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BackgroundMicrobial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset.ResultsThis non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Video abstract CONCLUSION: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.

The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C11H16O4, C18H34O4, and C6H15NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C6H15NO (assuming it presented as Diethylethanolamine).

Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material.

C-C Chemokine Receptor 7 (CCR7) mediates T-cell acute lymphoblastic leukemia (T-ALL) invasion of the central nervous system (CNS) mediated by chemotactic migration to C-C chemokine ligand 19 (CCL19). To determine if a CCL19 antagonist, CCL198-83, could inhibit CCR7-induced chemotaxis and signaling via CCL19 but not CCL21, we used transwell migration and Ca2+ mobilization signaling assays. We found that in response to CCL19, human T-ALL cells employ β2 integrins to invade human brain microvascular endothelial cell monolayers. In vivo, using an inducible mouse model of T-ALL, we found that we were able to increase the survival of the mice treated with CCL198-83 when compared to non-treated controls. Overall, our results describe a targetable cell surface receptor, CCR7, which can be inhibited to prevent β2-integrin-mediated T-ALL invasion of the CNS and potentially provides a platform for the pharmacological inhibition of T-ALL cell entry into the CNS. [ABSTRACT FROM AUTHOR]

Host-associated microbial dynamics are influenced by dietary and immune factors, but how exogenous microbial exposure shapes host-microbe dynamics remains poorly characterized. To investigate this phenomenon, we characterized the skin, rectum, and respiratory tract-associated microbiota in four aquarium-housed dolphins daily over a period of 6 weeks, including administration of a probiotic during weeks 4 to 6. The environmental bacterial sources were also characterized, including the animals' human handlers, the aquarium air and water, and the dolphins' food supply. Continuous microbial exposure occurred between all sites, yet each environment maintained a characteristic microbiota, suggesting that the majority of exposure events do not result in colonization. Small changes in water physicochemistry had a significant but weak correlation with change in dolphin-associated bacterial richness but had no influence on phylogenetic diversity. Food and air microbiota were the richest and had the largest conditional influence on other microbiota in the absence of probiotics, but during probiotic administration, food alone had the largest influence on the stability of the dolphin microbiota. Our results suggest that respiratory tract and gastrointestinal epithelium interactions with air- and food-associated microbes had the biggest influence on host-microbiota dynamics, while other interactions, such as skin transmission, played only a minor role. Finally, direct oral stimulation with a foreign exogenous microbial source can have a profound effect on microbial stability. IMPORTANCE These results provide valuable insights into the ecological influence of exogenous microbial exposure, as well as laying the foundation for improving aquarium management practices. By comparing data for dolphins from aquaria that use natural versus artificial seawater, we demonstrate the potential influence of aquarium water disinfection procedures on dolphin microbial dynamics.

Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman's rank correlation [rs] = >0.81; false-discovery rate [q] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Differences in the bacterial community structure associated with 7 skin sites in 71 healthy people over five days showed significant correlations with age, gender, physical skin parameters, and whether participants lived in urban or rural locations in the same city. While body site explained the majority of the variance in bacterial community structure, the composition of the skin-associated bacterial communities were predominantly influenced by whether the participants were living in an urban or rural environment, with a significantly greater relative abundance of Trabulsiella in urban populations. Adults maintained greater overall microbial diversity than adolescents or the elderly, while the intragroup variation among the elderly and rural populations was significantly greater. Skin-associated bacterial community structure and composition could predict whether a sample came from an urban or a rural resident ~5x greater than random.

Our growing awareness of the microbial worlds importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earths microbial diversity., Author(s): Luke R. Thompson [1, 2, 3]; Jon G. Sanders [1]; Daniel McDonald [1]; Amnon Amir [1]; Joshua Ladau [4]; Kenneth J. Locey [5]; Robert J. Prill [6]; Anupriya Tripathi [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.comnet.2005.10.021 Byline: Olfa Nasraoui (a), Carlos Rojas (a), Cesar Cardona (b) Keywords: Mining evolving data streams; Web clickstreams; Web mining; Text mining; User profiles Abstract: The expanding and dynamic nature of the Web poses enormous challenges to most data mining techniques that try to extract patterns from Web data, such as Web usage and Web content. While scalable data mining methods are expected to cope with the size challenge, coping with evolving trends in noisy data in a continuous fashion, and without any unnecessary stoppages and reconfigurations is still an open challenge. This dynamic and single pass setting can be cast within the framework of mining evolving data streams. The harsh restrictions imposed by the "you only get to see it once" constraint on stream data calls for different computational models that may furthermore bring some interesting surprises when it comes to the behavior of some well known similarity measures during clustering, and even validation. In this paper, we study the effect of similarity measures on the mining process and on the interpretation of the mined patterns in the harsh single pass requirement scenario. We propose a simple similarity measure that has the advantage of explicitly coupling the precision and coverage criteria to the early learning stages. Even though the cosine similarity, and its close relative such as the Jaccard measure, have been prevalent in the majority of Web data clustering approaches, they may fail to explicitly seek profiles that achieve high coverage and high precision simultaneously. We also formulate a validation strategy and adapt several metrics rooted in information retrieval to the challenging task of validating a learned stream synopsis in dynamic environments. Our experiments confirm that the performance of the MinPC similarity is generally better than the cosine similarity, and that this outperformance can be expected to be more pronounced for data sets that are more challenging in terms of the amount of noise and/or overlap, and in terms of the level of change in the underlying profiles/topics (known sub-categories of the input data) as the input stream unravels. In our simulations, we study the task of mining and tracking trends and profiles in evolving text and Web usage data streams in a single pass, and under different trend sequencing scenarios. Author Affiliation: (a) Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, United States (b) Magnify Inc., Chicago, United States

Abstract: Data mining has recently attracted attention as a set of efficient techniques that can discover patterns from huge data. More recent advancements in collecting massive evolving data streams created [...]

Growing cultivars that possess multiple disease-and-pest resistance minimizes crop losses, reduces the need for pesticides, and lowers production costs. Our objective was to use gamete selection (i.e., selection based on [F.sub.1]-derived families that come from crosses that are multiple-parent, heterogeneous, and heterogametic) to develop upright carioca-type beans (Phaseolus vulgaris L.) with resistance to angular leaf spot (ALS), anthracnose (ANT), bean common mosaic (BCM), bean golden mosaic (BGM), common bacterial blight (CBB), and leafhopper (LHP). Two multiple-parent, interracial crosses (BZ 9780 and GX 9792) were made, using plant-to-plant pollinations, in 1990-1991. The [F.sub.1]-derived [F.sub.2] ([F.sub.1.2]) families were evaluated for ALS and CBB, and [F.sub.1.3] families for ANT and LHP. in [F.sub.4], carioca-type seeds from promising families were saved. The [F.sub.1.4] families were then evaluated for BGM. All 127 [F.sub.1.2] families from BZ 9780 were discarded by [F.sub.4] because none segregated for six resistances and possessed carioca-type seeds. Of the GX 9792 population, 260 [F.sub.5]-derived [F.sub.9] ([F.sub.5.9] lines, originating from only 12 of 460 [F.sub.1.2] families, were evaluated for ALS, ANT, BCM, BGM, CBB, and LHP. Six parents, eight checks, and 86 [F.sub.5.9] lines resistant to at least ANT, BCM, and CBB were tested for yield in seven environments in 1995-1996, using a partially balanced lattice design with three replicates. Only eight lines, originating from four of the 460 [F.sub.1.2] families, possessed resistance to all five diseases and LHP. Of these lines, one outyielded the check cultivar Carioca, and that line with one other outyielded the two carioca-type parents (A 769 and EMP 250) used in the GX 9792 populations. Thus, the use of gamete selection and early generation testing was effective in developing high- yielding upright lines with resistance to multiple biotic stresses., REPORTED 30 yr ago from unknown origins, Carioca has become the most popular common bean cultivar in Brazil. It has also been introduced to neighboring Argentina and Bolivia and to [...]

Arcelin, a seed protein discovered in wild Phaseolus vulgaris L. accessions, gives high levels of resistance to the Mexican Bean Weevil [MBW; Zabrotes subfasciatus (Boheman)]. Five arcelin variants have been described. To better understand to genetic control of arcelin and MBW resistance, an inheritance study was conducted. Bioassay tests for insect response, and biochemical tests to detect the presence-absence of arcelin, were performed on the same individual seed. Accessions G12952 (arc-4) and G02771 (arc-5) had the highest level of resistance to MBW with no adults emerging from infested seed. Resistance was also found in G12882 (arc-1) and G12866 (arc-2), while G12922 (arc-3) and the commercial cultivar, Pijao, were susceptible to the insect. The genetic study confirmed that all arcelin variants were inherited as a single dominant gene based on biochemical evaluations for presence-absence of arcelin. Nevertheless, in bioassay tests with MBW, only crosses with arc-1 and arc-5 showed a single, completely dominant gene mode of inheritance, with the presence of arcelin being highly associated with resistance to the insect. For arc-1 and arc-5, biochemical tests can be reliably used to select for MBW resistance. For arc-2, a combination of biochemical and bioassay tests is needed. As arc-4 segregated few resistant individuals, and arc-3 gave only intermediate to susceptible offspring, the use of these two arcelin variants is not recommended in a routine resistance breeding program. Electrophoretic patterns and bioassay tests of F [sub1] and F [sub2] generations showed that arc-5 and arc-1 variants are inherited as a single unit and are codominant.

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