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https://www.readbyqxmd.com/read/27900683/constructing-and-screening-a-metagenomic-library-of-a-cold-and-alkaline-extreme-environment
#1
Mikkel A Glaring, Jan K Vester, Peter Stougaard
Natural cold or alkaline environments are common on Earth. A rare combination of these two extremes is found in the permanently cold (less than 6 °C) and alkaline (pH above 10) ikaite columns in the Ikka Fjord in Southern Greenland. Bioprospecting efforts have established the ikaite columns as a source of bacteria and enzymes adapted to these conditions. They have also highlighted the limitations of cultivation-based methods in this extreme environment and metagenomic approaches may provide access to novel extremophilic enzymes from the uncultured majority of bacteria...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900680/construction-of-small-insert-and-large-insert-metagenomic-libraries
#2
Carola Simon, Rolf Daniel
The vast majority of the Earth's biological diversity is hidden in uncultured and yet uncharacterized microbial genomes. The construction of metagenomic libraries is a cultivation-independent molecular approach to assess this unexplored genetic reservoir. High numbers of novel biocatalysts have been identified by function-based or sequence-based screening of metagenomic libraries derived from various environments. Here, we describe detailed protocols for the construction of metagenomic small-insert and large-insert libraries in plasmids and fosmids, respectively, from environmental DNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896730/scaling-up-the-phylogenetic-detection-of-lateral-gene-transfer-events
#3
Cheong Xin Chan, Robert G Beiko, Mark A Ragan
Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27890085/detection-of-n2o-producing-fungi-in-environment-using-nitrite-reductase-gene-nirk-targeting-primers
#4
Huaihai Chen, Fangbo Yu, Wei Shi
Fungal denitrification has been increasingly investigated, but its community ecology is poorly understood due to the lack of culture-independent tools. In this work, four pairs of nirK-targeting primers were designed and evaluated for primer specificity and efficiency using thirty N2O-producing fungal cultures and an agricultural soil. All primers amplified nirK from fungi and soil, but their efficiency and specificity were different. A primer set, FnirK_F3/R2 amplified ∼80 % of tested fungi, including Aspergillus, Fusarium, Penicillium, and Trichoderma, as compared to ∼40-70 % for other three primers...
December 2016: Fungal Biology
https://www.readbyqxmd.com/read/27884207/potential-contribution-of-the-uterine-microbiome-in-the-development-of-endometrial-cancer
#5
Marina R S Walther-António, Jun Chen, Francesco Multinu, Alexis Hokenstad, Tammy J Distad, E Heidi Cheek, Gary L Keeney, Douglas J Creedon, Heidi Nelson, Andrea Mariani, Nicholas Chia
BACKGROUND: Endometrial cancer studies have led to a number of well-defined but mechanistically unconnected genetic and environmental risk factors. One of the emerging modulators between environmental triggers and genetic expression is the microbiome. We set out to inquire about the composition of the uterine microbiome and its putative role in endometrial cancer. METHODS: We undertook a study of the microbiome in samples taken from different locations along the female reproductive tract in patients with endometrial cancer (n = 17), patients with endometrial hyperplasia (endometrial cancer precursor, n = 4), and patients afflicted with benign uterine conditions (n = 10)...
November 25, 2016: Genome Medicine
https://www.readbyqxmd.com/read/27882771/functional-marine-metagenomic-screening-for-anti-quorum-sensing-and-anti-biofilm-activity
#6
Karin Yaniv, Karina Golberg, Esti Kramarsky-Winter, Robert Marks, Alina Pushkarev, Oded Béjà, Ariel Kushmaro
Quorum sensing (QS), a cell-to-cell communication process, entails the production of signaling molecules that enable synchronized gene expression in microbial communities to regulate myriad microbial functions, including biofilm formation. QS disruption may constitute an innovative approach to the design of novel antifouling and anti-biofilm agents. To identify novel quorum sensing inhibitors (QSI), 2,500 environmental bacterial artificial chromosomes (BAC) from uncultured marine planktonic bacteria were screened for QSI activity using soft agar overlaid with wild type Chromobacterium violaceum as an indicator...
November 24, 2016: Biofouling
https://www.readbyqxmd.com/read/27878346/salinity-affects-the-composition-of-the-aerobic-methanotroph-community-in-alkaline-lake-sediments-from-the-tibetan-plateau
#7
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/27877167/polycyclic-aromatic-hydrocarbon-induced-changes-in-bacterial-community-structure-under-anoxic-nitrate-reducing-conditions
#8
Sophie-Marie Martirani-Von Abercron, Daniel Pacheco, Patricia Benito-Santano, Patricia Marín, Silvia Marqués
Although bacterial anaerobic degradation of mono-aromatic compounds has been characterized in depth, the degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene has only started to be understood in sulfate reducing bacteria, and little is known about the anaerobic degradation of PAHs in nitrate reducing bacteria. Starting from a series of environments which had suffered different degrees of hydrocarbon pollution, we used most probable number (MPN) enumeration to detect and quantify the presence of bacterial communities able to degrade several PAHs using nitrate as electron acceptor...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27876828/common-variants-in-the-parl-and-pink1-genes-increase-the-risk-to-leprosy-in-han-chinese-from-south-china
#9
Dong Wang, Deng-Feng Zhang, Jia-Qi Feng, Guo-Dong Li, Xiao-An Li, Xiu-Feng Yu, Heng Long, Yu-Ye Li, Yong-Gang Yao
Leprosy is a chronic infectious and neurological disease caused by Mycobacterium leprae, an unculturable pathogen with massive genomic decay and dependence on host metabolism. We hypothesized that mitochondrial genes PARL and PINK1 would confer risk to leprosy. Thirteen tag SNPs of PARL and PINK1 were analyzed in 3620 individuals with or without leprosy from China. We also sequenced the entire exons of PARL, PINK1 and PARK2 in 80 patients with a family history of leprosy by using the next generation sequencing technology (NGS)...
November 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27865394/recent-developments-in-genomics-bioinformatics-and-drug-discovery-to-combat-emerging-drug-resistant-tuberculosis
#10
REVIEW
Soumya Swaminathan, Jagadish Chandrabose Sundaramurthi, Alangudi Natarajan Palaniappan, Sujatha Narayanan
Emergence of drug-resistant tuberculosis (DR-TB) is a big challenge in TB control. The delay in diagnosis of DR-TB leads to its increased transmission, and therefore prevalence. Recent developments in genomics have enabled whole genome sequencing (WGS) of Mycobacterium tuberculosis (M. tuberculosis) from 3-day-old liquid culture and directly from uncultured sputa, while new bioinformatics tools facilitate to determine DR mutations rapidly from the resulting sequences. The present drug discovery and development pipeline is filled with candidate drugs which have shown efficacy against DR-TB...
December 2016: Tuberculosis
https://www.readbyqxmd.com/read/27854567/metagenomic-evaluation-of-bacteria-from-voles
#11
Katja A Koskela, Laura Kalin-Mänttäri, Heidi Hemmilä, Teemu Smura, Paula M Kinnunen, Jukka Niemimaa, Heikki Henttonen, Simo Nikkari
Voles (Arvicolinae, Rodentia) are known carriers of zoonotic bacteria such as Bartonella spp. and Francisella tularensis. However, apart from F. tularensis, the bacterial microbiome of voles has not previously been determined in Finland and rarely elsewhere. Therefore, we studied liver samples from 61 voles using 16S ribosomal RNA gene PCR analysis, followed by Sanger sequencing. Twenty-three of these samples were also studied with tag-encoded pyrosequencing. The samples originated from 21 field voles (Microtus agrestis), 37 tundra voles (Microtus oeconomus), and 3 bank voles (Myodes glareolus)...
November 17, 2016: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/27836273/microbial-communities-of-biomethanization-digesters-fed-with-raw-and-heat-pre-treated-microalgae-biomasses
#12
Jose Luis Sanz, Patricia Rojas, Ana Morato, Lara Mendez, Mercedes Ballesteros, Cristina González-Fernández
Microalgae biomasses are considered promising feedstocks for biofuel and methane productions. Two Continuously Stirred Tank Reactors (CSTR), fed with fresh (CSTR-C) and heat pre-treated (CSTR-T) Chlorella biomass were run in parallel in order to determine methane productions. The methane yield was 1.5 times higher in CSTR-T with regard to CSTR-C. Aiming to understand the microorganism roles within of the reactors, the sludge used as an inoculum (I), plus raw (CSTR-C) and heat pre-treated (CSTR-T) samples were analyzed by high-throughput pyrosequencing...
November 8, 2016: Chemosphere
https://www.readbyqxmd.com/read/27823963/new-approaches-to-antimicrobial-discovery
#13
REVIEW
Kim Lewis
The spread of resistant organisms is producing a human health crisis, as we are witnessing the emergence of pathogens resistant to all available antibiotics. An increase in chronic infections presents an additional challenge - these diseases are difficult to treat due to antibiotic-tolerant persister cells. vermining of soil Actinomycetes ended the golden era of antibiotic discovery in the 60s, and efforts to replace this source by screening synthetic compound libraries was not successful. Bacteria have an efficient permeability barrier, preventing penetration of most synthetic compounds...
November 4, 2016: Biochemical Pharmacology
https://www.readbyqxmd.com/read/27822555/novel-syntrophic-populations-dominate-an-ammonia-tolerant-methanogenic-microbiome
#14
J A Frank, M Ø Arntzen, L Sun, L H Hagen, A C McHardy, S J Horn, V G H Eijsink, A Schnürer, P B Pope
Biogas reactors operating with protein-rich substrates have high methane potential and industrial value; however, they are highly susceptible to process failure because of the accumulation of ammonia. High ammonia levels cause a decline in acetate-utilizing methanogens and instead promote the conversion of acetate via a two-step mechanism involving syntrophic acetate oxidation (SAO) to H2 and CO2, followed by hydrogenotrophic methanogenesis. Despite the key role of syntrophic acetate-oxidizing bacteria (SAOB), only a few culturable representatives have been characterized...
September 2016: MSystems
https://www.readbyqxmd.com/read/27819657/culture-of-previously-uncultured-members-of-the-human-gut-microbiota-by-culturomics
#15
Jean-Christophe Lagier, Saber Khelaifia, Maryam Tidjani Alou, Sokhna Ndongo, Niokhor Dione, Perrine Hugon, Aurelia Caputo, Frédéric Cadoret, Sory Ibrahima Traore, El Hadji Seck, Gregory Dubourg, Guillaume Durand, Gaël Mourembou, Elodie Guilhot, Amadou Togo, Sara Bellali, Dipankar Bachar, Nadim Cassir, Fadi Bittar, Jérémy Delerce, Morgane Mailhe, Davide Ricaboni, Melhem Bilen, Nicole Prisca Makaya Dangui Nieko, Ndeye Mery Dia Badiane, Camille Valles, Donia Mouelhi, Khoudia Diop, Matthieu Million, Didier Musso, Jônatas Abrahão, Esam Ibraheem Azhar, Fehmida Bibi, Muhammad Yasir, Aldiouma Diallo, Cheikh Sokhna, Felix Djossou, Véronique Vitton, Catherine Robert, Jean Marc Rolain, Bernard La Scola, Pierre-Edouard Fournier, Anthony Levasseur, Didier Raoult
Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism(1). The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms(2). We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization-time of flight and 16S rRNA for identification(2)...
November 7, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27815278/molecular-evidence-of-chlamydia-like-organisms-in-the-faeces-of-the-bat-myotis-daubentonii
#16
K Hokynar, E J Vesterinen, T M Lilley, A T Pulliainen, S J Korhonen, J Paavonen, M Puolakkainen
: Chlamydia-like organisms (CLOs) are recently identified members of the Chlamydiales order. CLOs share intracellular lifestyle and biphasic developmental cycle and they have been detected in environmental samples as well as in various hosts like amoebae and arthropods. In this study we screened bat faeces for the presence of CLOs by molecular analysis. Using Pan-Chlamydiales-PCR, targeting the 16S rRNA gene, Chlamydiales DNA was detected in 54% of the specimens. PCR amplification, sequencing and phylogenetic analysis of the 16S rRNA and 23S rRNA were used to classify positive specimens and infer their phylogenetic relationships...
November 4, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27815274/quantitative-metaproteomics-highlight-the-metabolic-contributions-of-uncultured-phylotypes-in-a-thermophilic-anaerobic-digester
#17
Live H Hagen, Jeremy A Frank, Mirzaman Zamanzadeh, Vincent G H Eijsink, Phillip B Pope, Svein J Horn, Magnus Ø Arntzen
: In this study, we used multiple meta-omic approaches to characterize the microbial community and the active metabolic pathways of a stable industrial biogas reactor with food waste as the dominant feedstock, operating at thermophilic temperatures (60°C) and elevated levels of free ammonia (367 mg NH3-N/L). The microbial community was strongly dominated (76% of all 16S rRNA amplicon reads) by populations affiliated to the proteolytic bacterium, Coprothermobacter proteolyticus. Multiple Coprothermobacter-affiliated strains were detected, introducing an additional level of complexity seldom explored in biogas studies...
November 4, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27815062/short-term-exposure-of-human-ovarian-follicles-to-cyclophosphamide-metabolites-seems-to-promote-follicular-activation-in-vitro
#18
Yechezkel Lande, Benjamin Fisch, Abraham Tsur, Jacob Farhi, Roni Prag-Rosenberg, Avi Ben-Haroush, Gania Kessler-Icekson, Muayad A Zahalka, Susan M Ludeman, Ronit Abir
How chemotherapy affects dormant ovarian primordial follicles is unclear. The 'burnout' theory, studied only in mice, suggests cyclophosphamide enhances primordial follicle activation. Using 4-hydroperoxycyclophosphamide (4hc) and phosphoramide mustard (PM), this study assessed how the active cyclophosphamide metabolites 4-hydroxycyclophosphamide (4-OHC) and PM, affect human primordial follicles. Frozen-thawed human ovarian samples were sliced and cultured with basic culture medium (cultured controls) or with 4hc/PM (3 µmol/l/10 µmol/l) (treated samples) for 24-48 h...
October 17, 2016: Reproductive Biomedicine Online
https://www.readbyqxmd.com/read/27801291/computational-workflow-for-the-fine-grained-analysis-of-metagenomic-samples
#19
Esteban Pérez-Wohlfeil, Jose A Arjona-Medina, Oscar Torreno, Eugenia Ulzurrun, Oswaldo Trelles
BACKGROUND: The field of metagenomics, defined as the direct genetic analysis of uncultured samples of genomes contained within an environmental sample, is gaining increasing popularity. The aim of studies of metagenomics is to determine the species present in an environmental community and identify changes in the abundance of species under different conditions. Current metagenomic analysis software faces bottlenecks due to the high computational load required to analyze complex samples...
October 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27800599/metabolic-engineering-of-methanosarcina-acetivorans-for-lactate-production-from-methane
#20
Michael J McAnulty, Venkata Giridhar Poosarla, Jine Li, Valerie W C Soo, Fayin Zhu, Thomas K Wood
We previously demonstrated anaerobic conversion of the greenhouse gas methane into acetate using an engineered archaeon that produces methyl-coenzyme M reductase (Mcr) from unculturable microorgansims from a microbial mat in the Black Sea to create the first culturable prokaryote that reverses methanogenesis and grows anaerobically on methane. In this work, we further engineered the same host with the goal of converting methane into butanol. Instead, we discovered a process for converting methane to the secreted valuable product, L-lactate, with sufficient optical purity for synthesizing the biodegradable plastic poly-lactic acid...
November 1, 2016: Biotechnology and Bioengineering
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