Increased levels of markers of microbial exposure in homes with indoor storage of organic household waste

As part of environmental management policies in Europe, separate collection of organic household waste and nonorganic household waste has become increasingly common. As waste is often stored indoors, this policy might increase microbial exposure in the home environment. In this study we evaluated the association between indoor storage of organic waste and levels of microbial agents in house dust. The levels of bacterial endotoxins, mold beta(1-->3)-glucans, and fungal extracellular polysaccharides (EPS) of Aspergillus and Penicillium species were determined in house dust extracts as markers of microbial exposure. House dust samples were collected in 99 homes in The Netherlands selected on the basis of whether separated organic waste was present in the house. In homes in which separated organic waste was stored indoors for 1 week or more the levels of endotoxin, EPS, and glucan were 3.2-, 7.6-, and 4. 6-fold higher, respectively (all P < 0.05), on both living room and kitchen floors than the levels in homes in which only nonorganic residual waste was stored indoors. Increased levels of endotoxin and EPS were observed, 2.6- and 2.1-fold (P < 0.1), respectively, when separated organic waste was stored indoors for 1 week or less, whereas storage of nonseparated waste indoors had no effect on microbial agent levels (P > 0.2). The presence of textile floor covering was another major determinant of microbial levels (P < 0.05). Our results indicate that increased microbial contaminant levels in homes are associated with indoor storage of separated organic waste. These increased levels might increase the risk of bioaerosol-related respiratory symptoms in susceptible people.     

Architectural design influences the diversity and structure of the built environment microbiome

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors.     

From molecules to dynamic biological communities

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.     

Metacommunity theory for transmission of heritable symbionts within insect communities

Microbial organisms are ubiquitous in nature and often form communities closely associated with their host, referred to as the microbiome. The microbiome has strong influence on species interactions, but microbiome studies rarely take interactions between hosts into account, and network interaction studies rarely consider microbiomes. Here, we propose to use metacommunity theory as a framework to unify research on microbiomes and host communities by considering host insects and their microbes as discretely defined “communities of communities” linked by dispersal (transmission) through biotic interactions. We provide an overview of the effects of heritable symbiotic bacteria on their insect hosts and how those effects subsequently influence host interactions, thereby altering the host community. We suggest multiple scenarios for integrating the microbiome into metacommunity ecology and demonstrate ways in which to employ and parameterize models of symbiont transmission to quantitatively assess metacommunity processes in host‐associated microbial systems. Successfully incorporating microbiota into community‐level studies is a crucial step for understanding the importance of the microbiome to host species and their interactions.     

Increased Levels of Markers of Microbial Exposure in Homes with Indoor Storage of Organic Household Waste

As part of environmental management policies in Europe, separate collection of organic household waste and nonorganic household waste has become increasingly common. As waste is often stored indoors, this policy might increase microbial exposure in the home environment. In this study we evaluated the association between indoor storage of organic waste and levels of microbial agents in house dust. The levels of bacterial endotoxins, mold β(1→3)-glucans, and fungal extracullar polysaccharides (EPS) of Aspergillus and Penicillium species were determined in house dust extracts as markers of microbial exposure. House dust samples were collected in 99 homes in The Netherlands selected on the basis of whether separated organic waste was present in the house. In homes in which separated organic waste was stored indoors for 1 week or more the levels of endotoxin, EPS, and glucan were 3.2-, 7.6-, and 4.6-fold higher, respectively (all P < 0.05), on both living room and kitchen floors than the levels in homes in which only nonorganic residual waste was stored indoors. Increased levels of endotoxin and EPS were observed, 2.6- and 2.1-fold (P < 0.1), respectively, when separated organic waste was stored indoors for 1 week or less, whereas storage of nonseparated waste indoors had no effect on microbial agent levels (P > 0.2). The presence of textile floor covering was another major determinant of microbial levels (P < 0.05). Our results indicate that increased microbial contaminant levels in homes are associated with indoor storage of separated organic waste. These increased levels might increase the risk of bioaerosol-related respiratory symptoms in susceptible people.     

Colliding and interacting microbiomes and microbial communities - consequences for human health

Living ‘things’ coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world – paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.     

An ecological perspective on U.S. industrial poultry production: the role of anthropogenic ecosystems on the emergence of drug-resistant bacteria from agricultural environments

The industrialization of food animal production, specifically the widespread use of antimicrobials, not only increased pressure on microbial populations, but also changed the ecosystems in which antimicrobials and bacteria interact. In this review, we argue that industrial food animal production (IFAP) is appropriately defined as an anthropogenic ecosystem. This paper uses an ecosystem perspective to frame an examination of these changes in the context of U.S. broiler chicken production. This perspective emphasizes multiple modes by which IFAP has altered microbiomes and also suggests a means of generating hypotheses for understanding and predicting the ecological impacts of IFAP in terms of the resistome and the flow of resistance within and between microbiomes.     

Population level virulence in polymicrobial communities associated with chronic disease

Renewed studies of chronic infection have shifted the focus from single pathogens to multi-microbial communities as culture-independent techniques reveal complex consortia of microbes associated with c...     

Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances

The indoor microbiome is a complex system that is thought to depend on dispersal from the outdoor biome and the occupants'' microbiome combined with selective pressures imposed by the occupants'' behaviors and the building itself. We set out to determine the pattern of fungal diversity and composition in indoor air on a local scale and to identify processes behind that pattern. We surveyed airborne fungal assemblages within 1-month time periods at two seasons, with high replication, indoors and outdoors, within and across standardized residences at a university housing facility. Fungal assemblages indoors were diverse and strongly determined by dispersal from outdoors, and no fungal taxa were found as indicators of indoor air. There was a seasonal effect on the fungi found in both indoor and outdoor air, and quantitatively more fungal biomass was detected outdoors than indoors. A strong signal of isolation by distance existed in both outdoor and indoor airborne fungal assemblages, despite the small geographic scale in which this study was undertaken (<500 m). Moreover, room and occupant behavior had no detectable effect on the fungi found in indoor air. These results show that at the local level, outdoor air fungi dominate the patterning of indoor air. More broadly, they provide additional support for the growing evidence that dispersal limitation, even on small geographic scales, is a key process in structuring the often-observed distance–decay biogeographic pattern in microbial communities.     

Microbiomes in Canidae

Because of their range expansion across North America, coyotes (Canis latrans) now occur sympatrically with numerous other predator species, including red foxes (Vulpes vulpes). This raises several interesting ecological questions, including if and how sympatry affects the diet and gut microbiomes of coyotes and red foxes. We examined the gut microbiomes of sympatric populations of coyotes and red foxes within two different National Parks in Virginia, USA, that differ in land use, vegetation, and anthropogenic disturbance: Prince William Forest Park (PRWI) and Manassas National Battlefield Park (MANA). From 2012 to 2017, scat samples from PRWI and MANA were collected and analyzed. Polymerase chain reaction (PCR) amplification of a region of the mitochondrial cytochrome‐b gene followed by restriction enzyme digestion of the PCR product was used to determine the origin of each scat sample. Next‐Generation DNA sequencing of a hypervariable 16S rRNA gene region was used to determine gut microbiome information about the scat samples. There was no evidence for a difference between the gut microbiomes of red foxes in either location, or for a difference between the gut microbiomes of red foxes at either location and coyotes at the location with lower human disturbance, PRWI. However, the gut microbiomes of coyotes at the location with higher anthropogenic disturbances, MANA, revealed a marked change from those found in red foxes at either location and from those in coyotes at the location with lower disturbances. The gut microbiomes of coyotes subjected to greater human impact may provide evidence of dysbiosis, indicative of increased physiological stress and reduced health. We discuss our observations in the context of understanding anthropogenic impacts on coyote and red fox interactions. Our results suggest that physiological stress in the form of human disturbance may play an important role in the composition of the gut microbiome of coyotes, which can affect their overall health.     

Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro‐ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolomes of four wild lowland gorilla groups in the Dzanga‐Sangha Protected Areas, Central African Republic. Results show that geographical range may be an important modulator of the gut microbiomes and metabolomes of these gorilla groups. Distinctions seemed to relate to feeding behaviour, implying energy harvest through increased fruit consumption or fermentation of highly fibrous foods. These observations were supported by differential abundance of metabolites and bacterial taxa associated with the metabolism of cellulose, phenolics, organic acids, simple sugars, lipids and sterols between gorillas occupying different geographical ranges. Additionally, the gut microbiomes of a gorilla group under increased anthropogenic pressure could always be distinguished from that of all other groups. By characterizing the interplay between environment, behaviour, diet and symbiotic gut microbes, we present an alternative perspective on primate ecology and on the forces that shape the gut microbiomes of wild primates from an evolutionary context.     

Comparison of different methods for determining lignin concentration and quality in herbaceous and woody plant residues

Background

The development and dispersal of seeds as well as their transition to seedlings represent perhaps the most critical stages of a plant’s life cycle. The endophytic and epiphytic microbial interactions that take place in, on, and around seeds during these stages of the plant’s life cycle may have profound impacts on plant ecology, health, and productivity. While our understanding of the seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now being made.

Scope

This review explores the microbial associations with seeds through various stages of the plant life cycle, beginning with the earliest stages of seed development on the parent plant and continuing through the development and establishment of seedlings in soil. This review represents a broad synthesis of the ecological and agricultural literature focused on seed-microbe interactions as a means of better understanding how these interactions may ultimately influence plant ecology, health, and productivity in both natural and agricultural systems. Our current understanding of seed-microbe associations will be discussed, with an emphasis on recent findings that specifically highlight the emerging contemporary understanding of how seed-microbe associations may ultimately impact plant health and productivity.

Conclusions

The diversity and dynamics of seed microbiomes represent the culmination of complex interactions with microbes throughout the plant life cycle. The richness and dynamics of seed microbiomes is revealing exciting new opportunities for research into plant-microbe interactions. Often neglected in plant microbiome studies, the renaissance of inquiry into seed microbiomes is offering exciting new insights into how the diversity and dynamics of the seed microbiome with plant and soil microbiomes as well as the microbiomes of dispersers and pollinators. It is clear that the interactions taking place in and around seeds indeed have significant impacts on plant health and productivity in both agricultural and natural ecosystems.

     

Changes amid constancy: Flower and leaf microbiomes along land use gradients and between bioregions

Microbial communities inhabiting above-ground parts of plants affect their host's development, fitness and function. Although studies on plant-associated microbes are of growing interest, environmental drivers of flower microbiomes in particular are poorly characterized. In this study, we investigated flower and leaf epiphytic bacterial microbiomes of Ranunculus acris and Trifolium pratense using metabarcoding of 16S ribosomal DNA in three German bioregions and along land-use intensity gradients. Our data suggests that the structures of bacterial communities clearly differed between plant species and tissue types. Also, floral bacterial communities of R. acris showed higher variability in comparison to T. pratense. Bacteria usually associated with pollinators were found solely in flower samples, while bacteria usually associated with the rhizosphere were only present in high abundances on leaves. We identified Pseudomonadaceae, Enterobacteriaceae and Sphingomonadaceae as the most abundant taxa on flowers, while Sphingomonadaceae, Methylobacteriaceae and Cytophagaceae dominated bacterial communities on leaves. We found that bacterial communities did not differ between long-distant regions. However, there was a turnover within each bioregion between short-distant locations. High land use intensity caused phylogenetically less diverse and more homogenous bacterial communities with an exception of T. pratense flowers. This was associated with a loss of rare bacterial families. Intensification of mowing affected the bacterial communities associated with leaves of T. pratense and fertilization led to more homogenous flower and leaf communities of R. acris, while grazing had no effects on the bacterial community composition. However, dominant taxa were not affected by land use intensification. Despite that, we identified indicator taxa for regularly disturbed environments in flower microbiomes. In conclusion, our study contributes to the knowledge about microbial community structures of the phyllosphere and extends the understanding of their community dynamics with respect to biogeographical separation and anthropogenic changes of the environment.     

Seasonal Variations of Indoor Microbial Exposures and Their Relation to Temperature,Relative Humidity,and Air Exchange Rate

Indoor microbial exposure has been related to adverse pulmonary health effects. Exposure assessment is not standardized, and various factors may affect the measured exposure. The aim of this study was to investigate the seasonal variation of selected microbial exposures and their associations with temperature, relative humidity, and air exchange rates in Danish homes. Airborne inhalable dust was sampled in five Danish homes throughout the four seasons of 1 year (indoors, n = 127; outdoors, n = 37). Measurements included culturable fungi and bacteria, endotoxin, N-acetyl-beta-d-glucosaminidase, total inflammatory potential, particles (0.75 to 15 μm), temperature, relative humidity, and air exchange rates. Significant seasonal variation was found for all indoor microbial exposures, excluding endotoxin. Indoor fungi peaked in summer (median, 235 CFU/m³) and were lowest in winter (median, 26 CFU/m³). Indoor bacteria peaked in spring (median, 2,165 CFU/m³) and were lowest in summer (median, 240 CFU/m³). Concentrations of fungi were predominately higher outdoors than indoors, whereas bacteria, endotoxin, and inhalable dust concentrations were highest indoors. Bacteria and endotoxin correlated with the mass of inhalable dust and number of particles. Temperature and air exchange rates were positively associated with fungi and N-acetyl-beta-d-glucosaminidase and negatively with bacteria and the total inflammatory potential. Although temperature, relative humidity, and air exchange rates were significantly associated with several indoor microbial exposures, they could not fully explain the observed seasonal variations when tested in a mixed statistical model. In conclusion, the season significantly affects indoor microbial exposures, which are influenced by temperature, relative humidity, and air exchange rates.     

Effects of discrete bioactive microbial volatiles on plants and fungi

Plants live in association with microorganisms, which are well known as a rich source of specialized metabolites, including volatile compounds. The increasing numbers of described plant microbiomes allowed manifold phylogenetic tree deductions, but less emphasis is presently put on the metabolic capacities of plant‐associated microorganisms. With the focus on small volatile metabolites we summarize (i) the knowledge of prominent bacteria of plant microbiomes; (ii) present the state‐of‐the‐art of individual (discrete) microbial organic and inorganic volatiles affecting plants and fungi; and (iii) emphasize the high potential of microbial volatiles in mediating microbe–plant interactions. So far, 94 discrete organic and five inorganic compounds were investigated, most of them trigger alterations of the growth, physiology and defence responses in plants and fungi but little is known about the specific molecular and cellular targets. Large overlaps in emission profiles of the emitters and receivers render specific volatile organic compound‐mediated interactions highly unlikely for most bioactive mVOCs identified so far.     

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a 'hot spot' for horizontal gene transfer between microbes.     

Engineering solutions for open microalgae mass cultivation and realistic indoor simulation of outdoor environments

Microalgae could become an important renewable source for chemicals, food, and energy if process costs can be reduced. In the past 60 years, relevant factors in open outdoor mass cultivation of microalgae were identified and elaborate solutions regarding bioprocesses and bioreactors were developed. An overview of these solutions is presented. Since the cost of most microalgal products from current mass cultivation systems is still prohibitively high, further development is required. The application of complex computational techniques for cost-effective process and reactor development will become more important if experimental validation of simulation results can easily be achieved. Due to difficulties inherent to outdoor experimentation, it can be useful to conduct validation experiments indoors. Considerations and approaches for realistic indoor reproduction of the most important environmental conditions in microalgae cultivation experiments—light, temperature, and substance concentrations, are discussed.     

Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals

Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.     

Metagenomic assessment of the global diversity and distribution of bacteria and fungi

Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross-habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host-associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria-to-fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross-habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host-associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats.     

Oral microbiomes: more and more importance in oral cavity and whole body

Microbes appear in every corner of human life, and microbes affect every aspect of human life. The human oral cavity contains a number of different habitats. Synergy and interaction of variable oral microorganisms help human body against invasion of undesirable stimulation outside. However, imbalance of microbial flora contributes to oral diseases and systemic diseases. Oral microbiomes play an important role in the human microbial community and human health. The use of recently developed molecular methods has greatly expanded our knowledge of the composition and function of the oral microbiome in health and disease. Studies in oral microbiomes and their interactions with microbiomes in variable body sites and variable health condition are critical in our cognition of our body and how to make effect on human health improvement.