Identifying a core human microbiome Microbiome healthy immunesystem diet prokaryotes eukaryotes virome gut NGSsequencing omics Nutrients_MDPI TNO_Research Unibo UninaIT VetmeduniVienna
By Nidhi Saha, BDSJul 19 2022Reviewed by Benedette Cuffari, M.Sc. In a recent Nutrients journal study, researchers provide a critical review of the concept of ‘the core human microbiome.’ Herein, researchers discuss the technical, analytical, and conceptual issues that must be resolved in order to obtain a comprehensive understanding of the core human microbiome.
What causes differences in the core microbiome? Across different geographies and populations, the core human microbiome varies greatly. These differences can be attributed to varying environmental and individual conditions such as diet, host genetics, and various other factors. Distinct differences also exist between Westernized and non-Westernized populations. In fact, studies have shown that several microbial species abundantly present in one human population may not ubiquitous in other human cohorts. However, Faecalibacterium prausnitzii has frequently been identified in more than 90% of the specimens within six human cohorts.
Community profiling of nine cohorts: HMP phases 1 , 2 , and 3 ; healthy individuals from Denmark ; individuals with IBD from Spain ; hunter-gatherers and traditional agriculturalists ; gorillas ; mice ; and chickens . The fraction of samples that contain each species for species detected in at least 70% of the samples in at least one cohort . Refer to Supplementary Table S3 for a complete list of all the detected species in all cohorts.
The European Nucleotide Archive has over 610,000 samples of the human microbiome, 85% of which are 16S ribosomal ribonucleic acid amplicons. Notably, in microbiome surveys, different sites of the 16S rRNA gene are commonly used to detect prokaryotes. In conjunction with additional samples that are accessible through other platforms, ENA samples provide a sufficient amount of data for evaluating the core human microbiome.
In addition to NMR, both gas and liquid high-performance chromatographic techniques coupled with quadrupole-TOF mass spectrometry have been successfully employed to describe a large number of metabolites from microbial samples. In contrast, TOF-based detection necessitates elaborate sample pretreatment and chromatographic fractionation techniques before yielding a suitable resolution in discovery-based metabolomics.
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