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https://www.readbyqxmd.com/read/28742071/drep-a-tool-for-fast-and-accurate-genomic-comparisons-that-enables-improved-genome-recovery-from-metagenomes-through-de-replication
#1
Matthew R Olm, Christopher T Brown, Brandon Brooks, Jillian F Banfield
The number of microbial genomes sequenced each year is expanding rapidly, in part due to genome-resolved metagenomic studies that routinely recover hundreds of draft-quality genomes. Rapid algorithms have been developed to comprehensively compare large genome sets, but they are not accurate with draft-quality genomes. Here we present dRep, a program that reduces the computational time for pairwise genome comparisons by sequentially applying a fast, inaccurate estimation of genome distance, and a slow, accurate measure of average nucleotide identity...
July 25, 2017: ISME Journal
https://www.readbyqxmd.com/read/28741705/house-dust-mites-as-potential-carriers-for-ige-sensitisation-to-bacterial-antigens
#2
Sheron Dzoro, Irene Mittermann, Yvonne Resch, Susanne Vrtala, Marion Nehr, Alexander M Hirschl, Gustav Wikberg, Lena Lundeberg, Catharina Johansson, Annika Scheynius, Rudolf Valenta
BACKGROUND: IgE-reactivity to antigens from gram-positive and negative bacteria is common in patients suffering from respiratory and skin manifestations of allergy, but the routes and mechanisms of sensitisation are not fully understood. The analysis of the genome, transcriptome and microbiome of house dust mites (HDM) has shown that S. aureus and E. coli species are abundant bacteria within the HDM microbiome. Therefore, our aim was to investigate if HDM are carriers of bacterial antigens leading to IgE sensitisation in patients suffering from atopic dermatitis...
July 25, 2017: Allergy
https://www.readbyqxmd.com/read/28732766/molecular-structural-and-functional-comparison-of-n-lobe-and-c-lobe-of-the-transferrin-from-rock-bream-oplegnathus-fasciatus-with-respect-to-its-immune-response
#3
N C N Perera, G I Godahewa, Jee Youn Hwang, Mun Gyeong Kwon, Seong Don Hwang, Jehee Lee
The iron-withholding strategy of innate immunity is an effective antimicrobial defense mechanism that combats microbial infection by depriving microorganisms of Fe(3+), which is important for their growth and propagation. Transferrins (Tfs) are a group of iron-binding proteins that exert their antimicrobial function through Fe(3+) sequestration. The current study describes both structural and functional characteristics of a transferrin ortholog from rock bream Oplegnathus fasciatus (RbTf). The RbTf cDNA possesses an open reading frame (ORF) of 2079 bp encoding 693 amino acids...
July 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28731846/presence-and-future-of-culturing-bacteria
#4
Jörg Overmann, Birte Abt, Johannes Sikorski
The cultivation of bacteria is highly biased toward a few phylogenetic groups. Many of the currently underexplored bacterial lineages likely have novel biosynthetic pathways and unknown biochemical features. New cultivation concepts have been developed based on an improved understanding of the ecology of previously not-cultured bacteria. Particularly successful were improved media that mimic the natural types and concentrations of substrates and nutrients, high-throughput cultivation techniques, and approaches that exploit biofilm formation and bacterial interactions...
July 21, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28731533/improvement-of-d-lactic-acid-production-in-saccharomyces-cerevisiae-under-acidic-conditions-by-evolutionary-and-rational-metabolic-engineering
#5
Seung-Ho Baek, Eunice Y Kwon, Sang-Jeong Bae, Bo-Ram Cho, Seon-Young Kim, Ji-Sook Hahn
Microbial lactic acid (LA) production under acidic fermentation conditions is favorable to reduce the production cost, but circumventing LA toxicity is a major challenge. We generated D-LA-producing Saccharomyces cerevisiae strain JHY5610 by expressing D-lactate dehydrogenase gene (Lm. ldhA) from Leuconostoc mesenteroides, while deleting genes involved in ethanol production (ADH1, ADH2, ADH3, ADH4, and ADH5), glycerol production (GPD1 and GPD2), and degradation of D-LA (DLD1). Adaptive laboratory evolution of JHY5610 led to a strain JHY5710 having higher LA tolerance and D-LA-production capability...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28731475/unusual-metabolic-diversity-of-hyperalkaliphilic-microbial-communities-associated-with-subterranean-serpentinization-at-the-cedars
#6
Shino Suzuki, Shun'ichi Ishii, Tatsuhiko Hoshino, Amanda Rietze, Aaron Tenney, Penny L Morrill, Fumio Inagaki, J Gijs Kuenen, Kenneth H Nealson
Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh<-550 mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#7
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731470/a-genomic-perspective-on-stoichiometric-regulation-of-soil-carbon-cycling
#8
Wyatt H Hartman, Rongzhong Ye, William R Horwath, Susannah G Tringe
Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731467/uncultivated-microbes-in-need-of-their-own-taxonomy
#9
Konstantinos T Konstantinidis, Ramon Rosselló-Móra, Rudolf Amann
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28729863/effects-of-physiochemical-factors-on-prokaryotic-biodiversity-in-malaysian-circumneutral-hot-springs
#10
Chia S Chan, Kok-Gan Chan, Robson Ee, Kar-Wai Hong, María S Urbieta, Edgardo R Donati, Mohd S Shamsir, Kian M Goh
Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729861/comparative-omics-and-trait-analyses-of-marine-pseudoalteromonas-phages-advance-the-phage-otu-concept
#11
Melissa B Duhaime, Natalie Solonenko, Simon Roux, Nathan C Verberkmoes, Antje Wichels, Matthew B Sullivan
Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729854/microbiome-of-trichodesmium-colonies-from-the-north-pacific-subtropical-gyre
#12
Mary R Gradoville, Byron C Crump, Ricardo M Letelier, Matthew J Church, Angelicque E White
Filamentous diazotrophic Cyanobacteria of the genus Trichodesmium, often found in colonial form, provide an important source of new nitrogen to tropical and subtropical marine ecosystems. Colonies are composed of several clades of Trichodesmium in association with a diverse community of bacterial and eukaryotic epibionts. We used high-throughput 16S rRNA and nifH gene sequencing, carbon (C) and dinitrogen (N2) fixation assays, and metagenomics to describe the diversity and functional potential of the microbiome associated with Trichodesmium colonies collected from the North Pacific Subtropical Gyre (NPSG)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#13
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28729274/genome-sequences-of-two-shewanella-spp-isolated-from-the-gut-of-the-sea-cucumber-apostichopus-japonicus-selenka-1867
#14
Hyun-Hee Hong, Hyunjun Choi, Seongmin Cheon, Hyun-Gwan Lee, Chungoo Park
In this study, we sequenced the genomes of two Shewanella spp., newly isolated from the gut of the sea cucumber Apostichopus japonicus (Selenka, 1867). The whole-genome sequences reported here will expand the repertoire of genomic information for the members of the genus Shewanella and will provide important insights into their roles within microbial communities.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28720731/an-in-vitro-chicken-gut-model-demonstrates-transfer-of-a-multidrug-resistance-plasmid-from-salmonella-to-commensal-escherichia-coli
#15
Roderick M Card, Shaun A Cawthraw, Javier Nunez-Garcia, Richard J Ellis, Gemma Kay, Mark J Pallen, Martin J Woodward, Muna F Anjum
The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#16
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28718274/-microbiome-and-next-generation-sequencing
#17
REVIEW
A Suárez Moya
The human microbiome is an internal ecosystem that refers to the community of microorganisms that populate the human body. These microorganisms are essential to support his health, because the interaction between the host immune system and microorganisms, provide the host with protection against pathogens, and contributes to the preservation of health. Bacteriological culture has been the basis for traditional microbiology; however, most of the bacterial forms observed in nature cannot be isolated with laboratory culture methods...
July 17, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#18
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28716113/whole-metagenome-profiles-of-particulates-collected-from-the-international-space-station
#19
Nicholas A Be, Aram Avila-Herrera, Jonathan E Allen, Nitin Singh, Aleksandra Checinska Sielaff, Crystal Jaing, Kasthuri Venkateswaran
BACKGROUND: The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized...
July 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28716079/the-human-jejunum-has-an-endogenous-microbiota-that-differs-from-those-in-the-oral-cavity-and-colon
#20
Olof H Sundin, Antonio Mendoza-Ladd, Mingtao Zeng, Diana Diaz-Arévalo, Elisa Morales, B Matthew Fagan, Javier Ordoñez, Philip Velez, Nishaal Antony, Richard W McCallum
BACKGROUND: The upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 10(11)-10(12) colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 10(3) to 10(5) CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics...
July 17, 2017: BMC Microbiology
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