LITERATURE UPDATE
Metagenomics sequencing: a selection of current research interest
Metagenomics sequencing analyses DNA from a sample containing mixed microbial communities, which allows the identification and characterisation of microbes without the need for cultivation. Here, Pathology in Practice Science Editor Brian Nation selects a small sample of relevant research papers in this area, all of which are free to access.
Deep learning methods in metagenomics: a review Roy G, Prifti E, Belda E, Zucker JD. Microb Genom. 2024 Apr;10(4):001231. doi: 10.1099/mgen.0.001231.
The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of
microbial environments, such as the human gut.
The gut microbiome plays a crucial
role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement
state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention- based models. These methods aggregate contextualised data and pave the way for improved patient care and a better understanding of the microbiome’s key role in our health.
An Insight into Functional Metagenomics: A High-Throughput Approach to Decipher Food- Microbiota-Host Interactions in the Human Gut Mathieu E, Léjard V, Ezzine C et al. Int J Mol Sci. 2023 Dec 18;24(24):17630. doi: 10.3390/ijms242417630.
Our understanding of the symbiotic relationship between the microbiota and its host has constantly evolved since our understanding that the “self” was not only defined by our genetic patrimony but also by the genomes of bugs living in us.
Oxford Nanopore MinION connected via USB to a laptop.
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The first culture-based methods highlighted the important functions of the microbiota. However, these methods had strong limitations and did not allow for a full understanding of the complex relationships that occur at the interface between the microbiota and the host. The recent development of metagenomic approaches has been a groundbreaking step towards this understanding. Its use has provided new insights and perspectives.
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