1,721,041 research outputs found
The Potential of Microbiome Big Data in Precision Medicine: Predicting Outcomes Through Machine Learning
No full textMassive sequencing techniques for compositional and functional profiling of the gut microbiome, a key modifier of human health, are generating thousands of data that are well suited to machine learning approaches. In particular, there is now full awareness that such microbiome data, if properly exploited, can improve the prediction of a range of clinical outcomes in disparate contexts. Here, we first discuss the importance of the gut microbiome in human physiology and pathophysiology and then provide some practical examples of machine learning applied to microbiome research in the context of specific disorders, such as obesity and cancer (with a particular focus on colorectal cancer [CRC]), in the field of personalized nutrition, and within the meta-community framework for inter-microbiome predictions. While there is still a long way to go to integrate machine learning into the clinical decision-making scheme, its potential in microbiome-based precision medicine is emerging more than ever
From whole-genome shotgun sequencing to viral community profiling: The viromescan tool
No full textViromeScan is an innovative metagenomic analysis tool that allows the viral community characterization in terms of taxonomy from raw data of metagenomics sequencing. It efficiently denoises samples from reads of other microorganisms. Users can adopt the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we apply ViromeScan pipeline to some examples, thus illustrating the processes computed from raw data to the final output
Ageing and Human Gut Microbiome: The Taxonomic and Functional Transition Towards an Elderly-Type Microbiome
No full textThe gut microbiome is recognized as an important component in determining the health status of ageing individuals due to its role in modulating digestive functions, immunity and resistance to pathogen infections, and cognitive functions. Microbial data from long-lived individuals showed the progressive transition to a peculiar elderly-type microbiome, often related to immunosenescence, inflammageing, and frailty, along with the emergence of some possibly ageing-supportive features. Here, we extensively describe the characteristics of such a microbiome configuration, with a focus on the concomitant ageing-associated unavoidable physiological modifications, in order to bring out the close connections between the human host and its microbial counterpart
Connect the dots: sketching out microbiome interactions through networking approaches
Full text linkMicrobiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment
Exploring clade differentiation of the Faecalibacterium prausnitzii complex
Full text linkFaecalibacterium prausnitzii is one of the most prevalent and abundant polyphyletic health-promoting components of the human gut microbiome with a propensity for dysbiotic decreases. To better understand its biology in the human gut, we specifically explored the divergence pressures acting on F. prausnitzii clades on a global scale. Five F. prausnitzii clades were de novo identified from 55 publicly available genomes and 92 high-quality metagenome assembled genomes. Divergence rate indices were constructed and validated to compare the divergence rates among the different clades and between each of the diverging genes. For each clade we identified specific patterns of diverging functionalities, probably reflecting different ecological propensities, in term of inter-host dispersion capacity or exploitation of different substrates in the gut environment. Finally, we speculate that these differences may explain, at least in part, the observed differences in the overall divergence rates of F. prausnitzii clades in human populations
Microbiota and lifestyle interactions through the lifespan
No full textBackground
The human intestinal microbiota is an adaptive entity, being capable of adjusting its phylogenetic and functional profile in response to changes in diet, lifestyle and environment. Providing the host with functions important to regulate energetic homeostasis and immunological function, the gut microbiota is strategic to keep metabolic and immunological homeostasis during the entire lifespan.
Scope and approach
In the present work we review studies exploring human gut microbiota variations at different age, describing the trajectory of ecosystem changes during the course of our life, from infancy to the old age. Gut microbiota variation mirroring subsistence strategy is also explored, with a particular focus on how the gut microbiota changes in response to modifications in the diet. Finally, we illustrate how an abnormal dietary intake could force microbiota to an obese-associated configuration, which concurs in compromising the host metabolic homeostasis.
Key findings and conclusions
Our work allows appreciating the importance of the physiological flexibility conferred by the microbiota for modulating our metabolic and immunological phenotype along the course of our life. Further, the key role of the gut microbiota in providing an extra means of adaptive potential during our evolutionary history is highlighted, suggesting the importance of the intestinal microbiota-host interplay for the maintenance of human health and homeostasis in changing environments. On the other hand, different lifestyle and dietary factors, such as sanitization and antibiotic usage or high-fat diet, can force maladaptive changes in the microbiota configuration which could have negative effects on human health. Thus, it is important to modulate diet and lifestyle habits to keep a mutualistic gut microbiota layout along the course of our life
Host microbiomes in tumor precision medicine: how far are we?
Full text linkThe human gut microbiome has received a crescendo of attention in recent years, due to the countless influences on human pathophysiology, including cancer. Research on cancer and anticancer therapy is constantly looking for new hints to improve the response to therapy while reducing the risk of relapse. In this scenario, the gut microbiome and the plethora of microbial-derived metabolites are considered a new opening in the development of innovative anticancer treatments for a better prognosis. This narrative review summarizes the current knowledge on the role of the gut microbiome in the onset and progression of cancer, as well as in response to chemo-immunotherapy. Recent findings regarding the tumor microbiome and its implications for clinical practice are also commented on. Current microbiome-based intervention strategies (i.e., prebiotics, probiotics, live biotherapeutics and fecal microbiota transplantation) are then discussed, along with key shortcomings, including a lack of long-term safety information in patients who are already severely compromised by standard treatments. The implementation of bioinformatic tools applied to microbiomics and other omics data, such as machine learning, has an enormous potential to push research in the field, enabling the prediction of health risk and therapeutic outcomes, for a truly personalized precision medicine
ViromeScan: a new tool for metagenomic viral community profiling
Full text linkBioinformatics tools available for metagenomic sequencing analysis are principally devoted to the identification of microorganisms populating an ecological niche, but they usually do not consider viruses. Only some software have been designed to profile the viral sequences, however they are not efficient in the characterization of viruses in the context of complex communities, like the intestinal microbiota, containing bacteria, archeabacteria, eukaryotic microorganisms and viruses. In any case, a comprehensive description of the host-microbiota interactions can not ignore the profile of eukaryotic viruses within the virome, as viruses are definitely critical for the regulation of the host immunophenotype
Over-feeding the gut microbiome: A scoping review on health implications and therapeutic perspectives
Full text linkThe human gut microbiome has gained increasing attention over the past two decades. Several findings have shown that this complex and dynamic microbial ecosystem can contribute to the maintenance of host health or, when subject to imbalances, to the pathogenesis of various enteric and non-enteric diseases. This scoping review summarizes the current knowledge on how the gut microbiota and microbially-derived compounds affect host metabolism, especially in the context of obesity and related disorders. Examples of microbiome-based targeted intervention strategies that aim to restore and maintain an eubiotic layout are then discussed. Adjuvant therapeutic interventions to alleviate obesity and associated comorbidities are traditionally based on diet modulation and the supplementation of prebiotics, probiotics and synbiotics. However, these approaches have shown only moderate ability to induce sustained changes in the gut microbial ecosystem, making the development of innovative and tailored microbiome-based intervention strategies of utmost importance in clinical practice. In this regard, the administration of next-generation probiotics and engineered microbiomes has shown promising results, together with more radical intervention strategies based on the replacement of the dysbiotic ecosystem by means of fecal microbiota transplantation from healthy donors or with the introduction of synthetic communities specifically designed to achieve the desired therapeutic outcome. Finally, we provide a perspective for future translational investigations through the implementation of bioinformatics approaches, including machine and deep learning, to predict health risks and therapeutic outcomes
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