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Microbial Dark Matter

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https://www.readbyqxmd.com/read/30397357/expanded-skin-virome-in-dock8-deficient-patients
#1
Osnat Tirosh, Sean Conlan, Clay Deming, Shih-Queen Lee-Lin, Xin Huang, Helen C Su, Alexandra F Freeman, Julia A Segre, Heidi H Kong
Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3 , mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4 ...
November 5, 2018: Nature Medicine
https://www.readbyqxmd.com/read/30355348/ecologically-informed-microbial-biomarkers-and-accurate-classification-of-mixed-and-unmixed-samples-in-an-extensive-cross-study-of-human-body-sites
#2
Janko Tackmann, Natasha Arora, Thomas Sebastian Benedikt Schmidt, João Frederico Matias Rodrigues, Christian von Mering
BACKGROUND: The identification of body site-specific microbial biomarkers and their use for classification tasks have promising applications in medicine, microbial ecology, and forensics. Previous studies have characterized site-specific microbiota and shown that sample origin can be accurately predicted by microbial content. However, these studies were usually restricted to single datasets with consistent experimental methods and conditions, as well as comparatively small sample numbers...
October 24, 2018: Microbiome
https://www.readbyqxmd.com/read/30298250/single-cell-genomics-of-microbial-dark-matter
#3
Christian Rinke
Single-cell genomics allows bypassing the culturing step and to directly access environmental microbes one cell at a time. The method has been successfully applied to explore archaeal and bacterial candidate phyla, referred to as microbial dark matter. Here I summarize the single-cell genomics workflow, including sample preparation and preservation, high-throughput fluorescence-activated cell sorting, cell lysis and amplification of environmental samples. Furthermore I describe phylogenetic screening based on 16S rRNA genes and suggest a suitable library preparation and sequencing approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30292286/dark-matter-in-host-microbiome-metabolomics-tackling-the-unknowns-a-review
#4
B Y Loulou Peisl, Emma L Schymanski, Paul Wilmes
The "dark matter" in metabolomics (unknowns) represents an exciting frontier with significant potential for discovery in relation to biochemistry, yet it also presents one of the largest challenges to overcome. This focussed review takes a close look at the current state-of-the-art and future challenges in tackling the unknowns with specific focus on the human gut microbiome and host-microbe interactions. Metabolomics, like metabolism itself, is a very dynamic discipline, with many workflows and methods under development, both in terms of chemical analysis and post-analysis data processing...
December 11, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/30273414/phylogenetically-novel-uncultured-microbial-cells-dominate-earth-microbiomes
#5
Karen G Lloyd, Andrew D Steen, Joshua Ladau, Junqi Yin, Lonnie Crosby
To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been studied well, their global abundances, or numbers of cells in any given environment, have not been assessed...
September 2018: MSystems
https://www.readbyqxmd.com/read/30250507/genetic-repertoires-of-anaerobic-microbiomes-driving-generation-of-biogas
#6
Anja Grohmann, Yevhen Vainshtein, Ellen Euchner, Christian Grumaz, Dieter Bryniok, Ralf Rabus, Kai Sohn
Background: Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limited to technological and chemical parameters. Currently, most of the efforts on microbial management system (MiMaS) are focused on process-specific marker species and community dynamics, but a practical implementation is in its infancy. The high number of unknown and uncharacterized microorganisms in general is one of the reasons hindering further advancements...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/30038663/a-year-of-monitoring-20-mesophilic-full-scale-bioreactors-reveals-the-existence-of-stable-but-different-core-microbiomes-in-bio-waste-and-wastewater-anaerobic-digestion-systems
#7
Magdalena Calusinska, Xavier Goux, Marie Fossépré, Emilie E L Muller, Paul Wilmes, Philippe Delfosse
Background: Anaerobic digestion (AD) is a microbe-driven process of biomass decomposition to CH4 and CO2 . In addition to renewable and cost-effective energy production, AD has emerged in the European Union as an environmentally friendly model of bio-waste valorisation and nutrient recycling. Nevertheless, due to the high diversity of uncharacterised microbes, a typical AD microbiome is still considered as "dark matter". Results: Using the high-throughput sequencing of small rRNA gene, and a monthly monitoring of the physicochemical parameters for 20 different mesophilic full-scale bioreactors over 1 year, we generated a detailed view of AD microbial ecology towards a better understanding of factors that influence and shape these communities...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/30037084/rna-phage-biology-in-a-metagenomic-era
#8
REVIEW
Julie Callanan, Stephen R Stockdale, Andrey Shkoporov, Lorraine A Draper, R Paul Ross, Colin Hill
The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities...
July 21, 2018: Viruses
https://www.readbyqxmd.com/read/29998600/feasting-on-terrestrial-organic-matter-dining-in-a-dark-lake-changes-microbial-decomposition
#9
Amelia Fitch, Chloe Orland, David Willer, Erik J S Emilson, Andrew J Tanentzap
Boreal lakes are major components of the global carbon cycle, partly because of sediment-bound heterotrophic microorganisms that decompose within-lake and terrestrially derived organic matter (t-OM). The ability for sediment bacteria to break down and alter t-OM may depend on environmental characteristics and community composition. However, the connection between these two potential drivers of decomposition is poorly understood. We tested how bacterial activity changed along experimental gradients in the quality and quantity of t-OM inputs into littoral sediments of two small boreal lakes, a dark and a clear lake, and measured the abundance of operational taxonomic units and functional genes to identify mechanisms underlying bacterial responses...
July 11, 2018: Global Change Biology
https://www.readbyqxmd.com/read/29980553/linking-uncultivated-microbial-populations-and-benthic-carbon-turnover-by-using-quantitative-stable-isotope-probing
#10
Ömer K Coskun, Monica Pichler, Sergio Vargas, Stuart Gilder, William D Orsi
Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [13 C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter...
September 15, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29968336/identifying-labile-dom-components-in-a-coastal-ocean-through-depleted-bacterial-transcripts-and-chemical-signals
#11
Alexey Vorobev, Shalabh Sharma, Mengyun Yu, Juhyung Lee, Benjamin J Washington, William B Whitman, Ford Ballantyne, Patricia M Medeiros, Mary Ann Moran
Understanding which compounds comprising the complex and dynamic marine dissolved organic matter (DOM) pool are important in supporting heterotrophic bacterial production remains a major challenge. We eliminated sources of labile phytoplankton products, advected terrestrial material and photodegradation products to coastal microbial communities by enclosing water samples in situ for 24 h in the dark. Bacterial genes for which expression decreased between the beginning and end of the incubation and chemical formulae that were depleted over this same time frame were used as indicators of bioavailable compounds, an approach that avoids augmenting or modifying the natural DOM pool...
July 2, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29967420/ecology-and-evolution-of-seafloor-and-subseafloor-microbial-communities
#12
REVIEW
William D Orsi
Vast regions of the dark ocean have ultra-slow rates of organic matter sedimentation, and their sediments are oxygenated to great depths yet have low levels of organic matter and cells. Primary production in the oxic seabed is supported by ammonia-oxidizing archaea, whereas in anoxic sediments, novel, uncultivated groups have the potential to produce H2 and CH4 , which fuel anaerobic carbon fixation. Subseafloor bacteria have very low mutation rates, and their evolution is likely dominated by selection of different pre-adapted subseafloor taxa under oxic and anoxic conditions...
July 2, 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29908491/go-with-the-flow-or-solitary-confinement-a-look-inside-the-single-cell-toolbox-for-isolation-of-rare-and-uncultured-microbes
#13
REVIEW
Geert Rb Huys, Jeroen Raes
With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual cells in microenvironment compartments can facilitate the isolation of previously uncultured species and the discovery of novel microbial taxa...
June 13, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29727057/raman-activated-cell-sorting-and-metagenomic-sequencing-revealing-carbon-fixing-bacteria-in-the-ocean
#14
Xiaoyan Jing, Honglei Gou, Yanhai Gong, Xiaolu Su, La Xu, Yuetong Ji, Yizhi Song, Ian P Thompson, Jian Xu, Wei E Huang
It is of great significance to understand CO2 fixation in the oceans. Using single cell Raman spectra (SCRS) as biochemical profiles, Raman activated cell ejection (RACE) was able to link phenotypes and genotypes of cells. Here, we show that mini-metagenomic sequences from RACE can be used as a reference to reconstruct nearly complete genomes of key functional bacteria by binning shotgun metagenomic sequencing data. By applying this approach to 13 C bicarbonate spiked seawater from euphotic zone of the Yellow Sea of China, the dominant bacteria Synechococcus spp...
May 4, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29721711/rare-taxa-and-dark-microbial-matter-novel-bioactive-actinobacteria-abound-in-atacama-desert-soils
#15
REVIEW
Michael Goodfellow, Imen Nouioui, Roy Sanderson, Feiyang Xie, Alan T Bull
An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry...
August 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29704757/metagenomic-binning-reveals-the-functional-roles-of-core-abundant-microorganisms-in-twelve-full-scale-biogas-plants
#16
Stefano Campanaro, Laura Treu, Panagiotis G Kougias, Gang Luo, Irini Angelidaki
The aim of this work was to elucidate the microbial ecology in twelve mesophilic and thermophilic full-scale biogas plants using a genome-centric metagenomic approach. In this study both biogas plants treating manure and those treating sludge from waste water treatment plants were considered. The identification of 132 Metagenome-Assembled Genomes (MAGs) and analysis of their abundance profile in different samples allowed the identification of the most abundant core members of the anaerobic digestion microbiome...
September 1, 2018: Water Research
https://www.readbyqxmd.com/read/29475108/intriguing-changes-in-molecular-size-and-composition-of-dissolved-organic-matter-induced-by-microbial-degradation-and-self-assembly
#17
Huacheng Xu, Laodong Guo
Dissolved organic matter (DOM) is ubiquitous and plays an important role in regulating water quality, ecological function, and the fate and transport of trace elements and pollutants in aquatic environments. Both the colloidal precursors (i.e. <1 kDa) and bulk DOM collected from a freshwater estuary were incubated in the dark for 21 days to examine dynamic changes in molecular size and composition induced by microbial degradation and self-assembly. Results showed that the concentrations of total organic carbon, carbohydrates, and protein-like substances decreased by 11-30% during incubation, while those of humic- and fulvic-like substances remained relatively constant, indicating humic substances are more resistant to microbial utilization compared to carbohydrates and protein-like DOM...
May 15, 2018: Water Research
https://www.readbyqxmd.com/read/29420719/microbial-dark-matter-investigations-how-microbial-studies-transform-biological-knowledge-and-empirically-sketch-a-logic-of-scientific-discovery
#18
Guillaume Bernard, Jananan S Pathmanathan, Romain Lannes, Philippe Lopez, Eric Bapteste
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29401383/metabolomic-dark-matter-dependent-on-peroxisomal-%C3%AE-oxidation-in-caenorhabditis-elegans
#19
Alexander B Artyukhin, Ying K Zhang, Allison E Akagi, Oishika Panda, Paul W Sternberg, Frank C Schroeder
Peroxisomal β-oxidation (pβo) is a highly conserved fat metabolism pathway involved in the biosynthesis of diverse signaling molecules in animals and plants. In Caenorhabditis elegans, pβo is required for the biosynthesis of the ascarosides, signaling molecules that control development, lifespan, and behavior in this model organism. Via comparative mass spectrometric analysis of pβo mutants and wildtype, we show that pβo in C. elegans and the satellite model P. pacificus contributes to life stage-specific biosynthesis of several hundred previously unknown metabolites...
February 28, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29380028/influence-of-darkness-and-aging-on-marine-and-freshwater-biofilm-microbial-communities-using-microcosm-experiments
#20
Niyati Hede, Lidita Khandeparker
Ballast tank biofilms pose an additional risk of microbial invasion if sloughed off during ballasting operations, yet their significance and invasion biology is poorly understood. In this study, biofilms developed in marine and freshwater locations were exposed to prolonged darkness and aging by mimicking ballast water conditions in the laboratory. Upon prolonged darkness, the decay of phytoplankton, as indicated by the decrease in chlorophyll a in marine biofilms, led to remineralization and enhanced bacterial and protist populations...
August 2018: Microbial Ecology
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