Search

Aims: To study the association between risk factors and chronic kidney disease (CKD), and characterize medication use in Finnish primary care type 2 diabetes (T2D) patients., Methods: Data on clinical characteristics, laboratory measurements, and medications were collected from medical records. The primary outcome measure was notable CKD (stage 3-5, eGFR <60 ml/min/1.73 m 2 ) and/or increased albuminuria. The explanatory variables were individual risk factors and risk factor groups based on their number (0-2, 3-4, 5-6, >7). Spearman's rank correlation coefficient and risk ratio analysis were used to analyze the association between the number of risk factors and CKD stage, and between the number of risk factors and notable CKD, respectively., Results: Altogether, 1335 patients with T2D in 60 Finnish primary care centers were recruited for this cross-sectional study. Three-quarters of T2D patients had 3 risk factors and 36% had ≥ 5 risk factors. Compared to patients with 0-2 risk factors, patients with 3-4, 5-6, and ≥ 7 risk factors had a 5.5-fold, 9.9-fold, and 15.9-fold risk of notable CKD (p < 0.001), respectively. Heart failure was most strongly associated with notable CKD (risk ratio, 3.7; p < 0.001)., Conclusions: Number of risk factors was strongly associated with advanced-stage CKD., (Copyright © 2023 Primary Care Diabetes Europe. Published by Elsevier Ltd. All rights reserved.)

The rising trend in non-communicable chronic inflammatory diseases coincides with changes in Western lifestyle. While changes in the human microbiota may play a central role in the development of chronic diseases, estimating the contribution of associated lifestyle factors remains challenging. We studied the influence of lifestyle-diet, antibiotic use, and residential environment with housing and family-on the gut microbiota of healthy and owner-reported atopic pet dogs, searching for associations between the lifestyle factors, atopy and microbiota. The results showed that atopic and healthy dogs had contrasting gut microbial composition. The gut microbiota also differed between two breeds, Labrador Retriever and Finnish Lapphund, selected for our study. Among all lifestyle factors studied, diet was most significantly associated with gut microbiota but only weakly with atopic symptoms. Thus, diet- and atopy-associated changes in the microbiota were not interrelated. Instead, the severity of symptoms was positively associated with the usage of antibiotics, which in turn was associated with the microbiota composition. Urban lifestyle was significantly associated with the increased prevalence of allergies but not with the gut microbiota. Our results from pet dogs supported previous evidence from humans, demonstrating that antibiotics, gut microbiota and atopic manifestation are interrelated. This congruence suggests that canine atopy might be a promising model for understanding the aetiology of human allergy., Competing Interests: The authors declare that they have no competing interests., (© 2023 The Authors.)

Contact with natural environments enriches the human microbiome, promotes immune balance and protects against allergies and inflammatory disorders. In Finland, the allergy & asthma epidemic became slowly visible in mid 1960s. After the World War II, Karelia was split into Finnish and Soviet Union (now Russia) territories. This led to more marked environmental and lifestyle changes in the Finnish compared with Russian Karelia. The Karelia Allergy Study 2002-2022 showed that allergic conditions were much more common on the Finnish side. The Russians had richer gene-microbe network and interaction than the Finns, which associated with better balanced immune regulatory circuits and lower allergy prevalence. In the Finnish adolescents, a biodiverse natural environment around the homes associated with lower occurrence of allergies. Overall, the plausible explanation of the allergy disparity was the prominent change in environment and lifestyle in the Finnish Karelia from 1940s to 1980s. The nationwide Finnish Allergy Programme 2008-2018 implemented the biodiversity hypothesis into practice by endorsing immune tolerance, nature contacts, and allergy health with favorable results. A regional health and environment programme, Nature Step to Health 2022-2032 , has been initiated in the City of Lahti, EU Green Capital 2021. The programme integrates prevention of chronic diseases (asthma, diabetes, obesity, depression), nature loss, and climate crisis in the spirit of Planetary Health . Allergic diseases exemplify inappropriate immunological responses to natural environment. Successful management of the epidemics of allergy and other non-communicable diseases may pave the way to improve human and environmental health., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2023 Haahtela, Alenius, Auvinen, Fyhrquist, von Hertzen, Jousilahti, Karisola, Laatikainen, Lehtimäki, Paalanen, Ruokolainen, Saarinen, Valovirta, Vasankari, Vlasoff, Erhola, Bousquet, Vartiainen and Mäkelä.)

Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies. Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (<18 years) microbiota in acute and chronic respiratory conditions, with >10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses. Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus . Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively. Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis., Competing Interests: MPi reports personal fees from Mérieux Université, grants from Abacus Diagnostica, outside the submitted work. AM reports grants and personal fees from Janssen, personal fees from Merck, personal fees from Sanofi-Pasteur, personal fees from Roche, outside the submitted work. EZ reports grants and personal fees from Cystic Fibrosis Foundation, outside the submitted work. OS is an employee of Nestlé Research – Societé des Produits Nestlé S.A. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Broderick, Waite, Marsh, Camargo, Cardenas, Chang, Cookson, Cuthbertson, Dai, Everard, Gervaix, Harris, Hasegawa, Hoffman, Hong, Josset, Kelly, Kim, Kong, Li, Mansbach, Mejias, O’Toole, Paalanen, Pérez-Losada, Pettigrew, Pichon, Ramilo, Ruokolainen, Sakwinska, Seed, van der Gast, Wagner, Yi, Zemanick, Zheng, Pillarisetti and Taylor.)

Increase of allergic conditions has occurred at the same pace with the Great Acceleration, which stands for the rapid growth rate of human activities upon earth from 1950s. Changes of environment and lifestyle along with escalating urbanization are acknowledged as the main underlying causes. Secondary (tertiary) prevention for better disease control has advanced considerably with innovations for oral immunotherapy and effective treatment of inflammation with corticosteroids, calcineurin inhibitors, and biological medications. Patients are less disabled than before. However, primary prevention has remained a dilemma. Factors predicting allergy and asthma risk have proven complex: Risk factors increase the risk, while protective factors counteract them. Interaction of human body with environmental biodiversity with micro-organisms and biogenic compounds as well as the central role of epigenetic adaptation in immune homeostasis have given new insight. Allergic diseases are good indicators of the twisted relation to environment. In various non-communicable diseases, the protective mode of the immune system indicates low-grade inflammation without apparent cause. Giving microbes, pro- and prebiotics, has shown some promise in prevention and treatment. The real-world public health programme in Finland (2008-2018) emphasized nature relatedness and protective factors for immunological resilience, instead of avoidance. The nationwide action mitigated the allergy burden, but in the lack of controls, primary preventive effect remains to be proven. The first results of controlled biodiversity interventions are promising. In the fast urbanizing world, new approaches are called for allergy prevention, which also has a major cost saving potential., (© 2021 The Authors. Allergy published by European Academy of Allergy and Clinical Immunology and John Wiley & Sons Ltd.)

Predicting the emergence and spread of infectious diseases is critical for the effective conservation of biodiversity. White-nose syndrome (WNS), an emerging infectious disease of bats, has resulted in high mortality in eastern North America. Because the fungal causative agent Pseudogymnoascus destructans is constrained by temperature and humidity, spread dynamics may vary by geography. Environmental conditions in the southern part of the continent are different than the northeast, where disease dynamics are typically studied, making it difficult to predict how the disease will manifest. Herein, we modelled WNS pathogen spread in Texas based on cave densities and average dispersal distances of hosts, projecting these results out to 10 years. We parameterized a predictive model of WNS epidemiology and its effects on bat populations with observed cave environmental data. Our model suggests that bat populations in northern Texas will be more affected by WNS mortality than southern Texas. As such, we recommend prioritizing the preservation of large overwintering colonies of bats in north Texas through management actions. Our model illustrates that infectious disease spread and infectious disease severity can become uncoupled over a gradient of environmental variation and highlight the importance of understanding host, pathogen and environmental conditions across a breadth of environments.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization., Competing Interests: Declaration of interests R.J.X. is a consultant to Novartis and Nestle. E.J.A. is a co-founder and shareholder of Finch Therapeutics, a company that specializes in microbiome-targeted therapeutics., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Both humans and pet dogs are more prone to develop allergies in urban than in rural environments, which has been associated with the differing microbial exposures between areas. However, potential similarities in the microbiota, that associate with environmental exposures, in allergic dogs and owners has not been investigated. We evaluated skin and gut microbiota, living environment, and lifestyle in 168 dog-owner pairs. Due to partly different manifestations of allergies between species, we focused on aeroallergen sensitized humans and dogs with owner-reported allergic symptoms. Our results agree with previous studies: dog-owner pairs suffered simultaneously from these allergic traits, higher risk associated with an urban environment, and the skin, but not gut, microbiota was partly shared by dog-owner pairs. We further discovered that urban environment homogenized both dog and human skin microbiota. Notably, certain bacterial taxa, which were associated with living environment and lifestyle, were also related with allergic traits, but these taxa differed between dogs and humans. Thus, we conclude that dogs and humans can be predisposed to allergy in response to same risk factors. However, as shared predisposing or protective bacterial taxa were not discovered, other factors than environmental microbial exposures can mediate the effect or furry dog and furless human skin select different taxa.

Background: After the Second World War, the population living in the Karelian region was strictly divided by the "iron curtain" between Finland and Russia. This resulted in different lifestyle, standard of living, and exposure to the environment. Allergic manifestations and sensitization to common allergens have been much more common on the Finnish compared to the Russian side., Objective: The remarkable allergy disparity in the Finnish and Russian Karelia calls for immunological explanations., Methods: Young people, aged 15-20 years, in the Finnish (n = 69) and Russian (n = 75) Karelia were studied. The impact of genetic variation on the phenotype was studied by a genome-wide association analysis. Differences in gene expression (transcriptome) were explored from the blood mononuclear cells (PBMC) and related to skin and nasal epithelium microbiota and sensitization., Results: The genotype differences between the Finnish and Russian populations did not explain the allergy gap. The network of gene expression and skin and nasal microbiota was richer and more diverse in the Russian subjects. When the function of 261 differentially expressed genes was explored, innate immunity pathways were suppressed among Russians compared to Finns. Differences in the gene expression paralleled the microbiota disparity. High Acinetobacter abundance in Russians correlated with suppression of innate immune response. High-total IgE was associated with enhanced anti-viral response in the Finnish but not in the Russian subjects., Conclusions and Clinical Relevance: Young populations living in the Finnish and Russian Karelia show marked differences in genome-wide gene expression and host contrasting skin and nasal epithelium microbiota. The rich gene-microbe network in Russians seems to result in a better-balanced innate immunity and associates with low allergy prevalence., (© 2020 The Authors. Clinical & Experimental Allergy published by John Wiley & Sons Ltd.)

Background: Allergic diseases are more common in Finland than in Estonia, which-according to the biodiversity hypothesis-could relate to differences in early microbial exposures., Methods: We aimed at defining possible microbial perturbations preceding early atopic sensitization. Stool, nasal and skin samples of 6-month-old DIABIMMUNE study participants with HLA susceptibility to type 1 diabetes were collected. We compared microbiotas of sensitized (determined by specific IgE results at 18 months of age) and unsensitized Estonian and Finnish children., Results: Sensitization was differentially targeted between populations, as egg-specific and birch pollen-specific IgE was more common in Finland. Microbial diversity and community composition also differed; the genus Acinetobacter was more abundant in Estonian skin and nasal samples. Particularly, the strain-level profile of Acinetobacter lwoffii was more diverse in Estonian samples. Early microbiota was not generally associated with later sensitization. Microbial composition tended to differ between children with or without IgE-related sensitization, but only in Finland. While land-use pattern (ie green areas vs. urban landscapes around the children's homes) was not associated with microbiota as a whole, it associated with the composition of the genus Acinetobacter. Breastfeeding affected gut microbial composition and seemed to protect from sensitization., Conclusions: In accordance with the biodiversity hypothesis, our results support disparate early exposure to environmental microbes between Finnish and Estonian children and suggest a significant role of the genus Acinetobacter in the allergy gap between the two populations. The significance of the observed differences for later allergic sensitization remains open., (© 2020 EAACI and John Wiley and Sons A/S. Published by John Wiley and Sons Ltd.)

Bats utilize forests as roosting sites and feeding areas. However, it has not been documented how bats utilize these habitats in the boreal zone with methods afforded by recent technological advances. Forest structure and management practices can create a variety of three-dimensional habitats for organisms capable of flight, such as bats. Here, we study the presence of boreal bats in a forest forming a mosaic of different age classes, dominant tree species, canopy cover, soil fertility, and other environmental variables, throughout their active season in the summer using passive ultrasound detectors. Our results indicate a preference for mature forest by Eptesicus nilssonii and a pooled set of Myotis bats . Both groups of bats also showed temporal changes in their habitat use regarding forest age. In June and July, both groups occurred more often in mature than young forests, but from August onwards, the difference in occurrence became less evident in Myotis and disappeared completely in E. nilssonii . In addition, E. nilssonii was more often present in forests with low canopy cover, and its occurrence shifted from coniferous forests to deciduous forests during the season. The results reflect the within-season dynamics of bat communities and their ability to utilize different types of forest as environmental conditions change. Yet, the results most importantly emphasize the importance of mature forests to bat diversity and the need to conserve such environments in the boreal zone., Competing Interests: No competing interests., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Children are in contact with local environments, which may affect respiratory symptoms and allergic sensitization. We aimed to assess the effect of the environment and the walkability surrounding schools on lung function, airway inflammation and autonomic nervous system activity. Data on 701 children from 20 primary schools were analysed. Lung function, airway inflammation and pH from exhaled breath condensate were measured. Pupillometry was performed to evaluate autonomic activity. Land use composition and walkability index were quantified within a 500 m buffer zone around schools. The proportion of effects explained by the school environment was measured by mixed-effect models. We found that green school areas tended to be associated with higher lung volumes (FVC, FEV1 and FEF25-75%) compared with built areas. FVC was significantly lower in-built than in green areas. After adjustment, the school environment explained 23%, 34% and 99.9% of the school effect on FVC, FEV1, and FEF25-75%, respectively. The walkability of school neighbourhoods was negatively associated with both pupil constriction amplitude and redilatation time, explaining -16% to 18% of parasympathetic and 8% to 29% of sympathetic activity. Our findings suggest that the environment surrounding schools has an effect on the lung function of its students. This effect may be partially mediated by the autonomic nervous system.

Inbreeding is common in nature, and many laboratory studies have documented that inbreeding depression can reduce the fitness of individuals. Demonstrating the consequences of inbreeding depression on the growth and persistence of populations is more challenging because populations are often regulated by density- or frequency-dependent selection and influenced by demographic and environmental stochasticity. A few empirical studies have shown that inbreeding depression can increase extinction risk of local populations. The importance of inbreeding depression at the metapopulation level has been conjectured based on population-level studies but has not been evaluated. We quantified the impact of inbreeding depression affecting the fitness of individuals on metapopulation persistence in heterogeneous habitat networks of different sizes and habitat configuration in a context of natural butterfly metapopulations. We developed a spatial individual-based simulation model of metapopulations with explicit genetics. We used Approximate Bayesian Computation to fit the model to extensive demographic, genetic and life-history data available for the well-studied Glanville fritillary butterfly (Melitaea cinxia) metapopulations in the Åland islands in SW Finland. We compared 18 semi-independent habitat networks differing in size and fragmentation. The results show that inbreeding is more frequent in small habitat networks, and consequently, inbreeding depression elevates extinction risks in small metapopulations. Metapopulation persistence and neutral genetic diversity maintained in the metapopulations increase with the total habitat amount in and mean patch size of habitat networks. Dispersal and mating behaviour interact with landscape structure to determine how likely it is to encounter kin while looking for mates. Inbreeding depression can decrease the viability of small metapopulations even when they are strongly influenced by stochastic extinction-colonization dynamics and density-dependent selection. The findings from this study support that genetic factors, in addition to demographic factors, can contribute to extinctions of small local populations and also of metapopulations., (© 2019 The Authors. Journal of Animal Ecology © 2019 British Ecological Society.)

Background: Sufficient exposure to natural environments, in particular soil and its microbes, has been suggested to be protective against allergies., Objective: We aim at gaining more direct evidence of the environment-microbiota-health axis by studying the colonization of gut microbiota in mice after exposure to soil and by examining immune status in both a steady-state situation and during allergic inflammation., Methods: The gastrointestinal microbiota of mice housed on clean bedding or in contact with soil was analyzed by using 16S rRNA gene sequencing, and the data were combined with immune parameters measured in the gut mucosa, lung tissue, and serum samples., Results: We observed marked differences in the small intestinal and fecal microbiota composition between mice housed on clean bedding or in contact with soil, with a higher proportion of Bacteroidetes relative to Firmicutes in the soil group. The housing environment also influenced mouse intestinal gene expression, as shown by upregulated expression of the immunoregulatory markers IL-10, forkhead box P3, and cytotoxic T lymphocyte-associated protein 4 in the soil group. Importantly, using the murine asthma model, we found that exposure to soil polarizes the immune system toward T H 1 and a higher level of anti-inflammatory signaling, alleviating T H 2-type allergic responses. The inflammatory status of the mice had a marked influence on the composition of the gut microbiota, suggesting bidirectional communication along the gut-lung axis., Conclusion: Our results provide evidence of the role of environmentally acquired microbes in alleviating against T H 2-driven inflammation, which relates to allergic diseases., (Copyright © 2018 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.)

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations., Competing Interests: The authors declare no conflict of interest., (Copyright © 2018 the Author(s). Published by PNAS.)

Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the effects of low concentrations of antibiotics on multispecies microbial communities. Here, we address this question by investigating the effects of low antibiotic concentration on community composition and horizontal transfer of an antibiotic resistance plasmid in a 62-strain bacterial community in response to manipulation of the spatial environment and presence of predation. The strong effects of antibiotic treatment on community composition depend on the presence of predation and spatial structuring that have strong community effects on their own. Overall, we find plasmid transfer to diverse recipient taxa. Plasmid transfer is likely to occur to abundant strains, occurs to a higher number of strains in the presence of antibiotic, and also occurs to low-abundance strains in the presence of spatial structures. These results fill knowledge gaps concerning the effects of low antibiotic concentrations in complex ecological settings., Competing Interests: The authors declare no competing interests.

Vertebrate gut microbiota form a key component of immunity and a dynamic link between an individual and the ecosystem. Microbiota might play a role in social systems as well, because microbes are transmitted during social contact and can affect host behaviour. Combining methods from behavioural and molecular research, we describe the relationship between social dynamics and gut microbiota of a group-living cooperative species of primate, the red-bellied lemur (Eulemur rubriventer). Specifically, we ask whether patterns of social contact (group membership, group size, position in social network, individual sociality) are associated with patterns of gut microbial composition (diversity and similarity) between individuals and across time. Red-bellied lemurs were found to have gut microbiota with slight temporal fluctuations and strong social group-specific composition. Contrary to expectations, individual sociality was negatively associated with gut microbial diversity. However, position within the social network predicted gut microbial composition. These results emphasize the role of the social environment in determining the microbiota of adult animals. Since social transmission of gut microbiota has the potential to enhance immunity, microbiota might have played an escalating role in the evolution of sociality., (© 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.)

Our companion-animals, dogs, suffer increasingly from non-communicable diseases, analogous to those common in humans, such as allergic manifestations. In humans, living in rural environments is associated with lower risk of allergic diseases. Our aim was to explore whether a similar pattern can be found in dogs, using a nation-wide survey in Finland (n = 5722). We characterised the land-use around dog's home at the time of birth as well as around its current home, and described several lifestyle factors. The severity of owner-reported allergic symptoms in dogs was estimated with a comprehensive set of questions, developed by experts of canine dermatology. Also, the prevalence of diagnosed allergies in dog owners was recorded. The results indicate that allergic symptoms are more prevalent in urban environments both in dog owners and in dogs (accounting the effect of dog breed). Several factors related to rural living, such as bigger family size and regular contact with farm animals and other pets, were also protective against allergic symptoms in dogs. Interestingly, allergic dogs were more likely to have allergic owners than healthy dogs were. Therefore, we suggest that the mutual presence of allergic symptoms in both species indicates common underlying causal factors of allergic diseases.

The epidemiological dynamics of potentially free-living pathogens are often studied with respect to a specific pathogen species (e.g., cholera) and most studies concentrate only on host-pathogen interactions. Here we show that metacommunity-level interactions can alter conventional spatial disease dynamics. We introduce a pathogen eating consumer species and investigate a deterministic epidemiological model of two habitat patches, where both patches can be occupied by hosts, pathogens, and consumers of free-living pathogens. An isolated habitat patch shows periodic disease outbreaks in the host population, arising from cyclic consumer-pathogen dynamics. On the other hand, consumer dispersal between the patches generate asymmetric disease prevalence, such that the host population in one patch stays disease-free, while disease outbreaks occur in the other patch. Such asymmetry can also arise with host dispersal, where infected hosts carry pathogens to the other patch. This indirect movement of pathogens causes also a counter-intuitive effect: decreasing morbidity in a focal patch under increasing pathogen immigration. Our results underline that community-level interactions influence disease dynamics and consistent spatial asymmetry can arise also in spatially homogeneous systems.

Social welfare, better health care, and urbanization have greatly improved human health and well-being. On the other hand, Western societies suffer from the downsides of the elevated standard of living. Among other factors, the Western diet (poor in dietary fiber), lack of contact with natural biodiversity, and excessive antibiotic use are known to be associated with the increase in chronic inflammatory disorders. Limited exposure to microbial biodiversity, in combination with severe lifestyle-related disturbances to commensal microbial communities, especially during early life, is changing the diversity and composition of human microbiota. In this review, we try to promote and apply ecological theory to understand the dynamics and diversity of human commensal microbiota. In this context, we explore the changes in the microbiota that are relevant to human health, especially in light of the rise of chronic inflammatory disorders. We try to elucidate the underlying ecological mechanisms behind these disorders and provide potential solutions for their avoidance., (© 2017 New York Academy of Sciences.)

Understanding the complex molecular alterations related to engineered nanomaterial (ENM) exposure is essential for carrying out toxicity assessment. Current experimental paradigms rely on both in vitro and in vivo exposure setups that often are difficult to compare, resulting in questioning the real efficacy of cell models to mimic more complex exposure scenarios at the organism level. Here, we have systematically investigated transcriptomic responses of the THP-1 macrophage cell line and lung tissues of mice, after exposure to several carbon nanomaterials (CNMs). Under the assumption that the CNM exposure related molecular alterations are mixtures of signals related to their intrinsic properties, we inferred networks of responding genes, whose expression levels are coordinately altered in response to specific CNM intrinsic properties. We observed only a minute overlap between the sets of intrinsic property-correlated genes at different exposure scenarios, suggesting specific transcriptional programs working in different exposure scenarios. However, when the effects of the CNM were investigated at the level of significantly altered molecular functions, a broader picture of substantial commonality emerged. Our results imply that in vitro exposures can efficiently recapitulate the complex molecular functions altered in vivo. In this study, altered molecular pathways in response to specific CNM intrinsic properties have been systematically characterized from transcriptomic data generated from multiple exposure setups. Our computational approach to the analysis of network response modules further revealed similarities between in vitro and in vivo exposures that could not be detected by traditional analysis of transcriptomics data. Our analytical strategy also opens a possibility to look for pathways of toxicity and understanding the molecular and cellular responses identified across predefined biological themes.

The composition of human microbiota is affected by a multitude of factors. Understanding the dynamics of our microbial communities is important for promoting human health because microbiota has a crucial role in the development of inflammatory diseases, such as allergies. We have studied the skin microbiota of both arms in 275 Finnish children of few months old to teenagers living in contrasting environments. We show that while age is a major factor affecting skin microbial composition, the living environment also discriminates the skin microbiota of rural and urban children. The effect of environment is age-specific; it is most prominent in toddlers but weaker for newborns and non-existent for teenagers. Within-individual variation is also related to age and environment. Surprisingly, variation between arms is smaller in rural subjects in all age groups, except in teenagers. We also collected serum samples from children for characterization of allergic sensitization and found a weak, but significant association between allergic sensitization and microbial composition. We suggest that physiological and behavioral changes, related to age and the amount of contact with environmental microbiota, jointly influence the dynamics of the skin microbiota, and explain why the association between the living environment skin microbiota is lost in teenager.

Purpose of Review: It has been proposed that biodiversity loss leads to reduced interaction between environmental and human microbiotas. This, in turn, may lead to immune dysfunction and impaired tolerance mechanisms in humans. That is, contact with environmental biodiversity is expected to protect from allergies. However, direct evidence linking contact with biodiversity and risk of allergy has been lacking. In this review, we consider the latest research on the biodiversity hypothesis of allergy., Recent Findings: It is becoming clear that what you eat, drink, inhale, and touch all contribute to the grand scheme of host-microbial crosstalk that is needed for a balanced, healthy immune system to develop and maintain a healthy recognition between harmful and harmless invasions. Microbes can either communicate directly with host immune cells or affect the host via metabolism that can even lead to epigenetic modifications. Our living environment plays a key role in this process. Although especially, early exposure to diverse, beneficial microbiota from the environment is repeatedly found crucial, studies on immigrants demonstrate that condition in later life can also be decisive., Conclusion: We are still lacking a more detailed understanding of the interaction between natural, environmental biodiversity, and health, which calls for new innovative and more long-term investigations. The outcomes should be utilized in policy and urban planning efforts, promoting human interaction with natural biodiversity, and supporting a healthy lifestyle.

Stable coexistence of ecologically identical species is not possible according to the established ecological theory. Many coexistence mechanisms have been proposed, but they all involve some form of ecological differentiation among the competing species. The aggregation model of coexistence would predict coexistence of identical species if there would be a mechanism that generates spatially aggregated distributions that are not completely correlated among the species. Our aim is to demonstrate that continued dispersal, triggered by reproductive interference between ecologically identical species, is such a mechanism. This study has been motivated by species using ephemeral patchy resources, such as decomposing fruits, fungal sporophores, carrion, and dung. We analyse an individual-based model with sexual reproduction, in which the progeny develops in ephemeral resource patches and the new generation disperses to a new set of patches. We assume spatially restricted dispersal, that patches differ in detectability, and that unmated females continue dispersal. In the model, reproductive interference (males spend some time searching for and/or attempting to mate with heterospecific females) reduces the mating rate of females, especially in the less common species, which leads to increased dispersal and reduces spatial correlation in species' distributions. For a wide range of parameter values, coexisting species show a systematic difference in their relative abundances due to two opposing forces: (1) uncommon species have reduced growth rate (Allee effect), which decreases abundance; (2) an abundance difference between the species reduces interspecific spatial correlation, which in turn reduces interspecific competition and allows the rarer species to persist at low density. Our results demonstrate a new mechanism for coexistence that is not based on ecological differentiation between species., (© 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.)

Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, prehibernating bats should adopt a less selective feeding behavior--yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual-level variation in prey preferences. DNA metabarcoding was used to characterize both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Nonbiting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators., (© 2016 John Wiley & Sons Ltd.)

Background: White-nose syndrome (WNS) has devastated bat populations in North America, with millions of bats dead. WNS is associated with physiological changes in hibernating bats, leading to increased arousals from hibernation and premature consumption of fat reserves. However, there is evidence of surviving populations of little brown myotis (Myotis lucifugus) close to where the fungus was first detected nearly ten years ago., Results: We examined the hibernation patterns of a surviving population of little brown myotis and compared them to patterns in populations before the arrival of WNS and populations at the peak of WNS mortality. Despite infection with Pseudogymnoascus destructans, the causative fungal agent, the remnant population displayed less frequent arousals from torpor and lower torpid body temperatures than bats that died from WNS during the peak of mortality. The hibernation patterns of the remnant population resembled pre-WNS patterns with some modifications., Conclusions: These data show that remnant populations of little brown myotis do not experience the increase in periodic arousals from hibernation typified by bats dying from WNS, despite the presence of the fungal pathogen on their skin. These patterns may reflect the use of colder hibernacula microclimates by WNS survivors, and/or may reflect differences in how these bats respond to the disease.

Many socio-economically important pathogens persist and grow in the outside host environment and opportunistically invade host individuals. The environmental growth and opportunistic nature of these pathogens has received only little attention in epidemiology. Environmental reservoirs are, however, an important source of novel diseases. Thus, attempts to control these diseases require different approaches than in traditional epidemiology focusing on obligatory parasites. Conditions in the outside-host environment are prone to fluctuate over time. This variation is a potentially important driver of epidemiological dynamics and affect the evolution of novel diseases. Using a modelling approach combining the traditional SIRS models to environmental opportunist pathogens and environmental variability, we show that epidemiological dynamics of opportunist diseases are profoundly driven by the quality of environmental variability, such as the long-term predictability and magnitude of fluctuations. When comparing periodic and stochastic environmental factors, for a given variance, stochastic variation is more likely to cause outbreaks than periodic variation. This is due to the extreme values being further away from the mean. Moreover, the effects of variability depend on the underlying biology of the epidemiological system, and which part of the system is being affected. Variation in host susceptibility leads to more severe pathogen outbreaks than variation in pathogen growth rate in the environment. Positive correlation in variation on both targets can cancel the effect of variation altogether. Moreover, the severity of outbreaks is significantly reduced by increase in the duration of immunity. Uncovering these issues helps in understanding and controlling diseases caused by environmental pathogens.

Background: The human commensal microbiota interacts in a complex manner with the immune system, and the outcome of these interactions might depend on the immune status of the subject., Objective: Previous studies have suggested a strong allergy-protective effect for Gammaproteobacteria. Here we analyze the skin microbiota, allergic sensitization (atopy), and immune function in a cohort of adolescents, as well as the influence of Acinetobacter species on immune responses in vitro and in vivo., Methods: The skin microbiota of the study subjects was identified by using 16S rRNA sequencing. PBMCs were analyzed for baseline and allergen-stimulated mRNA expression. In in vitro assays human monocyte-derived dendritic cells and primary keratinocytes were incubated with Acinetobacter lwoffii. Finally, in in vivo experiments mice were injected intradermally with A lwoffii during the sensitization phase of the asthma protocol, followed by readout of inflammatory parameters., Results: In healthy subjects, but not in atopic ones, the relative abundance of Acinetobacter species was associated with the expression of anti-inflammatory molecules by PBMCs. Moreover, healthy subjects exhibited a robust balance between anti-inflammatory and TH1/TH2 gene expression, which was related to the composition of the skin microbiota. In cell assays and in a mouse model, Acinetobacter species induced strong TH1 and anti-inflammatory responses by immune cells and skin cells and protected against allergic sensitization and lung inflammation through the skin., Conclusion: These results support the hypothesis that skin commensals play an important role in tuning the balance of TH1, TH2, and anti-inflammatory responses to environmental allergens., (Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.)

The physiological performance and behaviour of organisms are contingent on environmental conditions. When these conditions vary over time, this can have important consequences for the dynamics of individual populations and entire species communities. While the importance of environmental variation on the structuring and stability of natural food webs is recognised, little work has been done so far to build up a theoretical understanding of these processes. Here we investigate a simple model food web, where a consumer species forages flexibly upon two distinct, inter-competing resource species. Resource productivities or the resource intake rates by the consumer are assumed to depend on environmental conditions in a realistic manner. Fluctuations in these parameters drive variation in the strength of consumer-resource interactions, depending on whether the resource or the consumer is sensitive to environmental noise. The way resources and the consumer respond to changes in environmental conditions stems from the deterministic influence of each stochastic parameter on food web dynamics, which interact with the consumer adaptation process as well as between-resource competition. According to recent empirical reports, the mechanisms behind our results are likely to be relevant in natural systems and thus the model predictions are of potential importance in understanding food web responses to environmental stochasticity in general., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Natural populations experience environmental conditions that vary across space and over time. This variation is often correlated between localities depending on the geographical separation between them, and different species can respond to local environmental fluctuations similarly or differently, depending on their adaptation. How this emerging structure in environmental correlation (between-patches and between-species) affects spatial community dynamics is an open question. This paper aims at a general understanding of the interactions between the environmental correlation structure and population dynamics in spatial networks of local communities (metacommunities), by studying simple two-patch, two-species systems. Three different pairs of interspecific interactions are considered: competition, consumer-resource interaction, and host-parasitoid interaction. While the results paint a relatively complex picture of the effect of environmental correlation, the interaction between environmental forcing, dispersal, and local interactions can be understood via two mechanisms. While increasing between-patch environmental correlation couples immigration and local densities (destabilising effect), the coupling between local populations under increased between-species environmental correlation can either amplify or dampen population fluctuations, depending on the patterns in density dependence. This work provides a unifying framework for modelling stochastic metacommunities, and forms a foundation for a better understanding of population responses to environmental fluctuations in natural systems.

Environmentally transmitted pathogens face ecological interactions (e.g., competition, predation, parasitism) in the outside-host environment and host immune system during infection. Despite the ubiquitousness of environmental opportunist pathogens, traditional epidemiology focuses on obligatory pathogens incapable of environmental growth. Here we ask how competitive interactions in the outside-host environment affect the dynamics of an opportunist pathogen. We present a model coupling the classical SI and Lotka-Volterra competition models. In this model we compare a linear infectivity response and a sigmoidal infectivity response. An important assumption is that pathogen virulence is traded off with competitive ability in the environment. Removing this trade-off easily results in host extinction. The sigmoidal response is associated with catastrophic appearances of disease outbreaks when outside-host species richness, or overall competition pressure, decreases. This indicates that alleviating outside-host competition with antibacterial substances that also target the competitors can have unexpected outcomes by providing benefits for opportunist pathogens. These findings may help in developing alternative ways of controlling environmental opportunist pathogens.