The gut microbiota of critically ill patients: first steps in an unexplored world

Excerpt

The gut microbiota is a complex ecosystem encompassing all bacteria, fungi, archaea, viruses, and protozoa that colonize the intestinal tract, reaching in healthy humans an estimated total of 3.10¹³ microorganisms that roughly equals the number of host cells [1]. Bacterial commensals are divided up into seven main phyla that are physiologically dominated by Firmicutes and Bacteroidetes (Fig. 1), although their richness and diversity may exhibit substantial inter- as intra-individual variations depending on genetic, dietary, and environmental factors [2]. Several host-benefic functions have been linked to a “normal” gut microbiota and its symbiotic relationship with the intestinal mucosa, including contributions to hormonal homeostasis, carbohydrate and biliary acid metabolism, vitamin synthesis, anti-inflammatory pathways, and immune regulation [3]. Of note, most enteric bacteria are unculturable or exclusively grow under strict anaerobic conditions that are very demanding to achieve in experimental laboratories, which justifies the need for non-culture-based assays and bioinformatics to investigate the composition of this microbial community. Two main methods based on nucleic acid sequencing are currently available. The first one is 16S profiling, which relies on PCR-based amplification and sequencing of a fraction of the bacterial ubiquitous 16S rRNA-encoding gene. This approach is simple and cheap—less than 100 USD per sample; however, bacterial identifications are often limited to high taxonomic levels. The second one, referred to as shotgun metagenomics, consists in sequencing the whole DNA of a given sample without prior amplification. This method allows more accurate taxonomic assignments (down to species level, including for non-bacterial components of the microbiota) while providing information on resistance or virulence genes content. Yet, associated costs—more than 300 USD per sample—and the complex data analyses that it requires hamper the use of shotgun metagenomics in large clinical studies.

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