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https://www.readbyqxmd.com/read/27906039/peering-below-the-diffraction-limit-robust-and-specific-sorting-of-viruses-with-flow-cytometry
#1
Shea T Lance, David J Sukovich, Kenneth M Stedman, Adam R Abate
BACKGROUND: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population...
December 1, 2016: Virology Journal
https://www.readbyqxmd.com/read/27878346/salinity-affects-the-composition-of-the-aerobic-methanotroph-community-in-alkaline-lake-sediments-from-the-tibetan-plateau
#2
Yongcui Deng, Yongqin Liu, Marc Dumont, Ralf Conrad
Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied...
November 22, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27869614/cutaneous-granulomas-in-dolphins-caused-by-novel-uncultivated-paracoccidioides-brasiliensis
#3
Raquel Vilela, Gregory D Bossart, Judy A St Leger, Leslie M Dalton, John S Reif, Adam M Schaefer, Peter J McCarthy, Patricia A Fair, Leonel Mendoza
Cutaneous granulomas in dolphins were believed to be caused by Lacazia loboi, which also causes a similar disease in humans. This hypothesis was recently challenged by reports that fungal DNA sequences from dolphins grouped this pathogen with Paracoccidioides brasiliensis. We conducted phylogenetic analysis of fungi from 6 bottlenose dolphins (Tursiops truncatus) with cutaneous granulomas and chains of yeast cells in infected tissues. Kex gene sequences of P. brasiliensis from dolphins showed 100% homology with sequences from cultivated P...
December 2016: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/27864174/multilocus-sequence-analysis-of-phylogroup-1-and-2-oral-treponeme-strains
#4
Yong-Biao Huo, Yuki Chan, Donnabella C Lacap-Bugler, Sisu Mo, Patrick C Y Woo, W Keung Leung, Rory M Watt
: More than 75 'species-level' phylotypes of spirochete bacteria belonging to the genus Treponema reside within the human oral cavity. The majority of these oral treponeme phylotypes correspond to as-yet uncultivated taxa, or strains of uncertain standing in taxonomy. Here, we analyze phylogenetic and taxonomic relationships between oral treponeme strains using a multilocus sequence analysis (MLSA) scheme based on the highly-conserved 16S rRNA, pyrH, recA and flaA genes. We utilize this MLSA scheme to analyze genetic data from a curated collection of oral treponeme strains (n=71) of diverse geographical origins...
November 18, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27833995/cultivation-versus-molecular-analysis-of-banana-musa-sp-shoot-tip-tissue-reveals-enormous-diversity-of-normally-uncultivable-endophytic-bacteria
#5
Pious Thomas, Aparna Chandra Sekhar
The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes)...
November 10, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27819664/measurement-of-bacterial-replication-rates-in-microbial-communities
#6
Christopher T Brown, Matthew R Olm, Brian C Thomas, Jillian F Banfield
Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication...
November 7, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27812029/alterations-in-soil-microbial-community-composition-and-biomass-following-agricultural-land-use-change
#7
Qian Zhang, Junjun Wu, Fan Yang, Yao Lei, Quanfa Zhang, Xiaoli Cheng
The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature...
November 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27796326/shedding-light-on-cell-compartmentation-in-the-candidate-phylum-poribacteria-by-high-resolution-visualisation-and-transcriptional-profiling
#8
Martin T Jahn, Sebastian M Markert, Taewoo Ryu, Timothy Ravasi, Christian Stigloher, Ute Hentschel, Lucas Moitinho-Silva
Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal...
October 31, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27795254/complete-genome-sequence-of-a-bacterium-representing-a-deep-uncultivated-lineage-within-the-gammaproteobacteria-associated-with-the-degradation-of-polycyclic-aromatic-hydrocarbons
#9
David R Singleton, Allison N Dickey, Elizabeth H Scholl, Fred A Wright, Michael D Aitken
The bacterial strain TR3.2, representing a novel deeply branching lineage within the Gammaproteobacteria, was isolated and its genome sequenced. This isolate is the first cultivated representative of the previously described "Pyrene Group 2" (PG2) and represents a variety of environmental sequences primarily associated with petrochemical contamination and aromatic hydrocarbon degradation.
October 6, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27763339/evaluation-of-unclogging-aspects-in-horizontal-subsurface-flow-constructed-wetlands
#10
Suymara Toledo Miranda, Antonio Teixeira de Matos, Gheila Corrêa Ferres Baptestini, Alisson Carraro Borges
In horizontal subsurface flow constructed wetlands (HSSF-CWs), the main operational problem is clogging of the porous medium. In this study, the unclogging of HSSF-CWs was evaluated, at rest, by adding a nitrogen-based nutrient solution to the influent. For this, six HSSF-CWs were used, consisting of two uncultivated (CW-C), two cultivated with Tifton 85-grass (Cynodon spp.) (CW-T) and two cultivated with alligator weed (Alternanthera philoxeroides) (CW-A), which were fully clogged after being used for the treatment of swine wastewater...
October 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/27748767/genome-scale-analysis-of-the-non-cultivable-treponema-pallidum-reveals-extensive-within-patient-genetic-variation
#11
Miguel Pinto, Vítor Borges, Minia Antelo, Miguel Pinheiro, Alexandra Nunes, Jacinta Azevedo, Maria José Borrego, Joana Mendonça, Dina Carpinteiro, Luís Vieira, João Paulo Gomes
Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK)...
October 17, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27737357/bacterial-diversity-of-symptomatic-primary-endodontic-infection-by-clonal-analysis
#12
Letícia Maria Menezes Nóbrega, Francisco Montagner, Adriana Costa Ribeiro, Márcia Alves Pinto Mayer, Brenda Paula Figueiredo de Almeida Gomes
The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Samples were collected from 10 patients and submitted to bacterial DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. A bacterial genomic library was constructed and bacterial diversity was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84%) were different species and 29 (38...
October 10, 2016: Brazilian Oral Research
https://www.readbyqxmd.com/read/27723729/asynchronous-division-by-non-ring-ftsz-in-the-gammaproteobacterial-symbiont-of-robbea-hypermnestra
#13
Nikolaus Leisch, Nika Pende, Philipp M Weber, Harald R Gruber-Vodicka, Jolanda Verheul, Norbert O E Vischer, Sophie S Abby, Benedikt Geier, Tanneke den Blaauwen, Silvia Bulgheresi
The reproduction mode of uncultivable microorganisms deserves investigation as it can largely diverge from conventional transverse binary fission. Here, we show that the rod-shaped gammaproteobacterium thriving on the surface of the Robbea hypermnestra nematode divides by FtsZ-based, non-synchronous invagination of its poles-that is, the host-attached and fimbriae-rich pole invaginates earlier than the distal one. We conclude that, in a naturally occurring animal symbiont, binary fission is host-oriented and does not require native FtsZ to polymerize into a ring at any septation stage...
October 10, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27709433/risk-assessment-of-maize-damage-by-wireworms-coleoptera-elateridae-as-the-first-step-in-implementing-ipm-and-in-reducing-the-environmental-impact-of-soil-insecticides
#14
L Furlan, B Contiero, F Chiarini, M Colauzzi, E Sartori, I Benvegnù, F Fracasso, P Giandon
A survey of maize fields was conducted in northeast Italy from 1986 to 2014, resulting in a dataset of 1296 records including information on wireworm damage to maize, plant-attacking species, agronomic characteristics, landscape and climate. Three wireworm species, Agriotes brevis Candeze, A. sordidus Illiger and A. ustulatus Schäller, were identified as the dominant pest species in maize fields. Over the 29-year period surveyed, no yield reduction was observed when wireworm plant damage was below 15 % of the stand...
October 6, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27681128/bipartite-network-analysis-of-the-archaeal-virosphere-evolutionary-connections-between-viruses-and-capsidless-mobile-elements
#15
Jaime Iranzo, Eugene V Koonin, David Prangishvili, Mart Krupovic
: Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses...
December 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27679684/racial-disparity-in-colorectal-cancer-gut-microbiome-and-cancer-stem-cells
#16
REVIEW
Sachin Goyal, Pratima Nangia-Makker, Lulu Farhana, Yingjie Yu, Adhip Pn Majumdar
Over the past two decades there has been remarkable progress in cancer diagnosis, treatment and screening. The basic mechanisms leading to pathogenesis of various types of cancers are also understood better and some patients, if diagnosed at a particular stage go on to lead a normal pre-diagnosis life. Despite these achievements, racial disparity in some cancers remains a mystery. The higher incidence, aggressiveness and mortality of breast, prostate and colorectal cancers (CRCs) in African-Americans as compared to Caucasian-Americans are now well documented...
September 26, 2016: World Journal of Stem Cells
https://www.readbyqxmd.com/read/27645100/diversity-of-methane-oxidizing-bacteria-in-soils-from-hot-lands-of-medolla-italy-featured-by-anomalous-high-temperatures-and-biogenic-co2-emission
#17
Martina Cappelletti, Daniele Ghezzi, Davide Zannoni, Bruno Capaccioni, Stefano Fedi
"Terre Calde di Medolla" (TCM) (literally, "Hot Lands of Medolla") refers to a farming area in Italy with anomalously high temperatures and diffuse emissions of biogenic CO2, which has been linked to CH4 oxidation processes from a depth of 0.7 m to the surface. We herein assessed the composition of the total bacterial community and diversity of methane-oxidizing bacteria (MOB) in soil samples collected at a depth at which the peak temperature was detected (0.6 m). Cultivation-independent methods were used, such as: i) a clone library analysis of the 16S rRNA gene and pmoA (coding for the α-subunit of the particulate methane monooxygenase) gene, and ii) Terminal Restriction Fragment Length Polymorphism (T-RFLP) fingerprinting...
September 17, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27639084/rigidosticha-italiensis-n-gen-n-sp-ciliophora-spirotricha-a-novel-large-hypotrich-ciliate-from-the-soil-of-lombardia-italy
#18
Daizy Bharti, Santosh Kumar, Antonietta La Terza
The morphology of Rigidosticha italiensis n. gen., n. sp., which was found in a soil sample collected from an uncultivated field in Lombardia, Italy, was investigated using live observation and protargol staining. Rigidosticha n. gen. is characterised by a rigid body, undulating membranes resembling a Steinia pattern, oxytrichid frontal ciliature, distinct mid-ventral cirral pairs, transverse cirri, one right and one left row of marginal cirri, absence of dorsal kinety 3 fragmentation, more than two dorsomarginal rows, and caudal cirri...
August 25, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/27609915/draft-genome-sequence-of-helicobacter-suis-strain-sntw101-isolated-from-a-japanese-patient-with-nodular-gastritis
#19
Hidenori Matsui, Tetsufumi Takahashi, Somay Y Murayama, Ikuo Uchiyama, Katsushi Yamaguchi, Shuji Shigenobu, Masato Suzuki, Emiko Rimbara, Keigo Shibayama, Anders Øverby, Masahiko Nakamura
We present here the draft whole-genome shotgun sequence of an uncultivated strain SNTW101 of Helicobacter suis, which has been maintained in the stomachs of mice. This strain was originally isolated from gastric biopsy specimens of a urea breath test-negative Japanese patient suffering from nodular gastritis.
2016: Genome Announcements
https://www.readbyqxmd.com/read/27602526/bacterial-associates-of-hyalesthes-obsoletus-hemiptera-cixiidae-the-insect-vector-of-bois-noir-disease-with-a-focus-on-cultivable-bacteria
#20
Lilach Iasur-Kruh, Vered Naor, Tirtza Zahavi, Matthew J Ballinger, Rakefet Sharon, Wyatt E Robinson, Steve J Perlman, Einat Zchori-Fein
The planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae) is an important vector of phytoplasma diseases in grapevine. In the current study, the bacterial community compositions of symbionts of this insect were examined. Two dominant bacterial lineages were identified by mass sequencing: the obligate symbiont Candidatus Sulcia, and a facultative symbiont that is closely related to Pectobacterium sp. and to BEV, a cultivable symbiont of another phytoplasma vector, the leafhopper Euscelidius variegatus. In addition, one bacterium was successfully isolated in this study - a member of the family Xanthomonadaceae that is most closely related to the genus Dyella...
September 4, 2016: Research in Microbiology
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