A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation

Upregulation of Lactobacillus spp. in gut microbiota as a novel mechanism for environmental eustress-induced anti-pancreatic cancer effects

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with limited effective treatment options. Emerging evidence links enriched environment (EE)-induced eustress to PDAC inhibition. However, the underlying mechanisms remain unclear. In this study, we explored the role of gut microbiota in PDAC-suppressive effects of EE. We demonstrated that depletion of gut microbiota with antibiotics abolished EE-induced tumor suppression, while fecal microbiota transplantation (FMT) from EE mice significantly inhibited tumor growth in both subcutaneous and orthotopic PDAC models housed in standard environment. 16S rRNA sequencing revealed that EE enhanced gut microbiota diversity and selectively enriched probiotic Lactobacillus, particularly L. reuteri. Treatment with L. reuteri significantly suppressed PDAC tumor growth and increased natural killer (NK) cell infiltration into the tumor microenvironment. Depletion of NK cells alleviated the anti-tumor effects of L. reuteri, underscoring the essential role of NK cell-mediated immunity in anti-tumor response. Clinical analysis of PDAC patients showed that higher fecal Lactobacillus abundance correlated with improved progression-free and overall survival, further supporting the therapeutic potential of L. reuteri in PDAC. Overall, this study identifies gut microbiota as a systemic regulator of PDAC under psychological stress. Supplementation of psychobiotic Lactobacillus may offer a novel therapeutic strategy for PDAC.

Coevolutionary interplay: Helminths-trained immunity and its impact on the rise of inflammatory diseases

The gut biome, a complex ecosystem of micro- and macro-organisms, plays a crucial role in human health. A disruption in this evolutive balance, particularly during early life, can lead to immune dysregulation and inflammatory disorders. 'Biome repletion' has emerged as a potential therapeutic approach, introducing live microbes or helminth-derived products to restore immune balance. While helminth therapy has shown some promise, significant challenges remain in optimizing clinical trials. Factors such as patient genetics, disease status, helminth species, and the optimal timing and dosage of their products or metabolites must be carefully considered to train the immune system effectively. We aim to discuss how helminths and their products induce trained immunity as prospective to treat inflammatory and autoimmune diseases. The molecular repertoire of helminth excretory/secretory products (ESPs), which includes proteins, peptides, lipids, and RNA-carrying extracellular vesicles (EVs), underscores their potential to modulate innate immune cells and hematopoietic stem cell precursors. Mimicking natural delivery mechanisms like synthetic exosomes could revolutionize EV-based therapies and optimizing production and delivery of ESP will be crucial for their translation into clinical applications. By deciphering and harnessing helminth-derived products' diverse modes of action, we can unleash their full therapeutic potential and pave the way for innovative treatments.

Unveiling the potential antibacterial action of acetylcysteine for managing Staphylococcus aureus wound infections: in vitro and in vivo study

The global propagation of infections is a massive challenge in managing infected wounds. One of the most widely detected bacteria in wounds is Staphylococcus aureus. These bacteria possess multiple virulence factors, like biofilm formation, which hinder antibiotic treatment. Accordingly, it is vital to explore alternative therapeutics for managing these infections. We estimated the antibacterial and antibiofilm actions of N-acetylcysteine (NC). It revealed antibacterial action with minimum inhibitory concentration values of 256-2048 µg/mL. In addition, NC revealed antibiofilm action as exposed phenotypically from crystal violet assay. The NC diminished the percentages of strong and moderate biofilm-forming isolates from 75% (18 isolates out of 24) to 33.34% (8 isolates out of 24). Scanning electron microscopy and qRT-PCR confirmed NC's antibiofilm action. Furthermore, the antibacterial consequence of NC was investigated in vivo employing a burn wound infection model. NC revealed a remarkable (p < 0.05) enhancement of the macroscopic wound healing and a decline of the bacterial count in the infected wound tissues compared with the positive control. The histopathological and immunohistochemical investigations elucidated a considerable improvement of the skin wound tissues of the NC-treated group with a decrease in the inflammatory marker immunostained cells (TNF-α, IL-6, and Il-1β) compared to the positive control. Besides, the qRT-PCR exposed an induced upregulation of the platelet-derived growth factor (PDGF) and fibronectin genes, which have a role in renovating skin tissues. From the previous outcomes, NC could be a healing agent, mainly in S. aureus-infected wounds. To our knowledge, this is the first time to report the wound healing potential of NC for S. aureus-infected wounds.

Unlocking the Interactions Between the Whole-Body Microbiome and HPV Infection: A Literature Review

The human microbiome plays a vital role in maintaining human homeostasis, acting as a key regulator of host immunity and defense mechanisms. However, dysbiotic microbial communities may cause disruption of the symbiotic relationship between the host and the local microbiota, leading to the pathogenesis of various diseases, including viral infections and cancers. One of the most common infectious agents causing cancer is the human papilloma virus (HPV), which accounts for more than 90% of cervical cancers. In most cases, the host immune system is activated and clears HPV, whereas in some cases, the infection persists and can lead to precancerous lesions. Over the last two decades, the advent of next-generation sequencing (NGS) technology and bioinformatics has allowed a thorough and in-depth analysis of the microbial composition in various anatomical niches, allowing researchers to unveil the interactions and the underlying mechanisms through which the human microbiota could affect HPV infection establishment, persistence, and progression. Accordingly, the present narrative review aims to shed light on our understanding of the role of the human microbiome in the context of HPV infection and its progression, mainly to cervical cancer. Furthermore, we explore the mechanisms by which the composition and balance of microbial communities exert potential pathogenic or protective effects, leading to either HPV persistence and disease outcomes or clearance. Special interest is given to how the microbiome can modulate host immunity to HPV infection. Lastly, we summarize the latest findings on the therapeutic efficacy of probiotics and prebiotics in preventing and/or treating HPV infections and the potential of vaginal microbiota transplantation while highlighting the significance of personalized medicine approaches emerging from NGS-based microbiome profiling and artificial intelligence (AI) for the optimal management of HPV-related diseases.

New perspectives on gastric disorders: the relationship between innate lymphoid cells and microbes in the stomach

A growing number of studies in recent years have revealed the changes in the gastric microbiota during the development of gastric diseases, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. After a decade of intensive research, the discovery of innate lymphoid cells (ILCs) has provided a new perspective on the immune response in many diseases. In the context of defense against infectious pathogens, the pre-existing innate defense mechanism of tissue-resident ILCs can rapidly recognize and respond to microbes to eliminate infection at the earliest stages. Here, we outline the basic function of ILCs in the gastric mucosa and in shaping the gastric microbiome. We discuss the interactions between the gastric microbiota and ILCs, explaining how the ILCs actively drive the immune response against bacterial pathogens that can lead to the development of the gastric disease.

Symbiosis vs pathogenesis in plants: Reflections and perspectives

Plant-microbe partnerships constitute a complex and intricately woven network of connections that have evolved over countless centuries, involving both cooperation and antagonism. In various contexts, plants and microorganisms engage in mutually beneficial partnerships that enhance crop health and maintain balance in ecosystems. However, these associations also render plants susceptible to a range of pathogens. Understanding the fundamental molecular mechanisms governing these associations is crucial, given the notable susceptibility of plants to external environmental influences. Based on quorum sensing signals, phytohormone, and volatile organic carbon (VOC) production and others molecules, microorganisms influence plant growth, health, and defense responses. This review explores the multifaceted relationships between plants and their associated microorganisms, encompassing mutualism, commensalism, and antagonism. The molecular mechanisms of symbiotic and pathogenic interactions share similarities but lead to different outcomes. While symbiosis benefits both parties, pathogenesis harms the host. Genetic adaptations optimize these interactions, involving coevolution driving process. Environmental factors influence outcomes, emphasizing the need for understanding and manipulation of microbial communities for beneficial results. Research directions include employing multi-omics techniques, functional studies, investigating environmental factors, understanding evolutionary trajectories, and harnessing knowledge to engineer synthetic microbial consortia for sustainable agriculture and disease management.

Exploring the microbiome-gut-testis axis in testicular germ cell tumors

The microbiome-gut-testis axis has emerged as a significant area of interest in understanding testicular cancer, particularly testicular germ cell tumors (TGCTs), which represent the most common malignancy in young men. The interplay between the gut and testicular microbiomes is hypothesized to influence tumorigenesis and reproductive health, underscoring the complex role of microbial ecosystems in disease pathology. The microbiome-gut-testis axis encompasses complex interactions between the gut microbiome, systemic immune modulation, and the local microenvironment of the testis. Dysbiosis in the gut or testicular microbiomes may contribute to altered immune responses, inflammation, and hormonal imbalances, potentially playing a role in the pathogenesis of TGCTs. Concurrently, seminal microbiomes have been linked to variations in sperm quality, fertility potential, and possibly cancer susceptibility, underscoring the need for further evaluation. This review explores the emerging role of the microbiome-gut-testis axis in the context of testicular cancer, highlighting its implications for disease onset, progression, treatment efficacy, and toxicity. Identifying potential microbial biomarkers, followed by microbiota modulation to restore a balanced microbial community, might offer a novel supportive strategy for improving treatment efficacy in refractory TGCT patients while reducing chemotherapy-induced toxicity. We suggest a better understanding of the association between dysregulated microbial environments and TGCTs emphasizes potential pathways by which the gut microbiome might influence testicular cancer.

Best Practice Guidelines for Collecting Microbiome Samples in Research Studies

Microbiome research has the potential to provide valuable information regarding the complex relationship between microbial communities and the human body. To help facilitate the translation of this potentially revolutionary research to clinical medicine, common guidelines and best practices are necessary. These guidelines should be based on the key findings of recent research in the field and address the primary areas of discrepancy in the previously published literature. Based on this review's findings, future microbiome research should adopt a consistent and clear approach to nomenclature, using standardized terminology to mitigate confusion. Additionally, only sample collection methods proven to reduce the risk of contamination should be utilized. While sample storage often creates difficulty in microbiome research, there are proven techniques that can improve results. With the wide array of research methodologies in the literature, standardization of metadata collection, kits, and analysis software could also be beneficial. Finally, documentation and records are critical in ensuring reproducibility, as is the case with all basic research. This brief review provides a foundation for evidence-based guidelines in microbiome research. PATIENT SUMMARY: This report outlines general guidelines and best practices for conducting microbiome research, which could significantly advance the field of medicine.

Special Issue Introduction: Human Microbiota-Current Updates on Pathogenetic Mechanisms and Methodological Advances

Advances in sequencing technologies have made it possible to study microbial communities at a previously unimaginable resolution [...].