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https://www.readbyqxmd.com/read/28504576/is-the-role-of-human-female-reproductive-tract-microbiota-underestimated
#1
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
#2
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
#3
Yue Guan, Mohamed F Haroon, Intikhab Alam, James G Ferry, Ulrich Stingl
Pyrrolysine (Pyl), the 22(nd) 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28367142/diurnal-dynamics-of-gaseous-and-dissolved-metabolites-and-microbiota-composition-in-the-bovine-rumen
#14
Henk J van Lingen, Joan E Edwards, Jueeli D Vaidya, Sanne van Gastelen, Edoardo Saccenti, Bartholomeus van den Bogert, André Bannink, Hauke Smidt, Caroline M Plugge, Jan Dijkstra
Diurnal patterns of ruminal fermentation metabolites and microbial communities are not commonly assessed when investigating variation in ruminal CH4 production. The aims of this study were to monitor diurnal patterns of: (i) gaseous and dissolved metabolite concentrations in the bovine rumen, (ii) H2 and CH4 emitted, and (iii) the rumen microbiota. Furthermore, the effect of dietary inclusion of linseed oil on these patterns was assessed. Four rumen cannulated multiparous cows were used in a cross-over design with two 17 days periods and two dietary treatments: a control diet and a linseed oil supplemented diet [40% maize silage, 30% grass silage, 30% concentrate on dry matter (DM) basis for both diets; fat contents of 33 vs...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28359990/morphoanatomical-and-physiological-changes-in-bauhinia-variegata-l-as-indicators-of-herbicide-diuron-action
#15
Dêmily Andrômeda de Lima, Caroline Müller, Alan Carlos Costa, Priscila Ferreira Batista, Valdnéa Casagrande Dalvi, Marisa Domingos
The wide use of the herbicide diuron has compromised surrounding uncultivated areas, resulting in acute and/or chronic damage to non-target plants. Thus, the aim of this research was to evaluate physiological and morphoanatomical responses in Bauhinia variegata L. plants to different doses of diuron. Seedlings of 90-day-old B. variegata were transplanted into 10liter pots. After an acclimation period (about 30 days), treatments consisting of different diuron doses were applied: 0 (control), 400, 800, 1600, and 2400g ai ha(-1)...
March 27, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28350381/metagenome-sequencing-and-98-microbial-genomes-from-juan-de-fuca-ridge-flank-subsurface-fluids
#16
Sean P Jungbluth, Jan P Amend, Michael S Rappé
The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs)...
March 28, 2017: Scientific Data
https://www.readbyqxmd.com/read/28341674/interbacterial-adhesion-networks-within-the-early-oral-biofilm-of-individual-human-hosts
#17
Robert J Palmer, Nehal Shah, Alex Valm, Bruce Paster, Floyd Dewhirst, Taichi Inui, John O Cisar
Specific interbacterial adhesion, termed coaggregation, is well established for three early colonizers of the plaque biofilm: streptococci, actinomyces, and veillonellae. However, little is known about interactions of other early colonizers, and about the extent of interactions within the bacterial community from a single host. To address these gaps, subject-specific culture collections from two individuals were established using an intra-oral biofilm retrieval device. Molecular taxonomy (Human Oral Microbe Identification Microarray: HOMIM) of biofilm samples corroborated integrity and completeness of the collections...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28338684/seven-enzymes-create-extraordinary-molecular-complexity-in-an-uncultivated-bacterium
#18
Michael F Freeman, Maximilian J Helf, Agneya Bhushan, Brandon I Morinaka, Jörn Piel
Uncultivated bacteria represent a massive resource of new enzymes and bioactive metabolites, but such bacteria remain functionally enigmatic. Polytheonamides are potent peptide cytotoxins produced by uncultivated bacteria that exist as symbionts in a marine sponge. Outside glycobiology, polytheonamides represent the most heavily post-translationally modified biomolecules that are derived from amino acids. The biosynthesis of polytheonamides involves up to 50 site-specific modifications to create a membrane-spanning β-helical structure...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28314620/selenium-speciation-in-seleniferous-agricultural-soils-under-different-cropping-systems-using-sequential-extraction-and-x-ray-absorption-spectroscopy
#19
Hai-Bo Qin, Jian-Ming Zhu, Zhi-Qing Lin, Wen-Po Xu, De-Can Tan, Li-Rong Zheng, Yoshio Takahashi
Selenium (Se) speciation in soil is critically important for understanding the solubility, mobility, bioavailability, and toxicity of Se in the environment. In this study, Se fractionation and chemical speciation in agricultural soils from seleniferous areas were investigated using the elaborate sequential extraction and X-ray absorption near-edge structure (XANES) spectroscopy. The speciation results quantified by XANES technique generally agreed with those obtained by sequential extraction, and the combination of both approaches can reliably characterize Se speciation in soils...
March 14, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28283818/genome-sequences-of-a-capulavirus-infecting-plantago-lanceolata-in-the-%C3%A3-land-archipelago-of-finland
#20
Hanna Susi, Anna-Liisa Laine, Denis Filloux, Simona Kraberger, Kata Farkas, Pauline Bernardo, Mikko J Frilander, Darren P Martin, Arvind Varsani, Philippe Roumagnac
The discovery and full-genome sequences of two isolates of a fourth capulavirus species are reported. The viruses were discovered during a viral metagenomics survey of uncultivated Plantago lanceolata plants in the Åland archipelago of south western Finland. The newly discovered viruses apparently produce no symptoms in P. lanceolata. They have a genome organization that is very similar to that of the three known capulavirus species and additionally share between 62.9 and 67.1% genome-wide sequence identity with the isolates of these species...
March 10, 2017: Archives of Virology
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