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Community assembly

Aileen Y Chang, Edith C Tonui, Douglas Momanyi, Alex R Mills, Paul Wasike, Rakhi Karwa, Toby A Maurer, Sonak D Pastakia
INTRODUCTION: Compression therapy is well-established standard of care for chronic leg ulcers from venous disease and lymphedema. Chronic leg ulcers and lymphedema have a significant impact on quality of life, driven by pain, foul odor, and restricted mobility. Provision of layered compression therapy in resource-limited settings, as in Western Kenya and other regions of sub-Saharan Africa, is a major challenge due to several barriers: availability, affordability, and access to healthcare facilities...
June 15, 2018: Dermatology and Therapy
Luis M Rodriguez-R, Santosh Gunturu, William T Harvey, Ramon Rosselló-Mora, James M Tiedje, James R Cole, Konstantinos T Konstantinidis
The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts...
June 14, 2018: Nucleic Acids Research
Maisie V Nash, Alexandre M Anesio, Gary Barker, Martyn Tranter, Gilda Varliero, Emiley A Eloe-Fadrosh, Torben Nielsen, Thomas Turpin-Jelfs, Liane G Benning, Patricia Sánchez-Baracaldo
Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonization in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled contigs. The low number of recovered genes highlights the need for deeper sequencing in some diverse samples, to uncover the complete microbial populations...
June 12, 2018: FEMS Microbiology Ecology
Hannah Holland-Moritz, Julia Stuart, Lily R Lewis, Samantha Miller, Michelle C Mack, Stuart F McDaniel, Noah Fierer
Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local site conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with seven boreal moss species collected near Fairbanks, AK USA...
June 14, 2018: Environmental Microbiology
Yuanyuan Xue, Huihuang Chen, Jun R Yang, Min Liu, Bangqin Huang, Jun Yang
Plankton communities normally consist of few abundant and many rare species, yet little is known about the ecological role of rare planktonic eukaryotes. Here we used a 18S ribosomal DNA sequencing approach to investigate the dynamics of rare planktonic eukaryotes, and to explore the co-occurrence patterns of abundant and rare eukaryotic plankton in a subtropical reservoir following a cyanobacterial bloom event. Our results showed that the bloom event significantly altered the eukaryotic plankton community composition and rare plankton diversity without affecting the diversity of abundant plankton...
June 13, 2018: ISME Journal
Alexander L Greninger, Pavitra Roychoudhury, Hong Xie, Amanda Casto, Anne Cent, Gregory Pepper, David M Koelle, Meei-Li Huang, Anna Wald, Christine Johnston, Keith R Jerome
Herpes simplex viruses (HSVs) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover nearly complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run...
June 27, 2018: MSphere
Vanessa N Kavamura, Rifat Hayat, Ian M Clark, Maike Rossmann, Rodrigo Mendes, Penny R Hirsch, Tim H Mauchline
The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N) was sown with seeds of Triticum aestivum cv...
2018: Frontiers in Microbiology
Bosheng Chen, Kaiqian Du, Chao Sun, Arunprasanna Vimalanathan, Xili Liang, Yong Li, Baohong Wang, Xingmeng Lu, Lanjuan Li, Yongqi Shao
Bombyx mori, the domesticated silkworm, is of great importance as a silk producer and as a powerful experimental model for the basic and applied research. Similar to other animals, abundant microorganisms live inside the silkworm gut; however, surprisingly, the microbiota of this model insect has not been well characterized to date. Here, we comprehensively characterized the gut microbiota of the domesticated silkworm and its wild relatives. Comparative analyses with the mulberry-feeding moths Acronicta major and Diaphania pyloalis revealed a highly diverse but distinctive silkworm gut microbiota despite thousands of years of domestication, and stage-specific signatures in both total (DNA-based) and active (RNA-based) bacterial populations, dominated by the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes...
June 12, 2018: ISME Journal
Fernando Meyer, Peter Hofmann, Peter Belmann, Ruben Garrido-Oter, Adrian Fritz, Alexander Sczyrba, Alice C McHardy
Reconstructing the genomes of microbial community members is key to the interpretation of shotgun metagenome samples. Genome binning programs deconvolute reads or assembled contigs of such samples into individual bins, but assessing their quality is difficult due to the lack of evaluation software and standardized metrics. We present AMBER, an evaluation package for the comparative assessment of genome reconstructions from metagenome benchmark data sets. It calculates the performance metrics and comparative visualizations used in the first benchmarking challenge of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)...
June 8, 2018: GigaScience
David A Galbraith, Zachary L Fuller, Allyson M Ray, Axel Brockmann, Maryann Frazier, Mary W Gikungu, J Francisco Iturralde Martinez, Karen M Kapheim, Jeffrey T Kerby, Sarah D Kocher, Oleksiy Losyev, Elliud Muli, Harland M Patch, Cristina Rosa, Joyce M Sakamoto, Scott Stanley, Anthony D Vaudo, Christina M Grozinger
Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 4 continents and Oceania...
June 11, 2018: Scientific Reports
Emily Bacon, Gregory Budney, Jessica Bondy, Michael G Kahn, Emily V McCormick, John F Steiner, David Tabano, Jeanette A Waxmonsky, Rachel Zucker, Arthur J Davidson
Electronic health records (EHRs) provide an alternative to traditional public health surveillance surveys and administrative data for measuring the prevalence and impact of chronic health conditions in populations. As the infrastructure for secondary use of EHR data improves, many stakeholders are poised to benefit from data partnerships for regional access to information. Electronic health records can be transformed into a common data model that facilitates data sharing across multiple organizations and allows data to be used for surveillance...
June 7, 2018: Journal of Public Health Management and Practice: JPHMP
Margery L Evans, Elizabeth Gichana, Yizhou Zhou, Matthew R Chapman
Many bacteria can assemble functional amyloid fibers on their cell surface. Most bacterial amyloids contribute to biofilm or other community behaviors where cells interact with a surface or with other cells. Bacterial amyloids, like all functional amyloids, share structural and biochemical properties with disease-associated eukaryotic amyloids. The general ability of amyloids to bind specific dyes, like Congo red and Thioflavin T, and their resistance to denaturation have provided useful tools for scoring and quantifying bacterial amyloid formation...
2018: Methods in Molecular Biology
Henintsoa O Minoarivelo, Cang Hui
Ecological and evolutionary dynamics observed in mutualistic communities can be shaped by several mechanisms, including ecological interactions and their co-evolutionary consequences. Here we explore how intra and interspecific competition, together with mutualistic interactions, can affect community assembly through their effects on adaptive diversification and the emergence of biodiversity. To capture both ecological and evolutionary processes simultaneously, we used the adaptive dynamics approach based on a Lotka-Volterra framework and simulated the ecological dynamics of populations as well as the evolutionary dynamics of involved phenotypic traits...
June 6, 2018: Journal of Theoretical Biology
Jo M Wilmshurst, Alla Guekht, Mary Secco, J Helen Cross, Emilio Perucca
In May 2015 the World Health Assembly (WHA) approved the Resolution on the Global Burden of Epilepsy. This report addresses how the Resolution can be leveraged to improve the care of children with epilepsy worldwide. Children with epilepsy have unique needs and face unique challenges from stigma at all levels of society. Children lack a voice to lobby for their own needs, including their right to have access to education. Effective leadership and governance should be enhanced through the support of stakeholders empowered to counsel, advise, and lobby for appropriate care...
June 2018: Epilepsia Open
Yuanyuan Mo, Wenjing Zhang, Jun Yang, Yuanshao Lin, Zheng Yu, Senjie Lin
Unraveling the relative importance of ecological processes regulating microbial community structure is a central goal in microbial ecology. Here, we used high-throughput sequencing to examine the relative contribution of selective and neutral processes in the assembly of abundant and rare subcommunities from three subtropical bays of China. We found that abundant and rare bacterial taxa were distinctly different in diversity, despite the similar biogeographic patterns and strong distance-decay relationships, but the dispersal of rare bacterial taxa was more limited than that of abundant taxa...
June 7, 2018: ISME Journal
Marta Goberna, Miguel Verdú
The historical conditions under which bacterial lineages evolve determine their functional traits, and consequently their contribution to ecosystem functions (EFs). Under significant trait conservatism, which is common in prokaryotes, phylogeny may track the evolutionary history of species and predict their functionality. Productive communities can arise from: (i) the coexistence of functional, and therefore phylogenetically distant lineages, producing high EF rates at large phylogenetic diversity (PD); (ii) the dominance of productive lineages that outcompete other clades, generating high EF at low PD...
June 7, 2018: ISME Journal
Qanta A Ahmed, Ziad A Memish
Human behavior has long engaged in collective behavior assembling in crowds. The Christian pilgrimage to the Holy Land which has been recorded since the 4th century while the Hajj, Islam's great pilgrimage, has existed for fourteen centuries of which a body of literature devoted to the travelogues of the Hajj has existed for over ten centuries. Football, a sport played worldwide by more than 1.5 million teams and in 300,000 clubs. Most people however play outside of the officially organized sphere. More than 4 percent of the global population plays football, including 270 million amateur players...
June 4, 2018: Travel Medicine and Infectious Disease
Xing Liu, Shiyan Zhuo, Christopher Rensing, Shungui Zhou
Direct interspecies electron transfer (DIET) may prevail in microbial communities that show methanogenesis and anaerobic methane oxidation and can be an electron source to support anaerobic photosynthesis. Previous mutagenic studies on cocultures of defined Geobacter species indicate that both conductive pili and extracellular cytochromes are essential for DIET. However, the actual functional role of the pili in DIET is uncertain, as the pilus mutation strategy used in these studies affected the extracellular cytochrome profile...
June 6, 2018: ISME Journal
Stephen Wandro, Stephanie Osborne, Claudia Enriquez, Christine Bixby, Antonio Arrieta, Katrine Whiteson
The assembly and development of the gut microbiome in infants have important consequences for immediate and long-term health. Preterm infants represent an abnormal case for bacterial colonization because of early exposure to bacteria and frequent use of antibiotics. To better understand the assembly of the gut microbiota in preterm infants, fecal samples were collected from 32 very low birth weight preterm infants over the first 6 weeks of life. Infant health outcomes included health, late-onset sepsis, and necrotizing enterocolitis (NEC)...
June 27, 2018: MSphere
Thomas D Otto, Ulrike Böhme, Mandy Sanders, Adam Reid, Ellen I Bruske, Craig W Duffy, Pete C Bull, Richard D Pearson, Abdirahman Abdi, Sandra Dimonte, Lindsay B Stewart, Susana Campino, Mihir Kekre, William L Hamilton, Antoine Claessens, Sarah K Volkman, Daouda Ndiaye, Alfred Amambua-Ngwa, Mahamadou Diakite, Rick M Fairhurst, David J Conway, Matthias Franck, Chris I Newbold, Matt Berriman
Background : Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods : Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P...
2018: Wellcome Open Research
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