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Microbiome bioinformatics

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https://www.readbyqxmd.com/read/29780371/comparative-metatranscriptomics-of-wheat-rhizosphere-microbiomes-in-disease-suppressive-and-non-suppressive-soils-for-rhizoctonia-solani-ag8
#1
Helen L Hayden, Keith W Savin, Jenny Wadeson, Vadakattu V S R Gupta, Pauline M Mele
The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29774014/oral-microbiota-community-dynamics-associated-with-oral-squamous-cell-carcinoma-staging
#2
Chia-Yu Yang, Yuan-Ming Yeh, Hai-Ying Yu, Chia-Yin Chin, Chia-Wei Hsu, Hsuan Liu, Po-Jung Huang, Song-Nian Hu, Chun-Ta Liao, Kai-Ping Chang, Yu-Liang Chang
Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29765908/the-subgingival-microbiome-of-periodontal-pockets-with-different-probing-depths-in-chronic-and-aggressive-periodontitis-a-pilot-study
#3
Meng Shi, Yiping Wei, Wenjie Hu, Yong Nie, Xiaolei Wu, Ruifang Lu
Periodontitis is a kind of infectious disease initiated by colonization of subgingival periodontal pathogens, which cause destruction of tooth-supporting tissues, and is a predominant threat to oral health as the most common cause of loss of teeth. The aim of this pilot study was to characterize the subgingival bacterial biodiversity of periodontal pockets with different probing depths in patients with different forms of periodontitis. Twenty-one subgingival plaque samples were collected from three patients with chronic periodontitis (ChP), three patients with aggressive periodontitis (AgP) and three periodontally healthy subjects (PH)...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29755427/16s-rrna-gene-sequencing-for-deciphering-the-colorectal-cancer-gut-microbiome-current-protocols-and-workflows
#4
REVIEW
Muhammad-Afiq Osman, Hui-Min Neoh, Nurul-Syakima Ab Mutalib, Siok-Fong Chin, Rahman Jamal
The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29750384/effects-of-moderate-voluntary-ethanol-consumption-on-the-rat-and-human-gut-microbiome
#5
Kassi L Kosnicki, Jerrold C Penprase, Patricia Cintora, Pedro J Torres, Greg L Harris, Susan M Brasser, Scott T Kelley
Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans...
May 11, 2018: Addiction Biology
https://www.readbyqxmd.com/read/29703739/-tuf-gene-sequence-variation-in-bifidobacterium-longum-subspecies-infantis-detected-in-the-fecal-microbiota-of-chinese-infants
#6
Blair Lawley, Manuela Centanni, Jun Watanabe, Ian Sims, Susan Carnachan, Roland Broadbent, Pheng Soon Lee, Khai Hong Wong, Gerald W Tannock
Members of the bacterial genus Bifidobacterium generally dominate the faecal microbiota of infants. The species B. longum is prevalent, but the subspecies longum and infantis that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacity to metabolize Human Milk Oligosaccharides (HMO) and may have differing ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms...
April 27, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29700993/discovery-of-antimicrobial-lipodepsipeptides-produced-by-a-serratia-sp-within-mosquito-microbiomes
#7
Jack Ganley, Gavin Carr, Thomas Ioerger, James Sacchettini, Jon Clardy, Emily Derbyshire
The Anopheles mosquito that harbors the Plasmodium parasite contains a microbiota that can influence both the vector and parasite. In recent years, insect-associated microbes have highlighted the untapped potential of exploiting interspecies interactions to discover bioactive compounds. In this study, we report the discovery of nonribosomal lipodepsipeptides that are produced by a Serratia sp. within the midgut and salivary glands of A. stephensi mosquitoes. The lipodepsipeptides, stephensiolides A-K, have antibiotic activity and facilitate bacterial surface motility...
April 26, 2018: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29682676/how-human-microbiome-talks-to-health-and-disease
#8
REVIEW
Jing Cong, Xiaochun Zhang
Microbes are ubiquitous in the human body. They usually live in communities, and each of these communities has a distinct taxonomical structure. Due to its close relationship with human health and disease, the human microbiome has received great attention and is probably considered to be the most valuable biomarker in preventing and solving human diseases. In this paper, we first review the value of the human microbiome. Then, we focus on the role of the human microbiome in influencing human health and disease...
April 22, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29668831/using-standard-microbiome-reference-groups-to-simplify-beta-diversity-analyses-and-facilitate-independent-validation
#9
Marlena Maziarz, Ruth M Pfeiffer, Yunhu Wan, Mitchell H Gail
Motivation: Comparisons of microbiome communities across populations are often based on pairwise distance measures (beta-diversity). Standard analyses (principal coordinate plots, permutation tests, kernel methods) require access to primary data if another investigator wants to add or compare independent data.We propose using standard reference measurements to simplify microbiome beta-diversity analyses, to make them more transparent, and to facilitate independent validation and comparisons across studies...
April 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29666626/next-generation-immune-repertoire-sequencing-as-a-clue-to-elucidate-the-landscape-of-immune-modulation-by-host-gut-microbiome-interactions
#10
Tatsuo Ichinohe, Takahiko Miyama, Takakazu Kawase, Yasuko Honjo, Kazutaka Kitaura, Hiroyuki Sato, Tadasu Shin-I, Ryuji Suzuki
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29665003/the-inside-tract-the-appendicular-cecal-and-colonic-microbiome-of-captive-aye-ayes
#11
Lydia K Greene, Erin A McKenney
OBJECTIVES: The aye-aye (Daubentonia madagascariensis) is famous for its feeding strategies that target structurally defended, but high-quality resources. Nonetheless, the influence of this digestible diet on gut microbial contributions to aye-aye metabolism and nutrition remains unexplored. When four captive aye-ayes were unexpectedly lost to persin toxicity, we opportunistically collected samples along the animals' gastrointestinal tracts. Here we describe the diversity and composition of appendicular, cecal, and colonic consortia relative to the aye-aye's unusual feeding ecology...
April 17, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29660711/the-rhizosphere-microbiome-significance-in-rhizoremediation-of-polyaromatic-hydrocarbon-contaminated-soil
#12
REVIEW
Rhitu Kotoky, Jina Rajkumari, Piyush Pandey
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation...
April 13, 2018: Journal of Environmental Management
https://www.readbyqxmd.com/read/29657970/nonpareil-3-fast-estimation-of-metagenomic-coverage-and-sequence-diversity
#13
Luis M Rodriguez-R, Santosh Gunturu, James M Tiedje, James R Cole, Konstantinos T Konstantinidis
Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations of diversity. For instance, the completeness of reference databases cannot be generally estimated since it depends on the extant diversity sampled to date, which, with the exception of a few habitats such as the human gut, remains severely undersampled. Further, estimation of the degree of coverage of a microbial community by a metagenomic data set is prohibitively time-consuming for large data sets, and coverage values may not be directly comparable between data sets obtained with different sequencing technologies...
May 2018: MSystems
https://www.readbyqxmd.com/read/29629420/exploring-linkages-between-taxonomic-and-functional-profiles-of-the-human-microbiome
#14
Morgan G I Langille
Microbiome studies typically focus on characterizing the taxonomic and functional profiles of the microbes within a community. Functional profiling is generally thought to be superior to taxonomic profiling for investigating human-microbe interactions, but there are several limitations and challenges to existing approaches. This Perspective discusses the current sequencing and bioinformatic methods for producing taxonomic and functional profiles, recent studies utilizing and comparing these technologies, and the existing challenges and limitations of these data...
March 2018: MSystems
https://www.readbyqxmd.com/read/29618009/constructing-lightweight-and-flexible-pipelines-using-plugin-based-microbiome-analysis-pluma
#15
Trevor Cickovski, Giri Narasimhan
Motivation: Software pipelines have become almost standardized tools for microbiome analysis. Currently many pipelines are available, often sharing some of the same algorithms as stages. This is largely because each pipeline has its own source language and file formats, making it typically more economical to reinvent the wheel than to learn and interface to an existing package. We present PluMA, or Plugin-Based Microbiome Analysis, which addresses this problem by providing a lightweight back end that can be infinitely extended using dynamically loaded plugin extensions...
March 29, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29577086/katharoseq-enables-high-throughput-microbiome-analysis-from-low-biomass-samples
#16
Jeremiah J Minich, Qiyun Zhu, Stefan Janssen, Ryan Hendrickson, Amnon Amir, Russ Vetter, John Hyde, Megan M Doty, Kristina Stillwell, James Benardini, Jae H Kim, Eric E Allen, Kasthuri Venkateswaran, Rob Knight
Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), that outperforms single-tube extractions while processing at least five times as fast. KatharoSeq incorporates positive and negative controls to reveal the whole bacterial community from inputs of as few as 50 cells and correctly identifies 90...
May 2018: MSystems
https://www.readbyqxmd.com/read/29554948/species-classifier-choice-is-a-key-consideration-when-analysing-low-complexity-food-microbiome-data
#17
Aaron M Walsh, Fiona Crispie, Orla O'Sullivan, Laura Finnegan, Marcus J Claesson, Paul D Cotter
BACKGROUND: The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species...
March 20, 2018: Microbiome
https://www.readbyqxmd.com/read/29531234/influence-of-fecal-collection-conditions-and-16s-rrna-gene-sequencing-at-two-centers-on-human-gut-microbiota-analysis
#18
Jocelyn Sietsma Penington, Megan A S Penno, Katrina M Ngui, Nadim J Ajami, Alexandra J Roth-Schulze, Stephen A Wilcox, Esther Bandala-Sanchez, John M Wentworth, Simon C Barry, Cheryl Y Brown, Jennifer J Couper, Joseph F Petrosino, Anthony T Papenfuss, Leonard C Harrison
To optimise fecal sampling for reproducible analysis of the gut microbiome, we compared different methods of sample collection and sequencing of 16S rRNA genes at two centers. Samples collected from six individuals on three consecutive days were placed in commercial collection tubes (OMNIgeneGut OMR-200) or in sterile screw-top tubes in a home fridge or home freezer for 6-24 h, before transfer and storage at -80 °C. Replicate samples were shipped to centers in Australia and the USA for DNA extraction and sequencing by their respective PCR protocols, and analysed with the same bioinformatic pipeline...
March 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29523751/does-the-microbiome-and-virome-contribute-to-myalgic-encephalomyelitis-chronic-fatigue-syndrome
#19
REVIEW
Fiona Newberry, Shen-Yuan Hsieh, Tom Wileman, Simon R Carding
Myalgic encephalomyelitis (ME)/chronic fatigue syndrome (CFS) (ME/CFS) is a disabling and debilitating disease of unknown aetiology. It is a heterogeneous disease characterized by various inflammatory, immune, viral, neurological and endocrine symptoms. Several microbiome studies have described alterations in the bacterial component of the microbiome (dysbiosis) consistent with a possible role in disease development. However, in focusing on the bacterial components of the microbiome, these studies have neglected the viral constituent known as the virome...
March 15, 2018: Clinical Science (1979-)
https://www.readbyqxmd.com/read/29503702/acid-resistant-genes-of-oral-plaque-microbiome-from-the-functional-metagenomics
#20
Meng Zhang, Yuqiao Zheng, Yuhong Li, Han Jiang, Yuping Huang, Minquan Du
Acid resistance is one of key properties assisting the survival of cariogenic bacteria in a dental caries environment, but only a few genes conferring acid resistance have been identified to data. Functional metagenomics provides a systematic method for investigating commensal DNA to identify genes that encode target functions. Here, the host strain Escherichia coli DH10B and a constructed bidirectional transcription vector pSKII+ -lacZ contributed to the construction of a metagenomic library, and 46.6 Mb of metagenomic DNA was cloned from carious supragingival plaque of 8children along with screening for lethal functionality...
2018: Journal of Oral Microbiology
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