UNLABELLED: Contact with environmental microbial communities primes the human immune system. Factors determining the distribution of microorganisms, such as dispersal, are thus important for human health. Here, we used the relative number of bacteria shared between environmental and human samples as a measure of bacterial dispersal and studied these associations with living environment and lifestyles. We analyzed amplicon sequence variants (ASVs) of the V4 region of 16S rDNA gene from 347 samples of doormat dust as well as samples of saliva, skin swabs, and feces from 53 elderly people in urban and rural areas in Finland at three timepoints. We first enumerated the ASVs shared between doormat and one of the human sample types (i.e., saliva, skin swab, or feces) of each individual subject and calculated the shared ASVs as a proportion of all ASVs in the given sample type of that individual. We observed that the patterns for the proportions of shared ASVs differed among seasons and human sample type. In skin samples, there was a negative association between the proportion of shared ASVs and the coverage of built environment (a proxy for degree of urbanization), whereas in saliva data, this association was positive. We discuss these findings in the context of differing species pools in urban and rural environments. IMPORTANCE: Understanding how environmental microorganisms reach and interact with humans is a key question when aiming to increase human contacts with natural microbiota. Few methods are suitable for studying microbial dispersal at relatively large spatial scales. Thus, we tested an indirect method and studied patterns of bacterial taxa that are shared between humans and their living environment.

• Klíčová slova
• bacteria, biodiversity hypothesis, dispersal, hygiene hypothesis, land cover,
• MeSH
• Bacteria * klasifikace   genetika   izolace a purifikace   MeSH
• DNA bakterií genetika   MeSH
• feces * mikrobiologie   MeSH
• kůže mikrobiologie   MeSH
• lidé MeSH
• městské obyvatelstvo MeSH
• mikrobiologie životního prostředí MeSH
• mikrobiota * MeSH
• prach analýza   MeSH
• RNA ribozomální 16S * genetika   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• sliny * mikrobiologie   MeSH
• venkovské obyvatelstvo MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Finsko MeSH
• Názvy látek
• DNA bakterií MeSH
• prach MeSH
• RNA ribozomální 16S * MeSH

A resilient immune system is characterized by its capacity to respond appropriately to challenges, such as infections, and it is crucial in vaccine response. Here we report a paired randomized intervention-control trial in which we evaluated the effect of microbially rich soil on immune resilience and pneumococcal vaccine response. Twenty-five age and sex matched pairs of volunteers were randomized to intervention and control groups. The intervention group rubbed hands three times a day in microbially rich soil until participants received a pneumococcal vaccine on day 14. Vaccine response, skin and gut bacteriome and blood cytokine levels were analyzed on days 0, 14 and 35. Peripheral blood mononuclear cells (PBMCs) were stimulated with vaccine components and autoclaved soil for cytokine production. Commensal bacterial community shifted only in the intervention group during the 14-day intervention period. When PBMCs collected on day 14 before the vaccination were stimulated with the vaccine components, IFN-y production increased in the intervention but not in the control group. On day 35, vaccination induced a robust antibody response in both groups. In parallel, gut bacterial community was associated with TGF-β plasma levels and TGF-β decrease in plasma was lower in the intervention group. The results indicate that exposure to microbially rich soil can modulate the cell-mediated immunity to components in pneumococcal vaccine.

• MeSH
• buněčná imunita * MeSH
• cytokiny metabolismus   krev   MeSH
• dospělí MeSH
• kůže * imunologie   mikrobiologie   MeSH
• leukocyty mononukleární * imunologie   metabolismus   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mikrobiota imunologie   MeSH
• pneumokokové infekce prevence a kontrola   imunologie   MeSH
• pneumokokové vakcíny * imunologie   aplikace a dávkování   MeSH
• půdní mikrobiologie MeSH
• střevní mikroflóra imunologie   MeSH
• vakcinace MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• randomizované kontrolované studie MeSH
• Názvy látek
• cytokiny MeSH
• pneumokokové vakcíny * MeSH

The metagenomic data presented in this article are related to the published research of "A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children" This database contains 16S ribosomal RNA (rRNA) metagenomics of sandbox sand and skin and gut microbiota of children in the intervention and placebo daycares. In intervention daycares, children aged 3-5 years were exposed to playground sand enriched with microbially diverse soil. In placebo daycares, children were exposed to visually similar as in intervention daycares, but microbially poor sand colored with peat. Sand, skin and gut metagenomics were analyzed at baseline and after 14 and 28 days of intervention by high throughput sequencing of bacterial 16S rRNA gene on the Illumina MiSeq platform. This dataset shows how skin bacterial community composition, including classes Gammaproteobacteria and Bacilli, changed, and how the relative abundance of over 30 bacterial genera shifted on the skin of children in the intervention treatment, while no shifts occurred in the placebo group.

• Klíčová slova
• 16s rRNA metagenome, Biodiversity, Children, Gut bacteria, Human commensal microbiota, Placebo, Skin bacteria,
• Publikační typ
• časopisecké články MeSH