Editorial: The role of the bacteriome, mycobiome, archaeome and virome in animal health and disease

Zeineldin, Mohamed; Elolimy, Ahmed A.; Alharthi, Abdulrahman I.; Abdelmegeid, Mohamed

doi:10.3389/fvets.2022.1130187

Cited by 1 publication

(1 citation statement)

References 11 publications

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“…We suspect this finding to have resulted from the low relative amount of fungal organisms in human feces compared to bacteria and archaea 64 . Fecal sample composition varies with factors such as host species 65 , diet 66 , age 67 , and immune status 68 , thus we predict that fungal read abundance may be higher in some individuals and some hosts, which may explain the higher percentages of fungal reads in non-human primate samples (Fig. 5 ) than in human samples.…”

Section: Discussionmentioning

confidence: 97%

VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages

Owens,

Friant,

Martorelli Di Genova

et al. 2024

Nat Commun

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Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.

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