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Xiaohui Wang, Changdong Wang, Junkang Sui, Zhaoyang Liu, Qian Li, Chao Ji, Xin Song, Yurong Hu, Changqian Wang, Rongbo Sa, Jiamiao Zhang, Jianfeng Du, Xunli Liu
Rhizospheric microorganisms can increase phosphorus availability in the soil. In this regard, the ability of phosphofungi to dissolve insoluble phosphorus compounds is greater than that of phosphate-solubilizing bacteria. The aim of the current study was to identify efficient phosphofungi that could be developed as commercial microbial agents. Among several phosphate-solubilizing fungal isolates screened, strain CS-1 showed the highest phosphorus-solubilization ability. Based on phylogenetic analysis of the internal transcribed spacer region sequence, it was identified as Aspergillus niger...
April 20, 2018: AMB Express
Honglong Chu, Ming Tang, Haihua Wang, Chuyan Wang
AIMS: This study was to investigate pinewood nematode's impacts on root mycoflora of P. tabulaeformis. METHODS AND RESULTS: The biomass, colonization rate, community structure and diversity of root-associated fungi were investigated in pinewood nematode infected and non-infected P. tabulaeformis. The results indicated that the roots of P. tabulaeformis were colonized highly by root-associated fungi, mainly ectomycorrhizal fungi (ECMF) and dark septate endophytes...
April 19, 2018: Journal of Applied Microbiology
Sarah Potgieter, Ameet Pinto, Makhosazana Sigudu, Hein du Preez, Esper Ncube, Stephanus Venter
Long-term spatial-temporal investigations of microbial dynamics in full-scale drinking water distribution systems are scarce. These investigations can reveal the process, infrastructure, and environmental factors that influence the microbial community, offering opportunities to re-think microbial management in drinking water systems. Often, these insights are missed or are unreliable in short-term studies, which are impacted by stochastic variabilities inherent to large full-scale systems. In this two-year study, we investigated the spatial and temporal dynamics of the microbial community in a large, full scale South African drinking water distribution system that uses three successive disinfection strategies (i...
March 30, 2018: Water Research
Lei Xu, Xi Chen, Yuan Wang, Wen Jiang, Sa Wang, Zongxin Ling, Hui Chen
Dynamic alterations in oral microbiota are closely related to the development of dental caries;however, changes in salivary microbiota during this process have not been extensively studied. In addition, increasing evidence suggests that oral microbiome profiles differ according to dentition stages, but it is unclear whether they change with age during the same dentition, such as deciduous dentition. These two aspects were investigated in a 2-year follow-up study, and caries-free preschool children with complete deciduous dentition were enrolled...
2018: Frontiers in Physiology
Daniel Hagenfeld, Raphael Koch, Sebastian Jünemann, Karola Prior, Inga Harks, Peter Eickholz, Thomas Hoffmann, Ti-Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Ulrich Schlagenhauf, Benjamin Ehmke, Dag Harmsen
Empiric antibiotics are often used in combination with mechanical debridement to treat patients suffering from periodontitis and to eliminate disease-associated pathogens. Until now, only a few next generation sequencing 16S rDNA amplicon based publications with rather small sample sizes studied the effect of those interventions on the subgingival microbiome. Therefore, we studied subgingival samples of 89 patients with chronic periodontitis (solely non-smokers) before and two months after therapy. Forty-seven patients received mechanical periodontal therapy only, whereas 42 patients additionally received oral administered amoxicillin plus metronidazole (500 and 400 mg, respectively; 3x/day for 7 days)...
2018: PloS One
Tara G McDaneld, Larry A Kuehn, John W Keele
Bovine respiratory disease complex (BRDC) is a multifactor disease, and disease incidence may be associated with an animal's commensal bacterial populations (microbiome) in the upper nasal cavity. Identifying these commensal bacterial populations in the upper nasal cavity may help us to understand the impact of the microbiome on incidence of BRDC in cattle. Various sampling techniques have previously been utilized to evaluate the microbiome of different locations of the upper nasal cavity in cattle. Therefore, our objective was to determine whether bacterial populations of the nasal cavity vary based on these sampling locations...
April 12, 2018: Journal of Animal Science
Gui-Hua Lu, Xiao-Mei Hua, Li Liang, Zhong-Ling Wen, Mei-Hang Du, Fan-Fan Meng, Yan-Jun Pang, Jin-Liang Qi, Cheng-Yi Tang, Yong-Hua Yang
The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq...
April 16, 2018: Genes
Andrew Lucas, Owen Bodger, Berry J Brosi, Col R Ford, Dan W Forman, Carolyn Greig, Matthew Hegarty, Penelope J Neyland, Natasha de Vere
Pollination by insects is a key ecosystem service and important to wider ecosystem function. Most species-level pollination networks studied have a generalised structure, with plants having several potential pollinators, and pollinators in turn visiting a number of different plant species. This is in apparent contrast to a plant's need for efficient conspecific pollen transfer. The aim of this study was to investigate the structure of pollen transport networks at three levels of biological hierarchy: community, species and individual...
April 16, 2018: Journal of Animal Ecology
Dominika Salamon, Agnieszka Sroka-Oleksiak, Przemysław Kapusta, Magdalena Szopa, Sandra Mrozińska, Agnieszka H Ludwig-Słomczyńska, Paweł P Wołkow, Małgorzata Bulanda, Tomasz Klupa, Maciej T Małecki, Tomasz Gosiewski
INTRODUCTION    Scientific data indicate  a possible influence of the gastrointestinal tract microbiota on the development of type 1 (T1DM) and 2 (T2DM) diabetes. Sequence analysis of 16S rRNA identified several hundred bacterial species of the intestinal ecosystem, most of which cannot be cultured. OBJECTIVES    We aimed at evaluating the composition of the gut microbiota in adult patients with T1DM and T2DM and establishing a link between data obtained from microbiological testing and the patients' clinical data...
April 15, 2018: Polish Archives of Internal Medicine
Janko van Beek, Marjo Haanperä, Pieter W Smit, Silja Mentula, Hanna Soini
OBJECTIVES: Culture-based assays are currently the gold standard for drug susceptibility testing (DST) for Mycobacterium tuberculosis. They provide good sensitivity and specificity, but are time-consuming. The objective of this study was to evaluate whether whole genome sequencing (WGS), combined with software tools for data analysis, can replace routine culture based assays for drug susceptibility testing of M. tuberculosis. METHODS: M. tuberculosis cultures sent to the Finnish mycobacterial reference laboratory in 2014 (n=211) were phenotypically tested by Mycobacteria Growth Indicator Tube (MGIT) for first line drug susceptibilities...
April 10, 2018: Clinical Microbiology and Infection
Barbora Pafčo, Dagmar Čížková, Jakub Kreisinger, Hideo Hasegawa, Peter Vallo, Kathryn Shutt, Angelique Todd, Klára J Petrželková, David Modrý
Strongylid nematodes in large terrestrial herbivores such as great apes, equids, elephants, and humans tend to occur in complex communities. However, identification of all species within strongylid communities using traditional methods based on coproscopy or single nematode amplification and sequencing is virtually impossible. High-throughput sequencing (HTS) technologies provide opportunities to generate large amounts of sequence data and enable analyses of samples containing a mixture of DNA from multiple species/genotypes...
April 12, 2018: Scientific Reports
Bin Ji, Hui Qin, Shaodong Guo, Wei Chen, Xuechun Zhang, Jiechao Liang
Knowing the microbial compositions in fresh lakes is significant to explore the mechanisms of eutrophication and algal blooms. This study reported on the bacterial communities of the four adjacent fresh lakes at different trophic status by Illumina MiSeq Platform, which were Tangxun Lake (J1), Qingling Lake (J2), Huangjia Lake (J3) and Niushan Lake (J4) in Wuhan, China. J1 had the highest salinity and phosphorus. J2 was abundant in TC (Total Carbon)/TOC (Total Organic Carbon.), calcium and magnesium. J3 had the highest content of nitrogen, iron and pollution of heavy metals...
April 9, 2018: Ecotoxicology and Environmental Safety
Jeong A Kim, Sung-Hak Kim, In Sung Kim, Da Yoon Yu, Sung Chan Kim, Seung Ho Lee, Sang Suk Lee, Cheol-Heui Yun, In Soon Choi, Kwang Keun Cho
Atopic dermatitis is a chronic and recurrent inflammatory skin disease. Recently, probiotics have been shown to suppress allergic symptoms through immunomodulatory responses. In the present study, combinatorial effects on allergic symptoms were identified in BALB/c mice fed with a mixture of four species of probiotics, Bifidobacterium lactis, Lactobacillus casei, Lactobacillus rhamnosus, and Lactobacillus plantarum, and sodium butyrate. Following sensitization with whey protein, the mice were challenged and divided into two groups: (1) mice administered with phosphate-buffered saline as a control and (2) mice administered with the probiotic mixture and sodium butyrate...
March 20, 2018: Journal of Medicinal Food
Patricia J Simner, Annukka A R Antar, Stephanie Hao, James Gurtowski, Pranita D Tamma, Clare Rock, Belita N A Opene, Tsigereda Tekle, Karen C Carroll, Michael C Schatz, Winston Timp
Objectives: In this study, we characterize a concurrent disseminated infection with a virulent hypermucoviscous (HMV) Klebsiella pneumoniae and an OXA-181-producing XDR K. pneumoniae from a patient with recent hospitalization in India. During exposure to meropenem therapy, the highly susceptible HMV K. pneumoniae became resistant to carbapenems, consistent with the acquisition of blaOXA-181. Methods: Twelve K. pneumoniae isolates were recovered from the patient and the hospital room environment over a 3 month hospitalization...
April 10, 2018: Journal of Antimicrobial Chemotherapy
M Heath Farris, Andrew R Scott, Pamela A Texter, Marta Bartlett, Patricia Coleman, David Masters
BACKGROUND: Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA sequencing (MPS) technologies and human genome SNP databases allow for the design of suites of identity-linked target regions, amenable to sequencing in a multiplexed and massively parallel manner. Therefore, tools are needed for leveraging the genotypic information found within SNP databases for the discovery of genomic targets that can be evaluated on MPS platforms...
April 11, 2018: BMC Bioinformatics
Xiaojuan Wang, Jie Gu, Hua Gao, Xun Qian, Haichao Li
The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR) to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs) at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase ( intI1 ) gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3-V4 regions using MiSeq sequencing...
April 10, 2018: International Journal of Environmental Research and Public Health
Abdelhameed Elameen, Hans Geir Eiken, Ida Fløystad, Geir Knudsen, Snorre B Hagen
The apple fruit moth Argyresthia conjugella (Lepidoptera, Yponomeutidae) is a seed predator of rowan ( Sorbus aucuparia ) and is distributed in Europe and Asia. In Fennoscandia (Finland, Norway and Sweden), rowan fruit production is low every 2-4 years, and apple ( Malus domestica ) functions as an alternative host, resulting in economic loss in apple crops in inter-mast years. We have used Illumina MiSeq sequencing to identify a set of 19 novel tetra-nucleotide short tandem repeats (STRs) in Argyresthia conjugella ...
April 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Zhuo Zhang, Luyun Luo, Xinqiu Tan, Xiao Kong, Jianguo Yang, Duanhua Wang, Deyong Zhang, Decai Jin, Yong Liu
Phyllosphere microbiota play a crucial role in plant-environment interactions and their microbial community and function are influenced by biotic and abiotic factors. However, there is little research on how pathogens affect the microbial community of phyllosphere fungi. In this study, we collected 16 pumpkin ( Cucurbita moschata ) leaf samples which exhibited powdery mildew disease, with a severity ranging from L1 (least severe) to L4 (most severe). The fungal community structure and diversity was examined by Illumina MiSeq sequencing of the internal transcribed spacer (ITS) region of ribosomal RNA genes...
2018: PeerJ
Yuke Peng, Jie Li, Junling Lu, Lin Xiao, Liuyan Yang
Effluents from wastewater treatment plants (WWTPs) containing microorganisms and residual nutrients can influence the biofilm formation. Although the process and mechanism of bacterial biofilm formation have been well characterized, little is known about the characteristics and interaction of bacteria, archaea and eukaryotes in the early colonization, especially under the influence of WWTP effluent. The aim of this study was to characterize the important bacterial, archaeal and eukaryotic species in the early stage of biofilm formation downstream of the WWTP outlet...
April 2018: Journal of Environmental Sciences (China)
Zhongshuo Xu, Xiaohu Dai, Xiaoli Chai
Solid and liquid organic substances as carbon sources for denitrification process were deeply explored. In this study, the effect of three carbon sources, referred to as poly (3-hydroxybutyrate-co-3-hydroxyvalerate)/poly (lactic acid) (PHBV/PLA) polymer, glucose and CH3 COONa, on denitrification performance, microbial community and functional genes were investigated. It was found that maximum denitrification rates of 0.37, 0.46 and 0.39gN/(L·d) were achieved in PHBV/PLA, glucose and CH3 COONa supported denitrification systems, respectively...
April 5, 2018: Science of the Total Environment
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