Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood

Abstract

BackgroundLittle is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants’ nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers.ResultsFor our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection.ConclusionsOur findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1372-8) contains supplementary material, which is available to authorized users.

Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum

“…pseudotuberculosis [ 4 , 48 ], while DNA sequence analysis and Fourier-transform Infrared Spectroscopy would classify it as C . ulcerans [ 6 , 7 , 48 ].…”

“…The tox gene was found in only eight out of the 38 C . silvaticum strains (04–13, 05–13, KL0182, KL0884, KL0957, KL1196, PO100/5 and W25), although the strains lacking it were reported to be NTTB [ 6 ]. This can be seen in the circular map as a blank space in the tox gene region of the other 30 strains ( Fig 4 ).…”

“…silvaticum . This implies independent events of acquisition of virulence factors in zoonotic species that could influence their pathogenic potential [ 6 ].…”

Angucycline-like Aromatic Polyketide from a Novel Streptomyces Species Reveals Freshwater Snail Physa acuta as Underexplored Reservoir for Antibiotic-Producing Actinomycetes

“…Based on the 454 pyrosequencing method, the identified bacterial communities in the snails collected from coastal areas showed a higher abundance of Proteobacteria, while Actinobacteria were the more prominent phylum in the mountains of Sichuan and Yunnan Provinces, China [ 31 ]. Thus, the bacterial abundance may be affected by many factors, including the niche, diet, physiological states and genetic characteristics of the snail host [ 32 ]. In our study, despite the low abundance values of Actinobacteria and, especially, the genus Streptomyces , three Streptomyces strains (7NS1, 7NS2 and 7NS3) were isolated by using culture-based methods; among them, strain 7NS3 showed strong activity against Gram-positive bacteria.…”

Enteric Virome and Carcinogenesis in the Gut

“…There are, of course, other types of viruses included within the human virome, like archaeal viruses and virophages, which are not as deeply studied due to a limited understanding of their function within the environment of the human body [4]. By either directly affecting host cell behavior and structure or by preying upon certain species of bacteria and subsequently altering bacterial communities, viruses can alter their own environment and hold strong direct or indirect influence over host health and physiology [5,6]. While much research has focused on the role of the human bacteriome in the etiology and progression of diseases, such as cancer, cardiovascular disease, inflammatory bowel disease, among others, the human virome has been less studied.…”