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https://www.readbyqxmd.com/read/28630471/candidatus-mycoplasma-girerdii-replicates-diversifies-and-co-occurs-with-trichomonas-vaginalis-in-the-oral-cavity-of-a-premature-infant
#1
Elizabeth K Costello, Christine L Sun, Erica M Carlisle, Michael J Morowitz, Jillian F Banfield, David A Relman
Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis)...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28625077/microbiome-and-microbial-biofilm-profiles-of-peri-implantitis-a-systematic-review
#2
Gloria Inés Lafaurie, María Alejandra Sabogal, Diana Marcela Castillo, María Victoria Rincón, Luz Amparo Gómez, Yamil Augusto Lesmes, Leandro Chambrone
BACKGROUND: This systematic review assesses the microbiological profiles of peri-implantitis, periodontitis and healthy implants based on studies that evaluated microbial biofilms and entire microbiomes to establish their similarities and differences. METHODS: The Medical Literature Analysis and Retrieval System Online, via PubMed, EMBASE (Excerpta Medica Database) and Cochrane Central Register of Controlled Trials (CENTRAL) were searched without language restrictions through July 30, 2016...
June 19, 2017: Journal of Periodontology
https://www.readbyqxmd.com/read/28618189/comparative-genomics-of-the-dna-damage-inducible-network-in-the-patescibacteria
#3
Miquel Sánchez-Osuna, Jordi Barbé, Ivan Erill
Metagenomics provide unprecedented insights into the genetic diversity of uncultivated bacteria inhabiting natural environments. Recent surveys have uncovered a major radiation of candidate phyla encompassing the Patescibacteria superphylum. Patescibacteria have small genomes and a presumed symbiotic or parasitic lifestyle, but the difficulty in culturing representative members constrains the characterization of behavioral and adaptive traits. Here we combine in silico and in vitro approaches to characterize the SOS transcriptional response to DNA damage in the Patescibacteria superphylum...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28604068/comparison-of-the-effects-of-poultry-manure-and-its-biochar-on-barley-growth-in-petroleum-contaminated-soils
#4
Maryam Barati, Fereshteh Bakhtiari, Dariush Mowla, Sedigheh Safarzadeh
This study was conducted to evaluate and compare the effectiveness of two organic amendments (poultry manure (PM) and poultry manure biochar (PMB)) for the degradation of petroleum hydrocarbons in contaminated soils by barley plant at three levels of total petroleum hydrocarbons (TPHs) during 5 month under greenhouse conditions. TPHs removal efficiency and microbial respiration were shown to be higher at soil cultivated plant than uncultivated soil and in lowest level of contamination rather than other levels of contamination and at organic amendment treatment than unamended soil...
June 12, 2017: International Journal of Phytoremediation
https://www.readbyqxmd.com/read/28594267/a-plant-pathogenic-bacterium-exploits-the-tricarboxylic-acid-cycle-metabolic-pathway-of-its-insect-vector
#5
Nabil Killiny, Yasser Nehela, Faraj Hijaz, Christopher I Vincent
Huanglongbing in citrus is caused by a phloem-limited, uncultivable, gram-negative α-proteobacterium, Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by the phloem-sucking insect, Diaphorina citri (Hemiptera: Liviidae), in a persistent, circulative, and propagative manner. In this study, we investigated the metabolomic and respiration rates changes in D. citri upon infection with CLas using gas chromatography-mass spectrometry (GC-MS) and gas exchange analysis. The level of glycine, L-serine, L-threonine, and gamma-amino butyric acid were higher in CLas-infected D...
June 8, 2017: Virulence
https://www.readbyqxmd.com/read/28591840/novel-approaches-in-function-driven-single-cell-genomics
#6
Devin F R Doud, Tanja Woyke
Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology...
June 7, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28553195/characterization-of-the-cultivable-gut-microflora-in-wild-caught-%C3%A2-mediterranean-fish-species
#7
Ahmad Jammal, Michel Bariche, Heinrich Zu Dohna, Zakaria Kambris
BACKGROUND: Microflora of the gastrointestinal tract plays important roles in food digestion, nutrient absorption and in host defense against ingested pathogens. Several studies have focused on the microflora of farmed fishes, but the gut flora of wild fishes remains poorly characterized. The aim of this work was to provide an overview of the bacteria colonizing the gut of wild-caught fishes and to determine whether some bacterial species can be pathogenic. RESULTS: We isolated cultivable bacteria from fifteen wild-caught Mediterranean fish species corresponding to different habitat, diet and origin...
May 2017: Current Nutrition and Food Science
https://www.readbyqxmd.com/read/28504576/is-the-role-of-human-female-reproductive-tract-microbiota-underestimated
#8
D Kamińska, M Gajecka
An issue that is currently undergoing extensive study is the influence of human vaginal microbiota (VMB) on the health status of women and their neonates. Healthy women are mainly colonised with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners; however, other bacteria may be elements of the VMB, particularly in women with bacterial vaginosis. The implementation of culture-independent molecular methods in VMB characterisation, especially next-generation sequencing, have provided new information regarding bacterial diversity in the vagina, revealing a large number of novel, fastidious, and/or uncultivated bacterial species...
May 15, 2017: Beneficial Microbes
https://www.readbyqxmd.com/read/28502120/gut-microbial-communities-of-american-pikas-ochotona-princeps-evidence-for-phylosymbiosis-and-adaptations-to-novel-diets
#9
Kevin D Kohl, Johanna Varner, Jennifer L Wilkening, M Denise Dearing
1.Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. 2.We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences...
May 14, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28493460/single-cell-genomics-reveals-pyrrolysine-encoding-potential-in-members-of-uncultivated-archaeal-candidate-division-msbl1
#10
Yue Guan, Mohamed F Haroon, Intikhab Alam, James G Ferry, Ulrich Stingl
Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea...
May 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28488795/the-novel-bacterial-phylum-calditrichaeota-is-diverse-widespread-and-abundant-in-marine-sediments-and-has-the-capacity-to-degrade-detrital-proteins
#11
Ian P G Marshall, Piotr Starnawski, Carina Cupit, Eva Fernández Cáceres, Thijs J G Ettema, Andreas Schramm, Kasper U Kjeldsen
Calditrichaeota is a recently recognised bacterial phylum with three cultured representatives, isolated from hydrothermal vents. Here we expand the phylogeny and ecology of this novel phylum with metagenome-derived and single-cell genomes from six uncultivated bacteria previously not recognised as members of Calditrichaeota. Using 16S rRNA gene sequences from these genomes, we then identified 322 16S rRNA gene sequences from cultivation-independent studies that can now be classified as Calditrichaeota for the first time...
May 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28488147/advances-and-perspective-in-bioremediation-of-polychlorinated-biphenyl-contaminated-soils
#12
Jitendra K Sharma, Ravindra K Gautam, Sneha V Nanekar, Roland Weber, Brajesh K Singh, Sanjeev K Singh, Asha A Juwarkar
In recent years, microbial degradation and bioremediation approaches of polychlorinated biphenyls (PCBs) have been studied extensively considering their toxicity, carcinogenicity and persistency potential in the environment. In this direction, different catabolic enzymes have been identified and reported for biodegradation of different PCB congeners along with optimization of biological processes. A genome analysis of PCB-degrading bacteria has led in an improved understanding of their metabolic potential and adaptation to stressful conditions...
May 9, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28484210/identification-of-tp0751-pallilysin-as-a-treponema-pallidum-vascular-adhesin-by-heterologous-expression-in-the-lyme-disease-spirochete
#13
Wei-Chien Andrew Kao, Helena Pětrošová, Rhodaba Ebady, Karen V Lithgow, Pablo Rojas, Yang Zhang, Yae-Eun Kim, Yae-Ram Kim, Tanya Odisho, Nupur Gupta, Annette Moter, Caroline E Cameron, Tara J Moriarty
Treponema pallidum subsp. pallidum, the causative agent of syphilis, is a highly invasive spirochete pathogen that uses the vasculature to disseminate throughout the body. Identification of bacterial factors promoting dissemination is crucial for syphilis vaccine development. An important step in dissemination is bacterial adhesion to blood vessel surfaces, a process mediated by bacterial proteins that can withstand forces imposed on adhesive bonds by blood flow (vascular adhesins). The study of T. pallidum vascular adhesins is hindered by the uncultivable nature of this pathogen...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423426/the-invasive-liriomyza-huidobrensis-diptera-agromyzidae-understanding-its-pest-status-and-management-globally
#14
Phyllis G Weintraub, Sonja J Scheffer, Diedrich Visser, Graciela Valladares, Alberto Soares Correa, B Merle Shepard, Aunu Rauf, Sean T Murphy, Norma Mujica, Charles MacVean, Jürgen Kroschel, Miriam Kishinevsky, Ravindra C Joshi, Nina S Johansen, Rebecca H Hallett, Hasan S Civelek, Bing Chen, Helga Blanco Metzler
Liriomyza huidobrensis (Blanchard) is native to South America but has expanded its range and invaded many regions of the world, primarily on flowers and to a lesser extent on horticultural product shipments. As a result of initial invasion into an area, damage caused is usually significant but not necessarily sustained. Currently, it is an economic pest in selected native and invaded regions of the world. Adults cause damage by puncturing abaxial and adaxial leaf surfaces for feeding and egg laying sites. Larvae mine the leaf parenchyma tissues which can lead to leaves drying and wilting...
January 1, 2017: Journal of Insect Science
https://www.readbyqxmd.com/read/28396823/genomic-comparisons-of-a-bacterial-lineage-that-inhabits-both-marine-and-terrestrial-deep-subsurface-systems
#15
Sean P Jungbluth, Tijana Glavina Del Rio, Susannah G Tringe, Ramunas Stepanauskas, Michael S Rappé
It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth's crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of "Candidatus Desulforudis audaxviator" MP104C...
2017: PeerJ
https://www.readbyqxmd.com/read/28392745/cultivation-strategies-for-growth-of-uncultivated-bacteria
#16
Sonia R Vartoukian
BACKGROUND: The majority of environmental bacteria and around a third of oral bacteria remain uncultivated. Furthermore, several bacterial phyla have no cultivable members and are recognised only by detection of their DNA by molecular methods. Possible explanations for the resistance of certain bacteria to cultivation in purity in vitro include: unmet fastidious growth requirements; inhibition by environmental conditions or chemical factors produced by neighbouring bacteria in mixed cultures; or conversely, dependence on interactions with other bacteria in the natural environment, without which they cannot survive in isolation...
November 2016: Journal of Oral Biosciences
https://www.readbyqxmd.com/read/28387771/who-lives-in-a-fungus-the-diversity-origins-and-functions-of-fungal-endobacteria-living-in-mucoromycota
#17
Paola Bonfante, Alessandro Desirò
Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related)...
April 7, 2017: ISME Journal
https://www.readbyqxmd.com/read/28382330/metatranscriptomics-supports-the-mechanism-for-biocathode-electroautotrophy-by-candidatus-tenderia-electrophaga
#18
Brian J Eddie, Zheng Wang, W Judson Hervey, Dagmar H Leary, Anthony P Malanoski, Leonard M Tender, Baochuan Lin, Sarah M Strycharz-Glaven
Biocathodes provide a stable electron source to drive reduction reactions in electrotrophic microbial electrochemical systems. Electroautotrophic biocathode communities may be more robust than monocultures in environmentally relevant settings, but some members are not easily cultivated outside the electrode environment. We previously used metagenomics and metaproteomics to propose a pathway for coupling extracellular electron transfer (EET) to carbon fixation in "Candidatus Tenderia electrophaga," an uncultivated but dominant member of an electroautotrophic biocathode community...
March 2017: MSystems
https://www.readbyqxmd.com/read/28370791/cyanobacterial-ent-sterol-like-natural-products-from-a-deviated-ubiquinone-pathway
#19
Philipp Moosmann, Reiko Ueoka, Laura Grauso, Alfonso Mangoni, Brandon I Morinaka, Muriel Gugger, Jörn Piel
Natural products from marine animals show high potential for the development of new medicines, but drug development based on these compounds is commonly hampered by their low natural abundance. Since many of these metabolites are suspected or known to be produced by uncultivated bacterial symbionts, the rapidly growing diversity of sequenced prokaryotic genomes offers the opportunity to identify alternative, culturable sources of natural products computationally. In this work, we investigated the potential of using this sequenced resource to facilitate the production of meroterpenoid-like compounds related to those from marine sources...
March 30, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28368387/retroelement-guided-protein-diversification-abounds-in-vast-lineages-of-bacteria-and-archaea
#20
Blair G Paul, David Burstein, Cindy J Castelle, Sumit Handa, Diego Arambula, Elizabeth Czornyj, Brian C Thomas, Partho Ghosh, Jeff F Miller, Jillian F Banfield, David L Valentine
Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life(1-5). The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability(6-8), are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum...
April 3, 2017: Nature Microbiology
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