Challenges and opportunities of strain diversity in gut microbiome research

From microbes to medicine: harnessing the gut microbiota to combat prostate cancer

The gut microbiome (GM) has been identified as a crucial factor in the development and progression of various diseases, including cancer. In the case of prostate cancer, commensal bacteria and other microbes are found to be associated with its development. Recent studies have demonstrated that the human GM, including Bacteroides, Streptococcus, Bacteroides massiliensis, Faecalibacterium prausnitzii, Eubacterium rectale, and Mycoplasma genitalium, are involved in prostate cancer development through both direct and indirect interactions. However, the pathogenic mechanisms of these interactions are yet to be fully understood. Moreover, the microbiota influences systemic hormone levels and contributes to prostate cancer pathogenesis. Currently, it has been shown that supplementation of prebiotics or probiotics can modify the composition of GM and prevent the onset of prostate cancer. The microbiota can also affect drug metabolism and toxicity, which may improve the response to cancer treatment. The composition of the microbiome is crucial for therapeutic efficacy and a potential target for modulating treatment response. However, their clinical application is still limited. Additionally, GM-based cancer therapies face limitations due to the complexity and diversity of microbial composition, and the lack of standardized protocols for manipulating gut microbiota, such as optimal probiotic selection, treatment duration, and administration timing, hindering widespread use. Therefore, this review provides a comprehensive exploration of the GM's involvement in prostate cancer pathogenesis. We delve into the underlying mechanisms and discuss their potential implications for both therapeutic and diagnostic approaches in managing prostate cancer. Through this analysis, we offer valuable insights into the pivotal role of the microbiome in prostate cancer and its promising application in future clinical settings.

Pangenomics: A new era in the field of neurodegenerative diseases

A pangenome is composed of all the genetic variability of a group of individuals, and its application to the study of neurodegenerative diseases may provide valuable insights into the underlying aspects of genetic heterogenetiy for these complex ailments, including gene expression, epigenetics, and translation mechanisms. Furthermore, a reference pangenome allows for the identification of previously undetected structural commonalities and differences among individuals, which may help in the diagnosis of a disease, support the prediction of what will happen over time (prognosis) and aid in developing novel treatments in the perspective of personalized medicine. Therefore, in the present review, the application of the pangenome concept to the study of neurodegenerative diseases will be discussed and analyzed for its potential to enable an improvement in diagnosis and prognosis for these illnesses, leading to the development of tailored treatments for individual patients from the knowledge of the genomic composition of a whole population.

Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions

The study of microbiomes across organisms and environments has become a prominent focus in molecular ecology. This perspective article explores common challenges, methodological advancements, and future directions in the field. Key research areas include understanding the drivers of microbiome community assembly, linking microbiome composition to host genetics, exploring microbial functions, transience and spatial partitioning, and disentangling non-bacterial components of the microbiome. Methodological advancements, such as quantifying absolute abundances, sequencing complete genomes, and utilizing novel statistical approaches, are also useful tools for understanding complex microbial diversity patterns. Our aims are to encourage robust practices in microbiome studies and inspire researchers to explore the next frontier of this rapidly changing field.

Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference

A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.