Application of emerging technologies for gut microbiome research

Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy

INTRODUCTION

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.

AREAS COVERED

we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.

EXPERT OPINION

Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.

Interaction between post-tumor inflammation and vascular smooth muscle cell dysfunction in sepsis-induced cardiomyopathy

Background

Sepsis-induced cardiomyopathy (SIC) presents a critical complication in cancer patients, contributing notably to heart failure and elevated mortality rates. While its clinical relevance is well-documented, the intricate molecular mechanisms that link sepsis, tumor-driven inflammation, and cardiac dysfunction remain inadequately explored. This study aims to elucidate the interaction between post-tumor inflammation, intratumor heterogeneity, and the dysfunction of VSMC in SIC, as well as to evaluate the therapeutic potential of exercise training and specific pharmacological interventions.

Methods

Transcriptomic data from NCBI and GEO databases were analyzed to identify differentially expressed genes (DEGs) associated with SIC. Weighted gene co-expression network analysis (WGCNA), gene ontology (GO), and KEGG pathway enrichment analyses were utilized to elucidate the biological significance of these genes. Molecular docking and dynamics simulations were used to investigate drug-target interactions, and immune infiltration and gene mutation analyses were carried out by means of platforms like TIMER 2.0 and DepMap to comprehend the influence of DVL1 on immune responsiveness.

Results

Through the utilization of the datasets, we discovered the core gene DVL1 that exhibited remarkable up-regulated expression both in SIC and in diverse kinds of cancers, which were associated with poor prognosis and inflammatory responses. Molecular docking revealed that Digoxin could bind to DVL1 and reduce oxidative stress in SIC. The DVL1 gene module related to SIC was identified by means of WGCNA, and the immune infiltration analysis demonstrated the distinctive immune cell patterns associated with DVL1 expression and the impact of DVL1 on immunotherapeutic resistance.

Conclusions

DVL1 is a core regulator of SIC and other cancers and, therefore, can serve as a therapeutic target. The present study suggests that targeted pharmacological therapies to enhance response to exercise regimens may be a novel therapeutic tool to reduce the inflammatory response during sepsis, particularly in cancer patients. The identified drugs, Digoxin, require further in vivo and clinical studies to confirm their effects on SIC and their potential efforts to improve outcomes in immunotherapy-resistant cancer patients.

Promotion of Healthy Aging Through the Nexus of Gut Microbiota and Dietary Phytochemicals

Aging is associated with the decline of tissue and cellular functions, which can promote the development of age-related diseases like cancer, cardiovascular disease, neurodegeneration, and disorders of the musculoskeletal and immune systems. Healthspan is the length of time an individual is in good health and free from chronic diseases and disabilities associated with aging. Two modifiable factors that can influence healthspan, promote healthy aging, and prevent the development of age-related diseases, are diet and microbiota in the gastrointestinal tract (gut microbiota). This review will discuss how dietary phytochemicals and gut microbiota can work in concert to promote a healthy gut and healthy aging. First, an overview is provided of how the gut microbiota influences healthy aging through its impact on gut barrier integrity, immune function, mitochondria function, and oxidative stress. Next, the mechanisms by which phytochemicals effect gut health, inflammation, and nurture a diverse and healthy microbial composition are discussed. Lastly, we discuss how the gut microbiota can directly influence health by producing bioactive metabolites from phytochemicals in food like urolithin A, equol, hesperetin, and sulforaphane. These and other phytochemical-derived microbial metabolites that may promote healthspan are discussed. Importantly, an individual's capacity to produce health-promoting microbial metabolites from cruciferous vegetables, berries, nuts, citrus, and soy products will be dependent on the specific bacteria present in the individual's gut.

Unlocking the secrets of the human gut microbiota: Comprehensive review on its role in different diseases

The human gut microbiota, a complex and diverse community of microorganisms, plays a crucial role in maintaining overall health by influencing various physiological processes, including digestion, immune function, and disease susceptibility. The balance between beneficial and harmful bacteria is essential for health, with dysbiosis - disruption of this balance - linked to numerous conditions such as metabolic disorders, autoimmune diseases, and cancers. This review highlights key genera such as Enterococcus, Ruminococcus, Bacteroides, Bifidobacterium, Escherichia coli, Akkermansia muciniphila, Firmicutes (including Clostridium and Lactobacillus), and Roseburia due to their well-established roles in immune regulation and metabolic processes, but other bacteria, including Clostridioides difficile, Salmonella, Helicobacter pylori, and Fusobacterium nucleatum, are also implicated in dysbiosis and various diseases. Pathogenic bacteria, including Escherichia coli and Bacteroides fragilis, contribute to inflammation and cancer progression by disrupting immune responses and damaging tissues. The potential for microbiota-based therapies, such as probiotics, prebiotics, fecal microbiota transplantation, and dietary interventions, to improve health outcomes is examined. Future research directions in the integration of multi-omics, the impact of diet and lifestyle on microbiota composition, and advancing microbiota engineering techniques are also discussed. Understanding the gut microbiota's role in health and disease is essential for formulating personalized, efficacious treatments and preventive strategies, thereby enhancing health outcomes and progressing microbiome research.

Advances in bio-polymer coatings for probiotic microencapsulation: chitosan and beyond for enhanced stability and controlled release

This review paper analyzes recent advancements in bio-polymer coatings for probiotic microencapsulation, with a particular emphasis on chitosan and its synergistic combinations with other materials. Probiotic microencapsulation is essential for protecting probiotics from environmental stresses, enhancing their stability, and ensuring effective delivery to the gut. The review begins with an overview of probiotic microencapsulation, highlighting its significance in safeguarding probiotics through processing, storage, and gastrointestinal transit. Advances in chitosan-based encapsulation are explored, including the integration of chitosan with other bio-polymers such as alginate, gelatin, and pectin, as well as the application of nanotechnology and innovative encapsulation techniques like spray drying and layer-by-layer assembly. Detailed mechanistic insights are integrated, illustrating how chitosan influences gut microbiota by promoting beneficial bacteria and suppressing pathogens, thus enhancing its role as a prebiotic or synbiotic. Furthermore, the review delves into chitosan's immunomodulatory effects, particularly in the context of inflammatory bowel disease (IBD) and autoimmune diseases, describing the immune signaling pathways influenced by chitosan and linking gut microbiota changes to improvements in systemic immunity. Recent clinical trials and human studies assessing the efficacy of chitosan-coated probiotics are presented, alongside a discussion of practical applications and a comparison of in vitro and in vivo findings to highlight real-world relevance. The sustainability of chitosan sources and their environmental impact are addressed, along with the novel concept of chitosan's role in the gut-brain axis. Finally, the review emphasizes future research needs, including the development of personalized probiotic therapies and the exploration of novel bio-polymers and encapsulation techniques.

Changes in the gut microbial profile during long-term androgen deprivation therapy for prostate cancer

BACKGROUND

Recent studies have highlighted the association between androgen deprivation therapy (ADT) and the gut microbiota in prostate cancer. However, the impact of long-term ADT remains to be explored.

METHODS

To examine changes in the gut microbial profile from short-term (a median of 7 months), and middle-term (a median of 18 months) to long-term ADT (>33 months), 16S rRNA data from 56 fecal samples were reanalyzed. Additionally, a two-sample Mendelian randomization was employed to investigate the relationships between particular microbial signatures and prostate cancer as well as testosterone levels.

RESULTS

In contrast to the short- and middle-term ADT groups, the long-term ADT group had significant changes in alpha and beta diversity. In particular, the relative abundance of genera such as Catenibacterium and Holdemanella decreased in the long-term ADT group, whereas the opportunistic bacterium (Erysipelatoclostridium) and Ruminococcus gnavus showed increased abundance over ADT time. Moreover, a two-sample Mendelian randomization analysis revealed the negative associations between genetically predicated genera Coprobacter, Ruminococcaceae UCG002/011, and Defluviitaleacea-UCG-011, and testosterone levels.

CONCLUSIONS

In conclusion, long-term ADT use in prostate cancer patients was associated with detrimental changes in gut microbiota, including an increase in genera related to testosterone synthesis and opportunistic bacteria. These changes may be related to disease progression and side effects of long-term ADT while further longitudinal studies are required to prove this relationship.

Investigating the role of the intratumoral microbiome in thyroid cancer development and progression

The intratumoral microbiome (ITM) is in the spotlight due to its possible contribution to the initiation, progression, and invasion of a wide range of cancers. Its precise contribution to cancer tumorigenesis is still elusive, though. Thyroid cancer(TC), the ninth leading cause of cancer globally and the most prevalent endocrine malignancy with a rapidly rising incidence among all cancers, has attracted much attention nowadays. Still, the association between the tumor's microbiome and TC progression and development is an evolving area of investigation with significant consequences for disease understanding and intervention. Therefore, this review offers an appropriate perspective on this emerging concept in TC based on prior studies on the ITM among the most common tumors worldwide, concentrating on TC. Moreover, information on the origin of the ITM and practical methods can pave the way for researchers to opt for the most appropriate method for further investigations on the ITM more accurately.

Gut microbiota: Implications in pathogenesis and therapy to cardiovascular disease (Review)

The gut microbiota refers to the diverse bacterial community residing in the gastrointestinal tract. Recent data indicate a strong correlation between alterations in the gut microbiota composition and the onset of various diseases, notably cardiovascular disorders. Evidence suggests the gut-cardiovascular axis signaling molecules released by the gut microbiota play a pivotal role in regulation. This review systematically delineates the association between dysbiosis of the gut microbiota and prevalent cardiovascular diseases, including atherosclerosis, hypertension, myocardial infarction and heart failure. Furthermore, it provides an overview of the putative pathogenic mechanisms by which dysbiosis in the gut microbiota contributes to the progression of cardiovascular ailments. The potential modulation of gut microbiota as a preventive strategy against cardiovascular diseases through dietary interventions, antibiotic therapies and probiotic supplementation is also explored and discussed within the present study.

Exploring the Frontier: The Human Microbiome's Role in Rare Childhood Neurological Diseases and Epilepsy

Emerging research into the human microbiome, an intricate ecosystem of microorganisms residing in and on our bodies, reveals that it plays a pivotal role in maintaining our health, highlighting the potential for microbiome-based interventions to prevent, diagnose, treat, and manage a myriad of diseases. The objective of this review is to highlight the importance of microbiome studies in enhancing our understanding of rare genetic epilepsy and related neurological disorders. Studies suggest that the gut microbiome, acting through the gut-brain axis, impacts the development and severity of epileptic conditions in children. Disruptions in microbial composition can affect neurotransmitter systems, inflammatory responses, and immune regulation, which are all critical factors in the pathogenesis of epilepsy. This growing body of evidence points to the potential of microbiome-targeted therapies, such as probiotics or dietary modifications, as innovative approaches to managing epilepsy. By harnessing the power of the microbiome, we stand to develop more effective and personalized treatment strategies for children affected by this disease and other rare neurological diseases.

From gut to bone: deciphering the impact of gut microbiota on osteoporosis pathogenesis and management

Osteoporosis (OP) is characterized by decreased bone mineral density (BMD) and increased fracture risk, poses a significant global health burden. Recent research has shed light on the bidirectional relationship between gut microbiota (GM) and bone health, presenting a novel avenue for understanding OP pathogenesis and developing targeted therapeutic interventions. This review provides a comprehensive overview of the GM-bone axis, exploring the impact of GM on OP development and management. We elucidate established risk factors and pathogenesis of OP, delve into the diversity and functional changes of GM in OP. Furthermore, we examine experimental evidence and clinical observations linking alterations in GM composition or function with variations in BMD and fracture risk. Mechanistic insights into microbial mediators of bone health, such as microbial metabolites and products, are discussed. Therapeutic implications, including GM-targeted interventions and dietary strategies, are also explored. Finally, we identify future research directions and challenges in translating these findings into clinical practice.

The Impact of Surgical Bowel Preparation on the Microbiome in Colon and Rectal Surgery

Preoperative bowel preparation, through iterations over time, has evolved with the goal of optimizing surgical outcomes after colon and rectal surgery. Although bowel preparation is commonplace in current practice, its precise mechanism of action, particularly its effect on the human gut microbiome, has yet to be fully elucidated. Absent intervention, the gut microbiota is largely stable, yet reacts to dietary influences, tissue injury, and microbiota-specific byproducts of metabolism. The routine use of oral antibiotics and mechanical bowel preparation prior to intestinal surgical procedures may have detrimental effects previously thought to be negligible. Recent evidence highlights the sensitivity of gut microbiota to antibiotics, bowel preparation, and surgery; however, there is a lack of knowledge regarding specific causal pathways that could lead to therapeutic interventions. As our understanding of the complex interactions between the human host and gut microbiota grows, we can explore the role of bowel preparation in specific microbiome alterations to refine perioperative care and improve outcomes. In this review, we outline the current fund of information regarding the impact of surgical bowel preparation and its components on the adult gut microbiome. We also emphasize key questions pertinent to future microbiome research and their implications for patients undergoing colorectal surgery.

Caenorhabditis elegans as a Convenient Animal Model for Microbiome Studies

Microbes constitute the most prevalent life form on Earth, yet their remarkable diversity remains mostly unrecognized. Microbial diversity in vertebrate models presents a significant challenge for investigating host-microbiome interactions. The model organism Caenorhabditis elegans has many advantages for delineating the effects of host genetics on microbial composition. In the wild, the C. elegans gut contains various microbial species, while in the laboratory it is usually a host for a single bacterial species. There is a potential host-microbe interaction between microbial metabolites, drugs, and C. elegans phenotypes. This mini-review aims to summarize the current understanding regarding the microbiome in C. elegans. Examples using C. elegans to study host-microbe-metabolite interactions are discussed.

Current Trends and Challenges of Microbiome Research in Prostate Cancer

PURPOSE OF REVIEW

The role of the gut microbiome in prostate cancer is an emerging area of research interest. However, no single causative organism has yet been identified. The goal of this paper is to examine the role of the microbiome in prostate cancer and summarize the challenges relating to methodology in specimen collection, sequencing technology, and interpretation of results.

RECENT FINDINGS

Significant heterogeneity still exists in methodology for stool sampling/storage, preservative options, DNA extraction, and sequencing database selection/in silico processing. Debate persists over primer choice in amplicon sequencing as well as optimal methods for data normalization. Statistical methods for longitudinal microbiome analysis continue to undergo refinement. While standardization of methodology may help yield more consistent results for organism identification in prostate cancer, this is a difficult task due to considerable procedural variation at each step in the process. Further reproducibility and methodology research is required.

Epistemic misalignments in microbiome research

We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call "epistemic misalignment." An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epistemic misalignments, due to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporary microbiome science and urge microbiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole.

Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence

With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.

Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle

Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.