcerative Colitis

Ulcerative colitis (UC) is a chronic inflammatory bowel disease closely associated with dysbiosis of the gut microbiome, encompassing not only bacterial communities but also fungal populations. Despite the growing recognition of the gut microbiome's role in UC pathogenesis, the contribution of intestinal fungi has only recently garnered significant attention. In this review, we comprehensively examine the characteristics of intestinal fungi in both healthy individuals and UC patients, elucidating their role in disease pathogenesis and their interactions with bacterial communities. Additionally, we explore the impact of intestinal fungi on disease severity and therapeutic responses in UC. Furthermore, we evaluate the therapeutic potential of antifungal agents, probiotics, and fecal microbiota transplantation (FMT) in UC management, emphasizing the critical role of fungi in these treatment modalities. Future research should prioritize elucidating the multifunctional roles of fungi in UC pathogenesis and their implications for treatment strategies. Moreover, the identification of fungal biomarkers associated with FMT efficacy could pave the way for precision medicine approaches in FMT, offering novel insights into personalized therapeutic interventions for UC.

Replicating community dynamics reveals how initial composition shapes the functional outcomes of bacterial communities

Bacterial communities play key roles in global biogeochemical cycles, industry, agriculture, human health, and animal husbandry. There is therefore great interest in understanding bacterial community dynamics so that they can be controlled and engineered to optimise ecosystem services. We assess the reproducibility and predictability of bacterial community dynamics by creating a frozen archive of hundreds of naturally-occurring bacterial communities that we repeatedly revive and track in a standardised, complex resource environment. Replicate communities follow reproducible trajectories and the community dynamics closely map to ecosystem functioning. However, even under standardised conditions, the communities exhibit tipping-points, where small differences in initial community composition create divergent compositional and functional outcomes. The predictability of community trajectories therefore requires detailed knowledge of rugged compositional landscapes where ecosystem properties are not the inevitable result of prevailing environmental conditions but can be tilted toward different outcomes depending on the initial community composition. Our results shed light on the relationship between composition and function, opening new avenues to understand the feasibility and limitations of function prediction in complex microbial communities.

Fecal microbiota transplantation: transitioning from chaos and controversial realm to scientific precision era

With the popularization of modern lifestyles, the spectrum of intestinal diseases has become increasingly diverse, presenting significant challenges in its management. Traditional pharmaceutical interventions have struggled to keep pace with these changes, leaving many patients refractory to conventional pharmaceutical treatments. Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic approach for enterogenic diseases. Still, controversies persist regarding its active constituents, mechanism of action, scheme of treatment evaluation, indications, and contraindications. In this review, we investigated the efficacy of FMT in addressing gastrointestinal and extraintestinal conditions, drawing from follow-up data on over 8000 patients. We systematically addressed the controversies surrounding FMT's clinical application. We delved into key issues such as its technical nature, evaluation methods, microbial restoration mechanisms, and impact on the host-microbiota interactions. Additionally, we explored the potential colonization patterns of FMT-engrafted new microbiota throughout the entire intestine and elucidated the specific pathways through which the new microbiota modulates host immunity, metabolism, and genome.

Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients

OBJECTIVE

Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.

METHODS

In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.

RESULTS

Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R2>0.20), perceptual disturbance (maximum AUROC=0.763, R2=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.

CONCLUSIONS

Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.

Exercise-driven gut microbiota alterations enhance colonization resistance against methicillin-resistant Staphylococcus aureus

Gut microbiota plays a crucial role in resisting the invasion of pathogens, particularly multidrug-resistant (MDR) bacteria, which pose a significant threat to public health. While exercise offers numerous health benefits, its impact on host colonization resistance remains largely unclear. In this study, we demonstrate that moderate exercise significantly reduces gut colonization by methicillin-resistant Staphylococcus aureus (MRSA), a clinically important MDR pathogen. Moreover, we identify an understudied strain of the intestinal probiotic Dubosiella newyorkensis (L8) as a critical factor in mediating exercise-induced colonization resistance against MRSA. Mechanistically, L8 enhances the deprivation of fucose, a crucial carbon source essential for MRSA growth and pathogenicity. This process relies on the high binding affinity of pyruvate to the ILE257 site of the lactate dehydrogenase in L8. Overall, our work highlights the importance of moderate exercise in maintaining host colonization resistance and demonstrates L8 as a probiotic in protecting against MRSA colonization.

Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine

The intestinal tract extends several times the length of bodies, with varying environmental conditions across different segments (small intestinal and large intestinal), thereby harboring distinct gut microbiota. Most studies focused on the quantitative responses of gut microbiota upon probiotics entering the gut, without an in-depth analysis of how the genetic change in local gut microbiota. Therefore, in this experiment, C57BL/6J male mice were once administered Lactiplantibacillus plantarum HNU082 (Lp082). Then, the mice were euthanized on the 1st, 3rd, and 7th days after gavage, and the contents of the small and large intestines of the mice were scraped for metagenomic analysis. Based on the characterization of large intestine and small intestine bacteria, changes in the diversity and abundance of single-nucleotide variants (SNVs) of microbiota were analyzed. There were observable distinct responses at the genetic level. A significant number of SNVs were identified in Ligilactobacillus murinus in the large intestine. These SNVs may impact the utilization of carbohydrates in L. murinus. Ingested probiotics traversed the entire gut and interacted with the indigenous microbiota, driving the evolution of the indigenous gut microbiota in the different intestinal segments, thereby influencing microbial growth and metabolism. This study investigates the role of probiotics in the evolution of gut microbiota. It offers new probiotic insights and a basis for targeted interventions.

Protein Biomarkers of DNA Damage in Yeast Cells for Genotoxicity Screening

Providing an unbiased and comprehensive view of the DNA damage response in cells is critical in genotoxicity screening to identify substances that cause diverse types of DNA damage. Considering that S. cerevisiae is one of the most well-characterized model organisms in molecular and cellular biology, we created a map of the DNA damage response network containing the reported signaling pathways in yeast cells programmed to constitutively respond to DNA damage. A collection of GFP-fused S. cerevisiae yeast strains treated with typical genotoxic agents illuminated the cellular response to DNA damage, thereby identifying 15 protein biomarkers encompassing all eight documented DNA damage response pathways. Three statistical and one deep learning models were proposed to interpret the quantitative molecular toxicity end point, i.e. protein effect level index (PELI), by introducing weights of 15 biomarkers in genotoxicity assessment. The method based on standard deviation exhibited the best performance, with an R 2 of 0.916 compared to the SOS/umu test and an R 2 of 0.989 compared to the comet assay. The GFP-fused yeast-based proteomic assay has minute-level resolution of pathway activation data. It provides a concise alternative for fast, efficient, and mechanistic genotoxicity screening for various environmental and health applications.

Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition

Endotoxin-driven systemic immune activation is a common hallmark across various clinical conditions. During acute critical illness, elevated plasma lipopolysaccharide triggers non-specific systemic immune activation. In addition, a compositional shift in the gut microbiota, including an increase in gut-luminal opportunistic pathogens, is observed. Whether a causal link exists between acute endotoxemia and abundance of gut-luminal opportunistic pathogens is incompletely understood. Here, we model acute, pathophysiological lipopolysaccharide concentrations in mice and show that systemic exposure promotes a 100-10'000-fold expansion of Klebsiella pneumoniae, Escherichia coli, Enterococcus faecium and Salmonella Typhimurium in the gut within one day, without overt enteropathy. Mechanistically, this is driven by a Toll-like receptor 4-dependent increase in gut-luminal oxygen species levels, which transiently halts microbiota fermentation and fuels growth of gut-luminal facultative anaerobic pathogens through oxidative respiration. Thus, systemic immune activation transiently perturbs microbiota homeostasis and favours opportunistic pathogens, potentially increasing the risk of infection in critically ill patients.

Exploring the female genital tract mycobiome in young South African women using metaproteomics

BACKGROUND

Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women.

RESULTS

We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition.

CONCLUSIONS

The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract.

Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients

Colon cancer (CC) is one of the most common cancers globally, which is associated with the gut microbiota intimately. In current research, exploring the complex interaction between microbiomes and CC is a hotspot. However, the information on microbiomes in most previous studies is based on fecal, which does not fully display the microbial environment of CC. Herein, we collected mucosal and tissue samples from both the tumor and normal regions of 19 CC patients and clarified the composition of mucosal microbiota by 16S rRNA and metagenomic sequencing. Additionally, RNA-Seq was also conducted to identify the different expression genes between tumor and normal tissue samples. We revealed significantly different microbial community structures and expression profiles to CC. Depending on correlation analysis, we demonstrated that 1,472 genes were significantly correlated with CC tumor microbiota. Our study reveals a significant enrichment of Campylobacter jejuni in the mucosa of CC, which correlates with bile secretion. Additionally, we observe a negative correlation between C. jejuni and immune cells CD4+ Tem and mast cells. Finally, we discovered that metabolic bacterial endosymbiont of Bathymodiolus sp., Bacillus wiedmannii, and Mycobacterium tuberculosis had a significant survival value for CC, which was ignored by previous research. Overall, our study expands the understanding of the complex interplay between microbiota and CC and provides new targets for the treatment of CC.

IMPORTANCE

This study contributes to our understanding of the interaction between microbiota and colon cancer (CC). By examining mucosal and tissue samples rather than solely relying on fecal samples, we have uncovered previously unknown aspects of CC-associated microbiota. Our findings reveal distinct microbial community structures and gene expression profiles correlated with CC progression. Notably, the enrichment of Campylobacter jejuni in CC mucosa, linked to bile secretion, underscores potential mechanisms in CC pathogenesis. Additionally, observed correlations between microbial taxa and immune cell populations offer new avenues for immunotherapy research in CC. Importantly, this study introduces CC-associated microbiota with survival implications for CC, expanding therapeutic targets beyond conventional strategies. By elucidating these correlations, our study not only contributes to uncovering the potential role of gut microbiota in colon cancer but also establishes a foundation for mechanistic studies of gut microbiota in colon cancer, emphasizing the broader impact of microbiota research on cancer biology.

Mechanism of liver x receptor alpha in intestine, liver and adipose tissues in metabolic associated fatty liver disease

Metabolism associated fatty liver disease (MAFLD) has emerged as a growing global health challenge with limited effective treatments. Research on nuclear receptors offers promising new therapeutic avenues for MAFLD. The liver X receptor (LXR) has gained attention for its roles in tumors and metabolic and inflammatory diseases; However, its effects on MAFLD treatment remain a subject of debate. This review explores the therapeutic role of LXRα in MAFLD, focusing on its functions in the intestine, hepatic and adipose tissue, and summarizes recent advancements in LXRα ligands over the past five years. In the intestine, LXRα activation enhances the efflux of non-biliary cholesterol and reduces inflammation in the gut-liver axis by regulating intestinal high-density lipoprotein synthesis and its interaction with lipopolysaccharide. In the liver, LXRα activation facilitates cholesterol transport, influences hepatic lipid synthesis, and exerts anti-inflammatory effects. In adipose tissue, LXRα helps delay MAFLD progression by managing lipid autophagy and insulin resistance. Ligands that modulate LXRα transcriptional activity show considerable promise for MAFLD treatment.

Bile-Liver phenotype: Exploring the microbiota landscape in bile and intratumor of cholangiocarcinoma

Cholangiocarcinoma (CCA) arises within the peritumoral bile microenvironment, yet microbial translocation from bile to intracholangiocarcinoma (IntraCCA) tissues remains poorly understood. Previous studies on bile microbiota alterations from biliary benign disease (BBD) to CCA have yielded inconsistent results, highlighting the need for cross-study analysis. We presented a comprehensive analysis of five cohorts (N = 266), including our newly established 16S rRNA gene profiling (n = 42), to elucidate these microbiota transitions. The concordance of bacteria between CCA bile and intraCCA tissue, represented by Enterococcus and Staphylococcus, suggested microbiota migration from bile to intratumoral tissues. A computational random forest machine learning model effectively distinguished intraCCA tissue from CCA bile, identifying Rhodococcus and Ralstonia as diagnostically significant. The model also excelled in differentiating CCA bile from BBD bile, achieving an AUC value of 0.931 in external validation. Using unsupervised hierarchical clustering, we established Biletypes based on microbial signatures in our cohort. A combination of 17 genera effectively stratified patients into Biletype A and Biletype B. Biletype B robustly discerned CCA from BBD, with Sub-Biletype B1 correlating with advanced TNM stage and poorer prognosis. Among the 17 genera, bacterial Cluster 1, composed of Sphingomonas, Staphylococcus, Massilia, Paenibacillus, Porphyrobacter, Lawsonella, and Aerococcus, was enriched in Biletype B1 and predicted CCA with an AUC of 0.96. Staphylococcus emerged as a promising single-genus predictor for CCA diagnosis and staging. In conclusion, this study delineates a potential microbiota transition pathway from the gut through CCA bile to intra-CCA tissue, proposing Biletypes and Staphylococcus as biomarkers for CCA prognosis.

Alterations of gut microbiota for the onset and treatment of psoriasis: A systematic review

Psoriasis is a chronic, recurrent and systemic inflammatory skin disease which is mediated by immunoreaction. Its pathogenesis is multifactorial, and the exact driving factor remains unclear. Recent studies showed that gut microbiota, which maintain immune homeostasis of our bodies, is closely related with occurrence, development and prognosis of psoriasis. The intestinal microbial abundance and diversity in patients with psoriasis have changed significantly, including intestinal microbiota disorders and reduced production of short chain fatty acids (SCFAs), abnormalities in Firmicutes/Bacteroidetes (F/B), etc. Besides, the intestinal microbiota of psoriasis patients has also changed after treatment of systemic drugs, biologics and small molecule chemical drugs, suggesting that the intestinal microbiota may be a potential response-to-treatment biomarker for evaluating treatment effectiveness. Oral probiotics and prebiotics administration as well as fecal microbial transplantation were also reported to benefit well in psoriasis patients. Additionally, we also discussed the microbial changes from the skin and other organs, which regulated both the onset and treatment of psoriasis together with gut microbiota. Herein, we reviewed recent studies on the psoriasis-related microbiota in an attempt to confidently identify the "core" microbiota of psoriatic patients, understand how microbiota influence psoriasis through the gut-skin axis, and explore potential therapeutic strategies for psoriasis.

Gut microbiota and risk of heart failure in European population-A comprehensive Mendelian randomization study

AIMS

Gut dysbiosis is proven to be involved in the pathogenesis and progression of heart failure (HF). Hindering the detrimental effects of gut-heart axis is an emerging trend. Our goal is to investigate the causal relationship between gut microbiota and HF, with the aim of facilitating future exploration of microbiome-targeted approaches to prevent and delay the progression of HF.

METHODS AND RESULTS

Two-sample Mendelian randomization (MR) analysis was applied to investigate the causal association of the gut microbiome with HF among individuals of European ancestry. Genetic variants associated with the 196 bacterial taxa from MiBioGen consortium were used as exposure data, summary statistics for HF derived from Heart Failure Molecular Epidemiology for Therapeutic Targets (HERMES) consortium were used as outcome data. Five MR methods were applied, including inverse variance weighted, maximum likelihood, MR-Egger, weighted median, and weighted mode. Reverse causality of instrumental variables (IVs) was tested by MR Steiger test of directionality. Strength of IVs was evaluated by F-statistics. Cochrane's Q test, MR-Egger regression analysis, and MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) tests were used to detect heterogeneity and pleiotropy. Leave-one-out method was used for testing the stability of results. Seven microbiomes were found to be associated with HF. Five of them were associated with higher risks of developing HF, these included Order_Selenomonadales (odds ratio [OR] = 1.11, P = 0.024), Family_Peptococcaceae (OR = 1.07, P = 0.045), Genus_Eubacterium eligens group (OR = 1.14, P = 0.022), Genus_Eubacterium oxidoreducens group (OR = 1.12, P = 0.011) and Genus_Flavonifractor (OR = 1.14, P = 0.012). Genus_Anaerostipes and Order_Bacillales were associated with lower risks of HF (OR = 0.90, P = 0.014; OR = 0.95, P = 0.042, respectively). Evidence of pleiotropy or heterogeneity was not observed.

CONCLUSIONS

We identified seven intestinal microbiomes that were causally associated with HF at the level of gene prediction. This study will help with the discovery of potential preventive and therapeutic targets for HF.

Machine learning-derived diagnostic model of epithelial ovarian cancer based on gut microbiome signatures

BACKGROUND

Prior studies have elucidated that alterations in gut microbiota are associated with a spectrum of tumors and metabolic disorders. However, the diagnostic value of gut microbiota in epithelial ovarian cancer remains insufficiently investigated.

METHODS

A total of 34 patients with a diagnosis of epithelial ovarian cancer (EOC), 15 patients with benign ovarian tumors (TB), and 30 healthy volunteers (NOR) were enrolled in this study. Fecal samples were collected, followed by sequencing of the V3-V4 region of the 16S rRNA gene. The clinical data and pathological characteristics were comprehensively recorded for further analysis, PICRUSt2 was utilized to conduct an analysis of microbial functional predictions, WGCNA networks were constructed by integrating microbiome and clinical data. LEfSe analysis was employed to identify microbial diagnostic markers, LASSO and SVM analyses were used to screen microbial diagnostic markers in conjunction with the Cally index, to establish a Microbial-Cally diagnostic model. Bootstrap resampling was utilized for the internal validation of the model, whereas the Hosmer-Lemeshow test and decision curve analysis (DCA) were employed to evaluate the diagnostic performance of the model. Plasma samples were subjected to untargeted metabolomics profiling, followed by differential analysis to identify key metabolites that are significantly altered in epithelial ovarian cancer. At the same time, Spearman correlation analysis was used to study the association between key microbiota and differential metabolites. The supernatants from Escherichia coli and Bifidobacterium cultures were co-cultured with SKOV3 cells. Cell proliferation, migration, and invasion were evaluated using Cell Counting Kit-8 (CCK-8) assay, Transwell migration and invasion assays. Apoptosis was assessed by flow cytometry analysis of fluorescence signals from Annexin V and propidium iodide (PI) staining.

RESULTS

Compared to Nor and TB populations, individuals diagnosed with EOC demonstrated a significantly diminished gut microbiota diversity when contrasted with both normal controls and those presenting benign conditions. Specifically, the relative abundance of Bilophila, Bifidobacterium, and other probiotics was significantly reduced in patients diagnosed with epithelial ovarian cancer (EOC), while Escherichia and Shigella demonstrated a marked enrichment within this cohort. Differential microorganisms were identified through the application of machine learning techniques to delineate the characteristic microbial profiles associated with the EOC patients. A significant correlation was identified between the Cally index and microorganisms. In conclusion, we utilized microbial biomarkers alongside the Cally to establish a diagnostic model for epithelial ovarian cancer, receiver operating characteristic (ROC) curve Area Under Curve (AUC) of 0.976 (95%CI 0.943-1.00), The AUC obtained from the Bootstrap internal validation was 0.974. The Hosmer-Lemeshow test revealed a robust concordance between the observed probabilities and the predicted probabilities generated by the model. The decision curve analysis revealed that the model provided a significant net clinical benefit. A total of 233 differential metabolites were identified between the EOC group and the NT (NOR and TB) groups. Among these, eight specific metabolites (HMDB0243492, C09265, HMDB0242046, HMDB0240606, C04171, HMDB0060557, HMDB0252797, and C21412) were exclusively derived from the microbiome. Notably, metabolite HMDB0240606 exhibited a significant positive correlation with Escherichia coli and Shigella, while it showed a significant negative correlation with Ruminococcus. In vitro studies demonstrated that Bifidobacterium possessed anti-tumor activity, whereas Escherichia coli exhibited pro-tumor activity.

CONCLUSION

This study provides the inaugural comprehensive analysis of gut microbiota composition and its differential profiles among patients with epithelial ovarian cancer, those with benign ovarian tumors, and healthy controls in Hunan province, China.