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leaves metagenomics

Adriano Sofo, Alba N Mininni, Catia Fausto, Marina Scagliola, Carmine Crecchio, Cristos Xiloyannis, Bartolomeo Dichio
Under suitable conditions, low-quality, treated urban wastewater (TWW) is an additional water resource for irrigation in water-scarce environments but its use in agriculture requires a careful monitoring of a range of hygiene parameters, including human pathogenic bacteria (HPB). DNA-based microbiological analyses on soil, xylem sap, and leaves surface (phyllosphere) were carried out in an olive (Olea europaea L.) grove located in Southern Italy (Basilicata region). The experimental grove has been managed in two plots for 18 years...
December 18, 2018: Science of the Total Environment
J Musembi Mutuku, Francis O Wamonje, Gerardine Mukeshimana, Joyce Njuguna, Mark Wamalwa, Seung-Kook Choi, Trisna Tungadi, Appolinaire Djikeng, Krys Kelly, Jean-Baka Domelevo Entfellner, Sita R Ghimire, Hodeba D Mignouna, John P Carr, Jagger J W Harvey
Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean ( Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop...
2018: Frontiers in Microbiology
Juan C Castro, Luis M Rodriguez-R, William T Harvey, Michael R Weigand, Janet K Hatt, Michelle Q Carter, Konstantinos T Konstantinidis
Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets...
2018: PeerJ
Rodrigo G Taketani, Marta A Moitinho, Tim H Mauchline, Itamar S Melo
Background: Mangroves are important coastal ecosystems known for high photosynthetic productivity and the ability to support marine food chains through supply of dissolved carbon or particular organic matter. Most of the carbon found in mangroves is produced by its vegetation and is decomposed in root associated sediment. This process involves a tight interaction between microbial populations, litter chemical composition, and environmental parameters. Here, we study the complex interactions found during litter decomposition in mangroves by applying network analysis to metagenomic data...
2018: PeerJ
Xinyuan Hao, Weifu Zhang, Fumei Zhao, Ying Liu, Wenjun Qian, Yuchun Wang, Lu Wang, Jianming Zeng, Yajun Yang, Xinchao Wang
The tea plant ( Camellia sinensis (L.) O. Kuntze) is an economically important woody species. In this study, we collected 26 tea plant samples with typical discoloration symptoms from different tea gardens and performed metagenomic analysis based on next-generation sequencing. Homology annotation and PCR sequencing validation finally identified seven kinds of plant viruses from tea plant. Based on abundance distribution analysis, the two most abundant plant viruses were highlighted. Genetic characterization suggested that they are two novel virus species with relatively high homology to Blueberry necrotic ring blotch virus and American plum line pattern virus ...
2018: Frontiers in Microbiology
Melissa R Ingala, Nancy B Simmons, Susan L Perkins
Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear...
September 19, 2018: MSphere
Jean-Michel Hily, Thierry Candresse, Shahinez Garcia, Emmanuelle Vigne, Mélanie Tannière, Véronique Komar, Guillaume Barnabé, Antoine Alliaume, Sophie Gilg, Gérard Hommay, Monique Beuve, Armelle Marais, Olivier Lemaire
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species...
2018: Frontiers in Microbiology
Jeanmarie Verchot, Aastha Thapa, Dulanjani Wijayasekara, Peter R Hoyt
This metagenome approach is used to identify plant viruses with circular DNA genomes and their transcripts. Often plant DNA viruses that occur in low titers in their host or cannot be mechanically inoculated to another host are difficult to propagate to achieve a greater titer of infectious material. Infected leaves are ground in a mild buffer with optimal pH and ionic composition recommended for purifying most bacilliform Para retroviruses. Urea is used to break up inclusion bodies that trap virions and to dissolve cellular components...
July 27, 2018: Journal of Visualized Experiments: JoVE
Hanako Shimura, Chikara Masuta, Yasunori Koda
In nature, mycorrhizal association with soilborne fungi is indispensable for orchid families. Fungal structures from compatible endo-mycorrhizal fungi in orchid cells are digested in cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until shoots develop (leaves) and become photoautotrophic. Seeds of all orchid species surely geminate with the help of their own fungal partners, and this specific partnership has been acquired for a long evolutional history between orchids and fungi...
2018: Methods in Molecular Biology
Bo Jiang, Naifu Jin, Yi Xing, Yuping Su, Dayi Zhang
Uncultivable microorganisms account for over 99% of all species on earth, playing essential roles in ecological processes such as carbon/nitrogen cycle and chemical mineralization. Their functions remain unclear in ecosystems and natural habitats, requiring cutting-edge biotechnologies for a deeper understanding. Stable isotope probing (SIP) incorporates isotope-labeled elements, e.g. 13  C, 18  O or 15  N, into the cellular components of active microorganisms, serving as a powerful tool to link phylogenetic identities to their ecological functions in situ...
November 2018: Critical Reviews in Biotechnology
Alaine B Guerra, Jorge S Oliveira, Rita C B Silva-Portela, Wydemberg Araújo, Aline C Carlos, Ana Tereza R Vasconcelos, Ana Teresa Freitas, Yldeney Silva Domingos, Mirna Ferreira de Farias, Glauber José Turolla Fernandes, Lucymara F Agnez-Lima
Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers. Total DNA was extracted directly from the drill cutting samples and from two enriched consortia and sequenced using the Ion Torrent platform...
April 2018: Environmental Pollution
Tanja Woyke, Devin F R Doud, Frederik Schulz
Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and discuss some of the scientific endeavors that it has enabled. Specifically, we highlight newly added leaves and branches in the genomic tree of bacterial and archaeal life and illustrate the unique and exciting advantages that single-cell genomics offers over metagenomics, both now and in the near future...
October 31, 2017: Nature Methods
Sandra Blome, Martin Beer, Kerstin Wernike
Pestiviruses are a group of viruses of veterinary importance infecting livestock animals like pigs, cattle, and sheep, and also wildlife animals like wild boar and different deer species. While for decades only four classical species (Classical swine fever virus, Bovine viral diarrhea virus types 1 and 2, Border disease virus), and a few so-called atypical pestiviruses were known (e.g., Giraffe virus, Pronghorn virus, HoBi virus), a series of novel pestiviruses was identified in the last years (Bungowannah virus, Bat pestivirus, Norway rat pestivirus, Atypical porcine pestivirus, LINDA virus)...
2017: Advances in Virus Research
Yong-Wei Yan, Bin Zou, Ting Zhu, Wael N Hozzein, Zhe-Xue Quan
RNA-seq-based SSU (small subunit) rRNA (ribosomal RNA) analysis has provided a better understanding of potentially active microbial community within environments. However, for RNA-seq library construction, high quantities of purified RNA are typically required. We propose a modified RNA-seq method for SSU rRNA-based microbial community analysis that depends on the direct ligation of a 5' adaptor to RNA before reverse-transcription. The method requires only a low-input quantity of RNA (10-100 ng) and does not require a DNA removal step...
2017: PloS One
Wanping Aw, Shinji Fukuda
Recently, metagenomics and metabolomics are the two most rapidly advancing "omics" technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites) that specific cellular processes leave behind. Remarkable progress in DNA sequencing and mass spectrometry technologies has enabled the comprehensive collection of information on the gut microbiome and its metabolome in order to assess the influence of the gut microbiota on host physiology on a whole-systems level...
November 6, 2015: Diseases (Basel)
Qi Wu, Xiao Wang, Yun Ding, Yibo Hu, Yonggang Nie, Wei Wei, Shuai Ma, Li Yan, Lifeng Zhu, Fuwen Wei
Wild giant pandas use different parts of bamboo (shoots, leaves and stems) and different bamboo species at different times of the year. Their usage of bamboo can be classified temporally into a distinct leaf stage, shoot stage and transition stage. An association between this usage pattern and variation in the giant panda gut microbiome remains unknown. Here, we found associations using a gut metagenomic approach and nutritional analyses whereby diversity of the gut microbial community in the leaf and shoot stages was significantly different...
September 13, 2017: Proceedings. Biological Sciences
J Kipchirchir Bitok, Christophe Lemetre, Melinda A Ternei, Sean F Brady
The majority of environmental bacteria are not readily cultured in the lab, leaving the natural products they make inaccessible using culture-dependent discovery methods. Cloning and heterologous expression of DNA extracted from environmental samples (environmental DNA, eDNA) provides a means of circumventing this discovery bottleneck. To facilitate the identification of clones containing biosynthetic gene clusters, we developed a model heterologous expression reporter strain Streptomyces albus::bpsA ΔPPTase...
September 1, 2017: FEMS Microbiology Letters
Jessica D Forbes, Natalie C Knox, Jennifer Ronholm, Franco Pagotto, Aleisha Reimer
A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances...
2017: Frontiers in Microbiology
W K Mengesha, W M Gill, S M Powell, K J Evans, K M Barry
AIM: To investigate selected factors of two nonaerated compost teas (NCT) and mechanisms that influence the restriction of several fungal potato pathogens. METHODS AND RESULTS: Two NCTs, made from either commercial compost, (CCT) or vineyard compost (VCT), were tested for their ability to suppress potato pathogens. The VCT was more suppressive than CCT to mycelial growth of Alternaria solani and Rhizoctonia solani isolate 299, but not for R. solani isolate 422. Metagenomic studies of microbial diversity revealed that the CCT had higher fungal and bacterial diversity and richness than the VCT...
September 2017: Journal of Applied Microbiology
X Fernandez-Cassi, N Timoneda, E Gonzales-Gustavson, J F Abril, S Bofill-Mas, R Girones
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food...
September 18, 2017: International Journal of Food Microbiology
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