On November 5th Yaxin Xue successfully defended his PhD thesis with the title: Development and application of computational methods for NGS-based microbiome research.
In Earth, it is estimated that 100 million times as many bacteria as stars in the universe. Microbiome refers to a characteristic microbial community occupying a habitat which has distinct physio-chemical properties. The microbiome, which forms a dynamic and interactive micro-ecosystem with its habitat, thus plays a crucial role in environment and human. The application of Next Generation Sequencing (NGS) has greatly revolutionized the microbiome research with a deep understanding on their metabolic and physiological roles in various habits. However, the analysis of NGS data from microbiome remains challenge. This thesis focused on address several bioinformatic issues of marker gene (16S rRNA), metagenome and metatranscriptome analysis in microbiome research. The five articles in this thesis include airway and arctic soil microbiomes, as well as development of bioinformatic tools for analysis of this data.
Increasing evidence suggests that lung microbiome is highly associated to the appearance and severity of chronic obstructive pulmonary disease (COPD). The first two papers investigated the microbiomes of the airways in patients with the COPD and healthy subjects. The result supported the existence of a core airways-residing microbiome within individuals overtime.
The activity of permafrost microbiome is critical for global climate change and carbon-nitrogen cycle. However, we had limited knowledge on permafrost microbiome. The next two papers studied the metagenomes in permafrost soil samples from Svalbard obtained at different depths, which observed a markedly shift of microbial community with depth, and highlighted aerobic respiration and soil organic matter decomposition may play a crucial role in Svalbard permafrost.
Ribosomal RNA (rRNA) is the most commonly used marker genes due to the prevalent and unwavering nature of rRNA across all organisms.Reconstructing full-length rRNA will enable us to have a high-resolution taxonomic profile. The last paper described the new MetaRib tool for reconstructing full-length ribosomal gene sequences from total RNA metatranscriptomics. Compared to earlier tools, it could provide a faster alternative without loss of accuracy and support diverse samples.
Grønseth,R.*, Xue,Y et al. (2017) Protected sampling is preferable in bronchoscopic studies of the airway microbiome. ERJ Open Res., 3, 00019–02017.
Nielsen, R.*, Xue,Y*, et al. (2020) Repeated bronchoscopy in health and obstructive lung disease: Is the airway microbiome stable? (manuscript)
Xue,Y*. et al. (2019) Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost. Microbiol. Resour. Announc., 8.
Xue,Y*. et al. (2020) Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost. FEMS Microbiol. Ecol., 96.
Xue,Y*. et al. (2020) Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data. Bioinformatics, 36, 3365–3371.