Environmental and mucosal microbiota and their role in childhood asthma

BACKGROUND

High microbial diversity in the environment has been associated with lower asthma risk, particularly in children exposed to farming. It remains unclear whether this effect operates through an altered microbiome of the mucosal surfaces of the airways.

METHODS

DNA from mattress dust and nasal samples of 86 school age children was analyzed by 454 pyrosequencing of the 16S rRNA gene fragments. Based on operational taxonomic units (OTUs), bacterial diversity and composition were related to farm exposure and asthma status.

RESULTS

Farm exposure was positively associated with bacterial diversity in mattress dust samples as determined by richness (P = 8.1 × 10^-6 ) and Shannon index (P = 1.3 × 10^-5 ). Despite considerable agreement of richness between mattress and nasal samples, the association of richness with farming in nasal samples was restricted to a high gradient of farm exposure, that is, exposure to cows and straw vs no exposure at all. In mattress dust, the genera Clostridium, Facklamia, an unclassified genus within the family of Ruminococcaceae, and six OTUs were positively associated with farming. Asthma was inversely associated with richness [aOR = 0.48 (0.22-1.02)] and Shannon index [aOR = 0.41 (0.21-0.83)] in mattress dust and to a lower extent in nasal samples [richness aOR 0.63 = (0.38-1.06), Shannon index aOR = 0.66 (0.39-1.12)].

CONCLUSION

The stronger inverse association of asthma with bacterial diversity in mattress dust as compared to nasal samples suggests microbial involvement beyond mere colonization of the upper airways. Whether inhalation of metabolites of environmental bacteria contributes to this phenomenon should be the focus of future research.

Effects of multiple but low pesticide loads on aquatic fungal communities colonizing leaf litter

In the first tier risk assessment (RA) of pesticides, risk for aquatic communities is estimated by using results from standard laboratory tests with algae, daphnids and fish for single pesticides such as herbicides, fungicides, and insecticides. However, fungi as key organisms for nutrient cycling in ecosystems as well as multiple pesticide applications are not considered in the RA. In this study, the effects of multiple low pesticide pulses using regulatory acceptable concentrations (RACs) on the dynamics of non-target aquatic fungi were investigated in a study using pond mesocosm. For that, fungi colonizing black alder (Alnus glutinosa) leaves were exposed to multiple, low pulses of 11 different pesticides over a period of 60days using a real farmer's pesticide application protocol for apple cropping. Four pond mesocosms served as treatments and 4 as controls. The composition of fungal communities colonizing the litter material was analyzed using a molecular fingerprinting approach based on the terminal Restriction Fragment Length Polymorphism (t-RFLP) of the fungal Internal Transcribed Spacer (ITS) region of the ribonucleic acid (RNA) gene(s). Our data indicated a clear fluctuation of fungal communities based on the degree of leaf litter degradation. However significant effects of the applied spraying sequence were not observed. Consequently also degradation rates of the litter material were not affected by the treatments. Our results indicate that the nutrient rich environment of the leaf litter material gave fungal communities the possibility to express genes that induce tolerance against the applied pesticides. Thus our data may not be transferred to other fresh water habitats with lower nutrient availability.

Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions?

Type 1 diabetes (T1D) is a complex autoimmune disease, and first stages of the disease typically develop early in life. Genetic as well as environmental factors are thought to contribute to the risk of developing autoimmunity against pancreatic beta cells. Several environmental factors, such as breastfeeding or early introduction of solid food, have been associated with increased risk for developing T1D. During the first years of life, the gut microbial community is shaped by the environment, in particular by dietary factors. Moreover, the gut microbiome has been described for its role in shaping the immune system early in life and early data suggest associations between T1D risk and alterations in gut microbial communities. In this article, we discuss environmental factors influencing the colonization process of the gut microbial community. Furthermore, we review possible interactions between the microbiome and the host that might contribute to the risk of developing T1D.

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production

BACKGROUND

The development of anti-islet cell autoimmunity precedes clinical type 1 diabetes and occurs very early in life. During this early period, dietary factors strongly impact on the composition of the gut microbiome. At the same time, the gut microbiome plays a central role in the development of the infant immune system. A functional model of the association between diet, microbial communities, and the development of anti-islet cell autoimmunity can provide important new insights regarding the role of the gut microbiome in the pathogenesis of type 1 diabetes.

RESULTS

A novel approach was developed to enable the analysis of the microbiome on an aggregation level between a single microbial taxon and classical ecological measures analyzing the whole microbial population. Microbial co-occurrence networks were estimated at age 6 months to identify candidates for functional microbial communities prior to islet autoantibody development. Stratification of children based on these communities revealed functional associations between diet, gut microbiome, and islet autoantibody development. Two communities were strongly associated with breast-feeding and solid food introduction, respectively. The third community revealed a subgroup of children that was dominated by Bacteroides abundances compared to two subgroups with low Bacteroides and increased Akkermansia abundances. The Bacteroides-dominated subgroup was characterized by early introduction of non-milk diet, increased risk for early autoantibody development, and by lower abundances of genes for the production of butyrate via co-fermentation of acetate. By combining our results with information from the literature, we provide a refined functional hypothesis for a protective role of butyrate in the pathogenesis of type 1 diabetes.

CONCLUSIONS

Based on functional traits of microbial communities estimated from co-occurrence networks, we provide evidence that alterations in the composition of mucin degrading bacteria associate with early development of anti-islet cell autoimmunity. We hypothesize that lower levels of Bacteroides in favor of increased levels of Akkermansia lead to a competitive advantage of acetogens compared to sulfate reducing bacteria, resulting in increased butyrate production via co-fermentation of acetate. This hypothesis suggests that butyrate has a protective effect on the development of anti-islet cell autoantibodies.

Intracranial volume (ICV) in isolated sagittal craniosynostosis measured by 3D photocephalometry: A new perspective on a controversial issue

BACKGROUND

There are still controversies regarding the intracranial volumes in patients with isolated sagittal craniosynostosis compared to a healthy population. This study aimed to compare the intracranial volume of children with sagittal synostosis and scaphocephaly to an age- and gender-matched control cohort using three-dimensional (3D) photogrammetry.

METHODS

62 boys and nine girls with sagittal craniosynostosis were included in this study. The intracranial volume was measured at the first clinical presentation. However, 3D photogrammetry was performed at children not younger than 3 months. The 3D photogrammetric data of 547 healthy boys and 287 healthy girls between the ages of 3-10 month was analyzed to establish an age- and gender-matched control group.

RESULTS

Male patients with sagittal synostosis showed a significantly reduced intracranial volume compared to the reference group. For female patients, the intracranial volume was slightly lower compared to the norm group, but not significantly.

CONCLUSIONS

Male children with sagittal synostosis showed significantly decreased intracranial volume between the age of 3 and 10 months compared to an age- and gender-matched control group. Female patients in the same age group presented a lower intracranial volume compared to the norm group. Measuring intracranial volume using 3D photogrammetry is a comparable and valuable alternative to CT scans that leads to a significant reduction of radiation exposure to the growing brain.

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems

Phosphorus (P) is an important macronutrient for all biota on earth but similarly a finite resource. Microorganisms play on both sides of the fence as they effectively mineralize organic and solubilize precipitated forms of soil phosphorus but conversely also take up and immobilize P. Therefore, we analysed the role of microbes in two beech forest soils with high and low P content by direct sequencing of metagenomic deoxyribonucleic acid. For inorganic P solubilization, a significantly higher microbial potential was detected in the P-rich soil. This trait especially referred to Candidatus Solibacter usiatus, likewise one of the dominating species in the data sets. A higher microbial potential for efficient phosphate uptake systems (pstSCAB) was detected in the P-depleted soil. Genes involved in P starvation response regulation (phoB, phoR) were prevalent in both soils. This underlines the importance of effective phosphate (Pho) regulon control for microorganisms to use alternative P sources during phosphate limitation. Predicted genes were primarily harboured by Rhizobiales, Actinomycetales and Acidobacteriales.

Prokaryotes in Subsoil-Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks

Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of "everything is everywhere, but the environment selects." Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches.

Characterizing Aquifer Heterogeneity Using Bacterial and Bacteriophage Tracers

Gravel aquifers act as important potable water sources in central western Europe, yet they are subject to numerous contamination pressures. Compositional and textural heterogeneity makes protection zone delineation around groundwater supplies in these units challenging; artificial tracer testing aids characterization. This paper reappraises previous tracer test results in light of new geological and microbiological data. Comparative passive gradient testing, using a fluorescent solute (Uranine), virus (H40/1 bacteriophage), and comparably sized bacterial tracers and , was used to investigate a calcareous gravel aquifer's ability to remove microbiological contaminants at a test site near Munich, Germany. Test results revealed relative recoveries could exceed those of H40/1 at monitoring wells, 10 m and 20 m from an injection well, by almost four times; recoveries varied by a factor of up to three between wells. Application of filtration theory suggested greater attenuation of H40/1 relative to similarly charged occurred due to differences in microorganism size, while estimated collision efficiencies appeared comparable. By contrast, more positively charged experienced greater attenuation at one monitoring point, while lower attenuation rates at the second location indicated the influence of geochemical heterogeneity. Test findings proved consistent with observations from nearby fresh outcrops that suggested thin open framework gravel beds dominated mass transport in the aquifer, while discrete intervals containing stained clasts reflect localized geochemical heterogeneity. Study results highlight the utility of reconciling outcrop observations with artificial tracer test responses, using microbiological tracers with well-defined properties, to characterize aquifer heterogeneity.

pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils

In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.