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

Abstract

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