Pathogen Communities Research Articles

Illumina-based sequencing analysis of pathogenic microorganisms in dental caries patients of different Chinese ethnic groups.

ObjectiveTo analyze the pathogenic community diversity of dental caries patients from Tu, Hui, Tibetan, and Han Chinese ethnic groups.MethodsForty saliva samples were collected from the following patients with dental caries: Tu from Huzhu County (n = 10), Hui from Ping’an County (n = 10), Han from Xining city (n = 10), and Tibetan from Yushu (n = 10). High-throughput sequencing of bacterial 16S rRNA genes (V3-V4) was performed using the Illumina MiSeq sequencing platform.ResultsBased on 97% similarity clustering, operational taxonomic units of Tu, Hui, Tibetan, and Han ethnic groups were 181, 210, 38, and 67, respectively. In Tu patients, 11 phyla, 19 classes, and 89 genera were identified, compared with 13 phyla, 21 classes, and 113 genera in Hui patients, two phyla, four classes, and 21 genera in Tibetan patients, five phyla, nine classes, and 34 genera in Han patients, and four phyla, five classes, and 12 genera from the control group. The main pathogens of dental caries included Veillonella, Aggregatibacter, Leptotrichia, Bacteroides, Granulicatella, Streptococcus, and Prevotella.ConclusionThe pathogenic microorganisms of dental caries differ greatly among Tu, Hui, Tibetan, and Han ethnic groups. These findings provide a theoretical basis for the effective prevention and treatment of dental caries in different Chinese populations.

Using contact networks and next-generation sequencing for wildlife epidemiology

Horizontal transmission of infectious diseases is strongly determined by the contact network between hosts [1] . Environmental and ecological variables that define the probability of contacts between individuals, such as food resource quality and quantity, have been largely neglected in models studying the dynamics and epidemiology of wildlife diseases. In this work, we used pollinators and their pathogens to study the role of contact networks in a natural multi-host pathogen community. In agricultural landscapes, wild flowers are the most important food resources of insect pollinators such as bees and flies. To boost yields of agricultural crops and ensure pollinator conservation, the UK Environmental Stewardship scheme prompted farmers to grow pollinator-friendly wild flower margins along their fields ( Fig. 1 ). Wild flower margins ( Fig. 1 ) have proven to be efficient to increase both density and diversity of bees in agricultural areas, and to increase pollination success of surrounding crops. As the rate of disease transmission should increase with host density, we hypothesize that the success of wild flower margins may generate hubs for pathogen exchange within the bee community. Several recent studies have illustrated the frequent transmission of infectious diseases between managed and wild bees, potentially via the shared use of flowers [2] . However, the environmental and ecological drivers of disease dynamics between pollinators remain uncharacterised [3] . To understand the role of flower density and diversity for bee disease transmission, we reconstructed high-resolution plant–insect visitor networks from flower visitation data collected in ten farms in Southern England (five farms participating in the scheme vs. five control farms), as well as a record of bee pollen collection to describe the resource bees were exploiting (pollen vs. nectar). When analysing the plant–pollinator networks, we found that flower density and diversity strongly define pollinator density and foraging behaviour, and influence the structure of indirect ‘contact networks’ among pollinators (via the use of flower species). Particularly, we found flower diversity to be positively correlated with the reduction of niche overlap between insect species. This response of insect pollinators suggest that wild flower margins with high plant species richness may reduce insect competition for resources, and potentially reduce the risk of inter-specific disease transmission by supporting diverse diet for insects exploiting different flowers. To test the effect of plant diversity on pathogen dynamics in bees, we sampled pollinators on these farms and characterized their virome by deep transcriptome sequencing. We are now combining these environmental data to virus discovery in order to reveal the impact of the agri-environmental scheme on viral dynamics. Ultimately, we aim to identify environmental (flower density, agricultural practices) and ecological factors (plant taxa, insect community assemblage) that significantly enhance the transmission of plant and pollinator viral diseases within our model to eventually improve agricultural practises and wildlife management.

Cross-scale dynamics in community and disease ecology: relative timescales shape the community ecology of pathogens.

Communities of free-living organisms are shaped by processes operating within and among patches of habitat, whereas pathogen communities are shaped by analogous processes operating within and among hosts. Resource competition (R*) theory can describe dynamics within patches or hosts, and metacommunity dynamics describe competition-colonization trade-offs, extinction debts, and superinfection. However, models at this broader scale often assume instantaneous competitive exclusion in co-inhabited patches or co-infected hosts. Impacts of more gradual competitive exclusion on the abundance, distribution, and diversity of species are less clear. Here, we nest a general resource competition model within a metacommunity framework and manipulate the relative timescales for processes operating within and among patches/hosts. We focus on superinfection in pathogen communities. We compare cases where transmission depends on infection prevalence vs. the abundance of pathogens within hosts. Surprisingly, slowing the relative pace of competitive exclusion within hosts can decrease infection prevalence of the inferior competitor and increase prevalence of the superior competitor, depending on transmission and virulence. Slower within-host dynamics reduce the abundance of both pathogens within hosts and promote diversity at multiple scales: co-infections within individual hosts and co-occurrence in the host population. These results highlight surprising feedbacks that can emerge across scales and reinforce the rich cross-scale connections between community and disease ecology.

Summary bipartite networks: trees in Romanian forests – wood pathogenic and sapro-pathogenic fungi

The assembly of plant pathogenic communities is one of the central topics in community ecology. Based on collected metadata, a summary host-pathogen bipartite network was constructed, and network metrics such as connectance, node degree distribution, nestedness and modularity were employed to verify the non-random nature of host-pathogen interactions. The selected hosts (Quercus robur, Q. cerris, Q. frainetto, Q. pubescens, Q. petraea, Fagus sylvatica and Picea abies) are tree species characteristic for European forest ecosystems, covering large areas of Central and South-Eastern Europe including Romania. The selected tree species (based on their dominance in forest ecosystems) establish 109 forest ecosystem types in Romanian forest ecosystems’ typology. 105 species of wood pathogens and sapro-pathogens, covering whole area of Europe, were retrieved from published papers. The established bipartite network of wood pathogens and sapro-pathogens and their tree hosts was significantly modular, displaying four modules (Qnetwork = 0.24) and significantly nested (Nnetwork = 0.67), presented power law degree distribution, a common topology with mutualistic networks. Network topological characteristics generally encountered in parasitic networks described in literature, confirm the non-random assembly of the wood and bark pathogenic communities. Non-metric Multidimensional Scaling (NMDS) performed on wood pathogens ‘matrix and forest types’ matrix showed high resemblance in the positioning pattern of trees in ordination space. Mantel test confirmed the NMDS result - a significant correlation between similarities in pathogen share and similarities in tree composition of the forest ecosystems in Romanian forest classification. The network architecture resembles other published networks depicting symbiotic interactions. As tree species assemble in distinct forest types, the transmission of emerging or invasive pathogens is expected to continue in the future due to modular nature of the networks, triggered by major climatic changes.

Geographical Distribution of Fungal Plant Pathogens in Dust Across the United States

As the world’s population grows, global food production will need to increase. While food production efficiency has increased in recent decades through pathogen control, climate change poses new challenges in crop protection against pathogens. Understanding the natural geographical distribution and dispersal likelihood of fungal plant pathogens is essential for forecasting disease plant spread. Here we used cultivation-independent techniques to identify fungal plant pathogens in 1,289 near-surface dust samples collected across the United States. We found that overall fungal pathogen community composition is more related to environmental conditions (in particular soil pH, precipitation and frost) than to agricultural hosts and practices. We also delimited five susceptibility geographical areas in the United States where different sets of pathogens tend to occur.

Land use is a determinant of plant pathogen alpha- but not beta-diversity.

Little is known about the diversity patterns of plant pathogens and how they change with land use at a broad scale. We employed DNA metabarcoding to describe the diversity and composition of putative plant pathogen communities in three substrates (soil, roots, and leaves) across five major land uses at a national scale. Almost all plant pathogen communities (fungi, oomycetes, and bacteria) showed strong responses to land use and substrate type. Land use category could explain up to 24% of the variance in composition between communities. Alpha-diversity (richness) of plant pathogens was consistently lower in natural forests than in agricultural systems. In planted forests, there was also generally low pathogen alpha-diversity in soil and roots, but alpha-diversity in leaves was high compared with most other land uses. In contrast to alpha-diversity, differences in within-land use beta-diversity of plant pathogens (the predictability of plant pathogen communities within land use) were subtle. Our results show that large-scale patterns and distributions of putative plant pathogens can be determined using metabarcoding, allowing some of the first landscape level insights into these critically important communities.

Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next-generation sequencing strategy.

SummaryInfectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real‐time PCR and 16SrRNA gene‐based microbial profiling. A new target enrichment next‐generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas.

Individual tree traits shape insect and disease damage on oak in a climate-matching tree diversity experiment.

Diversifying planted forests by increasing genetic and species diversity is often promoted as a method to improve forest resilience to climate change and reduce pest and pathogen damage. In this study, we used a young tree diversity experiment replicated at two sites in the UK to study the impacts of tree diversity and tree provenance (geographic origin) on the oak (Quercus robur) insect herbivore community and a specialist biotrophic pathogen, oak powdery mildew. Local UK, French, and Italian provenances were planted in monocultures, provenance mixtures, and species mixes, allowing us to test whether: (a) local and nonlocal provenances differ in their insect herbivore and pathogen communities, and (b) admixing trees leads to associational effects on insect herbivore and pathogen damage. Tree diversity had variable impacts on foliar organisms across sites and years, suggesting that diversity effects can be highly dependent on environmental context. Provenance identity impacted upon both herbivores and powdery mildew, but we did not find consistent support for the local adaptation hypothesis for any group of organisms studied. Independent of provenance, we found tree vigor traits (shoot length, tree height) and tree apparency (the height of focal trees relative to their surroundings) were consistent positive predictors of powdery mildew and insect herbivory. Synthesis. Our results have implications for understanding the complex interplay between tree identity and diversity in determining pest damage, and show that tree traits, partially influenced by tree genotype, can be important drivers of tree pest and pathogen loads.

The role of long-term mineral and organic fertilisation treatment in changing pathogen and symbiont community composition in soil

Application of organic fertilisers to soil prevents erosion, improves fertility and may suppress certain soil-borne plant pathogens, but it is still unclear how different trophic groups of fungi and oomycetes respond to long-term fertilisation treatment. The objective of the study was to examine the effect of different fertilisation regimes on fungal and oomycete pathogen- and mycorrhizal symbiont diversity and community structure in both soil and roots, using PacBio SMRT sequencing. The field experiment included three fertilisation treatments that have been applied since 1989: nitrogen fertilisation (WOM), nitrogen fertilisation with manure amendment (FYM) and alternative organic fertilisation (AOF), each applied at five different rates. Soil samples were collected three times during the growing season, while root samples were collected during the flowering stage. There was no influence of the studied variables on soil and root pathogen richness. Contrary to our hypothesis, pathogen relative abundance in both soil and roots was significantly higher in plots with the AOF treatment. Furthermore, richness and relative abundance of arbuscular mycorrhizal (AM) fungi decreased significantly in the AOF treatment. Permutational analysis of variance (PERMANOVA) demonstrated the effect of fertilisation treatment on pathogen community composition in both soil and roots. Our findings indicate that organic fertilisers may not always benefit soil microbial community composition. Therefore, further studies are needed to understand how fertilisation affects mycorrhizal mutualists and pathogens.

An examination of the microbial community and occurrence of potential human pathogens in rainwater harvested from different roofing materials

While harvested rainwater can serve as an alternative water supply, microbial contaminants within the collection system can negatively affect water quality. Here, we investigated the impact of roofing material on the microbial quality of rainwater freshly harvested from pilot-scale roofs (concrete tile, cool, green, Galvalume® metal, and asphalt fiberglass shingle). The microbial quality of freshly harvested rainwater from six rain events over two years was analyzed by high-throughput sequencing and culture-dependent and -independent techniques. The concentrations of total coliform were significantly different among rainwaters harvested from the various roofing materials (p-value >0.05). However, the fecal coliform concentrations and the copy numbers of Enterococcus 23S rRNA genes and total Bacteria 16S rRNA genes did not vary by type of roofing material in a statistically significant way. Potential human pathogens such as Legionella, Escherichia coli O157:H7, Shiga-toxin-producing Escherichia coli, and adenovirus were detected at least once in rainwater harvested from the different roofing materials, even though the lowest occurrence of those potential human pathogens was noted from the metal roof. Also, substantial variation in the microbial communities from the different roofing materials was observed at the family and genus levels. These results demonstrate that the type of roofing material affects the microbial quality of freshly harvested rainwater, indicating that the choice of roofing material could shape the microbial community structure entering a rainwater storage tank. Given that detection of potential pathogens in the freshly harvested rainwater also differed between roofing materials, the type of roofing used to capture rainwater needs to be considered in rainwater harvesting system design, particularly if the water is intended for potable use.

Late Quaternary climate change explains soil fungal community composition rather than fungal richness in forest ecosystems.

The dramatic climate fluctuations of the late Quaternary have influenced the diversity and composition of macroorganism communities, but how they structure belowground microbial communities is less well known. Fungi constitute an important component of soil microorganism communities. They play an important role in biodiversity maintenance, community assembly, and ecosystem functioning, and differ from many macroorganisms in many traits. Here, we examined soil fungal communities in Chinese temperate, subtropical, and tropic forests using Illumina MiSeq sequencing of the fungal ITS1 region. The relative effect of late Quaternary climate change and contemporary environment (plant, soil, current climate, and geographic distance) on the soil fungal community was analyzed. The richness of the total fungal community, along with saprotrophic, ectomycorrhizal (EM), and pathogenic fungal communities, was influenced primarily by the contemporary environment (plant and/or soil) but not by late Quaternary climate change. Late Quaternary climate change acted in concert with the contemporary environment to shape total, saprotrophic, EM, and pathogenic fungal community compositions and with a stronger effect in temperate forest than in tropic–subtropical forest ecosystems. Some contemporary environmental factors influencing total, saprotrophic, EM, and pathogenic fungal communities in temperate and tropic–subtropical forests were different. We demonstrate that late Quaternary climate change can help to explain current soil fungal community composition and argue that climatic legacies can help to predict soil fungal responses to climate change.

Effect of Composting Under Semipermeable Film on the Sewage Sludge Virome.

The addition of compost from sewage sludge to soils represents a sustainable option from an environmental and economic point of view, which involves the valorisation of these wastes. However, before their use as a soil amendment, compost has to reach the quality levels according to the normative, including microbial parameters. Viruses are not included in this regulation and they can produce agricultural problems and human diseases if the compost is not well sanitised. In this study, we carried out the analysis of the viral populations during a composting process with sewage sludge at an industrial scale, using semipermeable cover technology. Viral community was characterised by the presence of plant viruses and bacteriophages of enteric bacteria. The phytopathogen viruses were the group with the highest relative abundance in the sewage sludge sample and at 70days of the composting process. The diversity of bacterial viruses and their specificity, with respect to the more abundant bacterial taxa throughout the process, highlights the importance of the interrelations between viral and bacterial communities in the control of pathogenic communities. These results suggest the possibility of using them as a tool to predict the effectiveness of the process.

Potential pathogen communities in highly polluted river ecosystems: Geographical distribution and environmental influence.

Risks of pathogenic bacteria to the health of both human beings and water ecosystems have been widely acknowledged. However, traditional risk assessment methods based on fecal indicator bacteria and/or pure culture are not comprehensive at the community level, mainly owing to the limited taxonomic coverage. Here, we combined the technique of high-throughput sequencing and the concept of metacommunity to assess the potential pathogenic bacterial communities in an economically and ecologically crucial but highly polluted river-the North Canal River (NCR) in Haihe River Basin located in North China. NCR presented a significant environmental gradient, with the highest, moderate, and lowest levels of pollution in the up-, middle, and downstream. After multiple analyses, we successfully identified 48 genera, covering nine categories of potential pathogens (mainly human pathogens). The most abundant genus was Acinetobacter, which was rarely identified as a pathogen bacterium in previous studies of NCR. At the community level, we observed significant geographical variation of community composition and structure. Such a high level of geographical variation was mainly derived from differed abundance of species among sections along the river, especially the top seven Operational Taxonomic Units (OTUs). For example, relative abundance of OTU1 (Gammaproteobacteria/Acinetobacter) increased significantly from upstream towards downstream. Regarding the underlying mechanisms driving community geographical variation, environmental filtering was identified as the dominant ecological process and total nitrogen as the most influential environmental variable. Altogether, this study provided a comprehensive profile of potential pathogenic bacteria in NCR and revealed the underlying mechanisms of community succession. Owing to their high abundance and wide geographical distribution, we suggest that potential pathogens identified in this study should be incorporated into future monitoring and management programs in NCR. By revealing the correlation between environmental factors and community composition, the results obtained in this study have significant implications for early warning and risk assessment of potential pathogen bacteria, as well as management practices in highly polluted river ecosystems.

Floc-size effects of the pathogenic bacteria in a membrane bioreactor plant

The size nature of sludge flocs could affect the occurrence and distribution of bacterial pathogens in wastewater treatment plants (WWTPs). In this study, the floc-size dependence of bacterial pathogens in the activated sludge of a WWTP was investigated using high-throughput metagenomic sequencing approaches. The results showed that a total of 423 pathogenic species belonging to 123 genera were identified in the three size-fractionated flocs. Also, we found that all the pathogens on the WHO's global priority pathogens list were detected in the size-fractionated flocs, with relative abundance of 0.4%, 0.3% and 0.3% for large-size, medium-size and small-size flocs, respectively, indicating the severe human and environmental health risks of activated sludge. Importantly, our results revealed that the pathogenic species showed a clear floc-size dependent distribution manner, leading to significant differences (P < 0.05) of pathogenic communities among the size-fractionated flocs. Additionally, by partitioning pathogens based on the occurrence and significant difference in abundances, we suggested the following distribution features: 1) large flocs-associated pathogens, such as Borrelia recurrentis, Actinobacillus ureae and Campylobacter gracilis; 2) medium flocs-associated pathogens, such as Mycobacterium szulgai and Ureaplasma urealyticum; and 3) small flocs-associated pathogens, such as Rickettsia akari, Staphylococcus anginosus and Helicobacter cinaedi. Overall, this study provides a comprehensive understanding of pathogens in activated sludge, which is expected to aid in assessment and management of pathogen risks.

Host plant phylogeny and abundance predict root‐associated fungal community composition and diversity of mutualists and pathogens

Abstract Interactions between plants and their root‐associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant–soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant–RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. Synthesis. We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant–soil feedback. Going forward, mechanisms underlying the host abundance‐RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.

How green alternatives to chemical pesticides are environmentally friendly and more efficient

Various soil management strategies that use disinfestation are important in the control of soil‐borne diseases before planting. However, only a few studies pay attention to preventing pathogen reinfestation during host plant cultivation, which is also important for the stable control of soil‐borne diseases. Here we used various pre‐planting management strategies to disinfest a field severely infested with Fusarium oxysporum, and then investigated changes in the potential pathogen and microbial communities during the 11 months of host plant cultivation. The soil microbial numbers, diversity, community structure and composition varied considerably across the soils treated by dazomet fumigation and reductive soil disinfestations (RSDs) using ethanol, bagasse and bean dregs. The Fusarium inoculum decreased to the same degree in the disinfested soils with the various methods. After the cultivation of lisianthus (Eustoma russellianum (Hook.) G. Don), microbial numbers, diversity and community structure tended to be similar and Fusarium increased markedly in these soils. Furthermore, the increase in relative abundance of Fusarium, especially in the RSD‐treated soils amended with bagasse, was significantly less than in the soils amended with non‐plant residues. Further analyses showed that the increases in microbial diversity and relative abundance of Zopfiella and Mycothermus were significantly and negatively correlated with the increase in Fusarium relative abundance. The additional sources of carbon supplied in the disinfested soil positively affected the development of the soil microbiota and prevented Fusarium reinfestation resulting from host plant cultivation, which should be considered for achieving stable disease suppression in the future.Highlights We studied Fusarium reinfestation resulting from host plant cultivation in various soil environments. Plant cultivation led to uniformity in the development of different soil microbiota. Fusarium reinfestation depended strongly on soil environment. Increased microbial diversity and specific microbial groups prevented Fusarium reinfestation.

Investigation of a Farm-scale Multitrophic Recirculating Aquaculture System with the Addition of Rhodovulum sulfidophilum for Milkfish (Chanos chanos) Coastal Aquaculture

Globally, coastal aquaculture is growing due to the large demand for marine products. Specific impacts caused by coastal aquaculture on the environment include the discharge of culture farm effluents, stress on ground water (the absence of recycling), nutrient pollution, and diseases of cultured animals. Three methods, integrated multitrophic aquaculture (IMTA), recirculating aquaculture system (RAS), and beneficial bacteria for aquaculture, have been developed to solve these problems. In this study, the advantages of IMTA and RAS were integrated to develop a novel multitrophic recirculating aquaculture system (MRAS) to adapt to the farm-scale culturing of milkfish (Chanos chanos). The photosynthetic bacteria Rhodovulum sulfidophilum was added to enhance the performance of the farm-scale milkfish MRAS. This setting could promote growth of beneficial bacteria, such as the nitrogen cycle-associated microbial community and the anoxygenic phototrophic Acidobacteria community. The ammonia level was reduced, and the total phosphorous level was stable in the water recycled in the MRAS. The cyanobacteria, algae, Vibrio, Escherichia, and other potential pathogenic bacteria communities were inhibited in the MRAS. This study provides an effective design of a water recycling aquaculture system. Milkfish, Asian tiger shrimp (Penaeus monodon), Asian hard clam (Meretrix lusoria), and seaweed (Gracilaria sp.) can be cultured and simultaneously produced in the system.

Characteristics of airborne opportunistic pathogenic bacteria during autumn and winter in Xi'an, China

Bacteria are ubiquitous throughout the earth's lower atmosphere. Bacteria, especially pathogenic bacteria, play an important role in human health. The diversity, composition, and dynamics of airborne bacteria has been widely studied; however, the characteristics of pathogenic bacteria remain poorly understood. In this study, a high throughput sequencing method was used to explore the airborne opportunistic pathogenic bacteria during autumn and winter in Xi'an, China. An aggregated boosted tree (ABT) was developed to determine the relative influence of environmental factors on the proportions of opportunistic pathogenic bacteria. Results showed that significantly more opportunistic pathogenic bacteria were found in winter than in autumn, and more opportunistic pathogenic bacteria were found in fine particulate matters (<2.5 μm) than in PM10 (<10 μm). However, the composition of opportunistic pathogenic bacteria varied in autumn and winter. PM was the main factor affecting the proportions of opportunistic pathogenic bacteria, and air contaminants (PM, sulfur dioxide, nitrogen oxide, carbon monoxide, and ozone) influenced the proportion of opportunistic pathogenic bacteria more than meteorological factors (relative humidity, temperature, and wind speed). Different factors may be responsible for the variances in opportunistic pathogenic bacterial communities in different seasons. This study may provide a reference to support the control of pathogenic bacteria in urban environments during haze events.

Immunosuppression-induced alterations in fish gut microbiota may increase the susceptibility to pathogens

Intestinal bacteria play an important role in the health and provide a variety of beneficial effects to host. Immunosuppressant can reduce the immunity of host and increase the susceptibility to pathogens. But it is not clear whether the increased susceptibility caused by immunosuppressant is related to changes of gut microbiota. In this study, we used crucian carp administrated with dexamethasone to explore the effects of immunosuppressants on gut microbial communities and further evaluate the potential association between changes in gut microbiota and susceptibility to pathogens. The results of MANOVA based on the top 10 PCoA axis scores from unweighed/weighted UniFrac distances showed that administration of dexamethasone (P = 0.021) and the administration time (P = 0.027) had a significant impact on the gut microbial composition, regardless of pathogens infection status (P = 0.35). After administration with dexamethasone, the fish had higher abundance of Cetobacterium and lower abundance of Bacillus and Lactococcus, and the abundance of genus Bacillus, Pseudomonas and Lactococcus decreased along with prolong administration time of dexamethasone. The results may help us understand the correlation between the host susceptibility to pathogenic bacteria and gut microbial community shift, and extend our knowledge regarding the role of gut microbiota in keeping the balance between pathogenic and symbiotic bacteria.

Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats (Eonycteris spelaea).

Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission. Here we investigate the diversity and abundance of viral communities from a colony of Eonycteris spelaea residing in Singapore. Our results detected 47 and 22 different virus families from bat fecal and urine samples, respectively. Among these, we identify a large number of virus families including Adenoviridae, Flaviviridae, Reoviridae, Papillomaviridae, Paramyxoviridae, Parvoviridae, Picornaviridae, and Polyomaviridae. In most cases, viral sequences from Eonycteris spelaea are genetically related to a group of bat viruses from other bat genera (e.g., Eidolon, Miniopterus, Rhinolophus and Rousettus). The results of this study improve our knowledge of the host range, spread and evolution of several important viral pathogens. More significantly, our findings provide a baseline to study the temporal patterns of virus shedding and how they correlate with bat phenological trends.