Differential virome composition and richness between children's diarrheagenic stools kept at ultra-low temperatures for long-term

Abstract

Introduction: Diarrhoeal illness is the second cause of morbidity/mortality among children from less-developed regions worldwide. Nonetheless, there is scarce information regarding their gut microbiome.

Aim: Microbiome characterization, with an emphasis on the virome, of children's stools with diarrhoea, by a commercial microbiome array.

Methodology: Nucleic acids extraction, optimised for viral identification, of stool samples from 20 Mexican children with diarrhoea (10 children < 2 and 10 ≥ 2-years-old), collected 16 years ago and kept at -70 °C, were analysed for the presence of viruses, bacteria, archaea, protozoa, and fungi species sequences.

Results: Only viral and bacterial species sequences were identified among children's stools. Most stool samples harboured species belonging to the bacteriophages (95%), anellovirus (60%), diarrhoeagenic viruses (40%), and non-human pathogens viruses (45% avian virus and 40% plant viruses) groups. Among the children's stools, virome inter-individual species composition was observed, even in presence of illness. The < 2-years-old children group has significantly higher viral richness (p = 0.01), conferred mainly by bacteriophages and diarrheagenic-viruses (p = 0.01) species, in comparison with the ≥ 2-years-old group.

Conclusions: The virome of stools of children with diarrhoea revealed inter-individual viral species composition. Similarly, to the few virome studies in healthy young children, the bacteriophages group was the most abundant. A significantly higher viral richness, conferred by bacteriophages and diarrheagenic-viral species, was observed among < 2-years-old children in comparison with older children. Stools preserved at -70 °C for long term can successfully be used for microbiome studies.

Keywords: Children with diarrhoea; anelloviruses; bacteriophages; gut virome; plant viruses.