Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens

Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host–microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens.

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Understanding the host-microbe interactions using metabolic modeling

Microbiome ◽

10.1186/s40168-020-00955-1 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Jack Jansma ◽

Sahar El Aidy

Keyword(s):

Human Health ◽

Flux Balance Analysis ◽

Bacterial Species ◽

Flux Balance ◽

Interaction Field ◽

In Silico Simulation ◽

Balance Analysis ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Genome Scale

AbstractThe human gut harbors an enormous number of symbiotic microbes, which is vital for human health. However, interactions within the complex microbiota community and between the microbiota and its host are challenging to elucidate, limiting development in the treatment for a variety of diseases associated with microbiota dysbiosis. Using in silico simulation methods based on flux balance analysis, those interactions can be better investigated. Flux balance analysis uses an annotated genome-scale reconstruction of a metabolic network to determine the distribution of metabolic fluxes that represent the complete metabolism of a bacterium in a certain metabolic environment such as the gut. Simulation of a set of bacterial species in a shared metabolic environment can enable the study of the effect of numerous perturbations, such as dietary changes or addition of a probiotic species in a personalized manner. This review aims to introduce to experimental biologists the possible applications of flux balance analysis in the host-microbiota interaction field and discusses its potential use to improve human health.

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Cross-species RNA-seq for deciphering host–microbe interactions

Nature Reviews Genetics ◽

10.1038/s41576-021-00326-y ◽

2021 ◽

Author(s):

Alexander J. Westermann ◽

Jörg Vogel

Keyword(s):

Rna Seq ◽

Microbe Interactions ◽

Host Microbe Interactions

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