Best practices for analysing microbiomes
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …
Correlation and association analyses in microbiome study integrating multiomics in health and disease
Y Xia - Progress in molecular biology and translational …, 2020 - Elsevier
Correlation and association analyses are one of the most widely used statistical methods in
research fields, including microbiome and integrative multiomics studies. Correlation and …
research fields, including microbiome and integrative multiomics studies. Correlation and …
NetCoMi: network construction and comparison for microbiome data in R
Motivation Estimating microbial association networks from high-throughput sequencing data
is a common exploratory data analysis approach aiming at understanding the complex …
is a common exploratory data analysis approach aiming at understanding the complex …
An introduction to next generation sequencing bioinformatic analysis in gut microbiome studies
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than
the human host and plays an essential role in human health and disease pathogenesis …
the human host and plays an essential role in human health and disease pathogenesis …
Metatranscriptome of human faecal microbial communities in a cohort of adult men
The gut microbiome is intimately related to human health, but it is not yet known which
functional activities are driven by specific microorganisms' ecological configurations or …
functional activities are driven by specific microorganisms' ecological configurations or …
Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions
Candida species overgrowth in the human gut is considered a prerequisite for invasive
candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth is …
candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth is …
Chromosomally normal miscarriage is associated with vaginal dysbiosis and local inflammation
K Grewal, YS Lee, A Smith, JJ Brosens, T Bourne… - BMC medicine, 2022 - Springer
Background Emerging evidence supports an association between vaginal microbiota
composition and risk of miscarriage; however, the underlying mechanisms are poorly …
composition and risk of miscarriage; however, the underlying mechanisms are poorly …
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria
Background Antibiotic treatment has a well-established detrimental effect on the gut
bacterial composition, but effects on the fungal community are less clear. Bacteria in the …
bacterial composition, but effects on the fungal community are less clear. Bacteria in the …
Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin
The subsurface is among Earth's largest biomes, but the extent to which microbial
communities vary across tectonic plate boundaries or interact with subduction-scale …
communities vary across tectonic plate boundaries or interact with subduction-scale …
A statistical model for describing and simulating microbial community profiles
Many methods have been developed for statistical analysis of microbial community profiles,
but due to the complex nature of typical microbiome measurements (eg sparsity, zero …
but due to the complex nature of typical microbiome measurements (eg sparsity, zero …