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Microbial genomics

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https://www.readbyqxmd.com/read/28934590/the-relationship-between-the-human-genome-and-microbiome-comes-into-view
#1
Julia K Goodrich, Emily R Davenport, Andrew G Clark, Ruth E Ley
The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28933075/-key-technologies-in-synthetic-biology-of-natural-products
#2
Xue-Jun Kuang, Li-Qiu Zou, Ying Li, Chao Sun, Shi-Lin Chen
Natural products with complex and diverse structures are the major sources of new drugs. The biosynthesis of natural products is considered to be one of the best ways to solve the problems of complex and scarce natural products. DNA assembly technology and genome editing technology are two key technologies in the emerging interdisciplinary field of synthetic biology. A number of novel DNA assembly methods developed in the last few years have paved the way for the engineering of high molecular weight DNA molecules, including whole genomes, hence, it can realize the reconstruction of the metabolic pathways and speed up optimization process...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932815/a-multicenter-study-to-evaluate-the-performance-of-high-throughput-sequencing-for-virus-detection
#3
Arifa S Khan, Siemon H S Ng, Olivier Vandeputte, Aisha Aljanahi, Avisek Deyati, Jean-Pol Cassart, Robert L Charlebois, Lanyn P Taliaferro
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics...
September 2017: MSphere
https://www.readbyqxmd.com/read/28931629/selinene-volatiles-are-essential-precursors-for-maize-defense-promoting-fungal-pathogen-resistance
#4
Yezhang Ding, Alisa Huffaker, Tobias G Köllner, Philipp Weckwerth, Christelle A M Robert, Joseph L Spencer, Alexander E Lipka, Eric A Schmelz
To ensure food security, maize (Zea mays) is a model crop for understanding useful traits underlying stress resistance. In contrast to foliar biochemicals, root defenses limiting the spread of disease remain poorly described. To better understand below-ground defenses in the field, we performed root metabolomic profiling and uncovered unexpectedly high levels of the sesquiterpene volatile β-selinene and the corresponding non-volatile antibiotic derivative, β-costic acid. The application of metabolite-based quantitative trait loci (mQTL) mapping using bi-parental populations, genome wide association studies, and near-isogenic lines (NILs) enabled the identification of terpene synthase 21 (ZmTps21) on chromosome 9 as a β-costic acid pathway candidate gene...
September 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28931373/improving-contig-binning-of-metagenomic-data-using-formula-see-text-oligonucleotide-frequency-dissimilarity
#5
Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
BACKGROUND: Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. RESULTS: According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes...
September 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28930530/genetic-organization-of-streptococcus-salivarius-24smbc-blp-like-bacteriocin-locus
#6
Maria Santagati, Marina Scillato, Stefania Stefani
In this paper, we describe, for the first time, the genetic organization of the blpU-like cassette in Streptococcus salivarius24SMBc by entire genome sequencing. This strain has recently been found useful and widely applied as an oral probiotic in the prevention of recurrent otitis media. The 24SMBc blpU-like cassette  is 8,023 bp in length, organized in 11 orfs,of which orf8 encodes for the pore-forming peptide bacteriocin, belonging to class IIc, with a double-glycine leader peptide. The first characterization of blplocus was described inStreptococcus pneumoniae, showing a crucial role in interspecies competition within the nasopharynx...
January 1, 2018: Frontiers in Bioscience (Scholar Edition)
https://www.readbyqxmd.com/read/28929383/evaluation-of-the-impact-of-six-different-dna-extraction-methods-for-the-representation-of-the-microbial-community-associated-with-human-chronic-wound-infections-using-a-gel-based-dna-profiling-method
#7
Ayomi Dilhari, Asanga Sampath, Chinthika Gunasekara, Neluka Fernando, Deepaka Weerasekara, Chris Sissons, Andrew McBain, Manjula Weerasekera
Infected chronic wounds are polymicrobial in nature which include a diverse group of aerobic and anaerobic microorganisms. Majority of these communal microorganisms are difficult to grow in vitro. DNA fingerprinting methods such as polymerase chain reaction-denaturation gradient gel electrophoresis (PCR-DGGE) facilitate the microbial profiling of complex ecosystems including infected chronic wounds. Six different DNA extraction methods were compared for profiling of the microbial community associated with chronic wound infections using PCR-DGGE...
September 19, 2017: AMB Express
https://www.readbyqxmd.com/read/28928752/climate-clever-clovers-new-paradigm-to-reduce-the-environmental-footprint-of-ruminants-by-breeding-low-methanogenic-forages-utilizing-haplotype-variation
#8
Parwinder Kaur, Rudi Appels, Philipp E Bayer, Gabriel Keeble-Gagnere, Jiankang Wang, Hideki Hirakawa, Kenta Shirasawa, Philip Vercoe, Katia Stefanova, Zoey Durmic, Phillip Nichols, Clinton Revell, Sachiko N Isobe, David Edwards, William Erskine
Mitigating methane production by ruminants is a significant challenge to global livestock production. This research offers a new paradigm to reduce methane emissions from ruminants by breeding climate-clever clovers. We demonstrate wide genetic diversity for the trait methanogenic potential in Australia's key pasture legume, subterranean clover (Trifolium subterraneum L.). In a bi-parental population the broadsense heritability in methanogenic potential was moderate (H(2) = 0.4) and allelic variation in a region of Chr 8 accounted for 7...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#9
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28927699/biochemical-mechanisms-of-pathogen-restriction-by-intestinal-bacteria
#10
REVIEW
Kavita J Rangan, Howard C Hang
The intestine is a highly complex ecosystem where many bacterial species interact with each other and host cells to influence animal physiology and susceptibility to pathogens. Genomic methods have provided a broad framework for understanding how alterations in microbial communities are associated with host physiology and infection, but the biochemical mechanisms of specific intestinal bacterial species are only emerging. In this review, we focus on recent studies that have characterized the biochemical mechanisms by which intestinal bacteria interact with other bacteria and host pathways to restrict pathogen infection...
September 16, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28927397/detection-of-bacterial-pathogens-from-clinical-specimens-using-conventional-microbial-culture-and-16s-metagenomics-a-comparative-study
#11
Lalanika M Abayasekara, Jennifer Perera, Vishvanath Chandrasekharan, Vaz S Gnanam, Nisala A Udunuwara, Dileepa S Liyanage, Nuwani E Bulathsinhala, Subhashanie Adikary, Janith V S Aluthmuhandiram, Chrishanthi S Thanaseelan, D Portia Tharmakulasingam, Tharaga Karunakaran, Janahan Ilango
BACKGROUND: Infectious disease is the leading cause of death worldwide, and diagnosis of polymicrobial and fungal infections is increasingly challenging in the clinical setting. Conventionally, molecular detection is still the best method of species identification in clinical samples. However, the limitations of Sanger sequencing make diagnosis of polymicrobial infections one of the biggest hurdles in treatment. The development of massively parallel sequencing or next generation sequencing (NGS) has revolutionized the field of metagenomics, with wide application of the technology in identification of microbial communities in environmental sources, human gut and others...
September 19, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28925595/determination-of-crassphage-in-water-samples-and-applicability-for-tracking-human-faecal-pollution
#12
Cristina García-Aljaro, Elisenda Ballesté, Maite Muniesa, Juan Jofre
In recent decades, considerable effort has been devoted to finding microbial source-tracking (MST) markers that are suitable to assess the health risks of faecally polluted waters, with no universal marker reported so far. In this study, the abundance and prevalence of a crAssphage-derived DNA marker in wastewaters of human and animal origins were studied by a new qPCR assay with the ultimate aim of assessing its potential as an MST marker. crAssphage showed up to 10(6) GC/ml in the sewage samples of human origin, in both the total DNA and the viral DNA fraction...
September 19, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28924834/diversity-of-family-gh46-chitosanases-in-kitasatospora-setae-km-6054
#13
Mina Zitouni, Pascal Viens, Mariana G Ghinet, Ryszard Brzezinski
The genome of Kitasatospora setae KM-6054, a soil actinomycete, has three genes encoding chitosanases belonging to GH46 family. The genes (csn1-3) were cloned in Streptomyces lividans and the corresponding enzymes were purified from the recombinant cultures. The csn2 clone yielded two proteins (Csn2BH and Csn2H) differing by the presence of a carbohydrate-binding domain. Sequence analysis showed that Csn1 and Csn2H were canonical GH46 chitosanases, while Csn3 resembled chitosanases from bacilli. The activity of the four chitosanases was tested in a variety of conditions and on diverse chitosan forms, including highly N-deacetylated chitosan or chitosan complexed with humic or polyphosphoric acid...
September 18, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28924496/challenging-a-bioinformatic-tool-s-ability-to-detect-microbial-contaminants-using-in-silico-whole-genome-sequencing-data
#14
Nathan D Olson, Justin M Zook, Jayne B Morrow, Nancy J Lin
High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives...
2017: PeerJ
https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#15
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28921406/genome-annotation-and-validation-of-keratin-hydrolyzing-proteolytic-enzymes-from-serratia-marcescens-egd-hp20
#16
Priya Fuke, Vaibhav V Gujar, Anshuman A Khardenavis
Stabilization and utilization of poultry waste demand efficient biodegradation either by mixture of enzymes or by microbial system that can produce different types of protein-hydrolyzing enzymes. For utilization of this keratinous biomass, in the present study, genome was sequenced and annotated for a bacterium having multiple enzymatic options for hydrolysis of different soluble and insoluble protein fractions of poultry waste. Among the soluble protein substrates, optimum production of enzyme and soluble protein was observed in case of casein, whereas among the insoluble protein substrates, maximum production of enzyme was achieved when broken nails were used...
September 18, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28919884/secretome-of-intestinal-bacilli-a-natural-guard-against-pathologies
#17
REVIEW
Olga N Ilinskaya, Vera V Ulyanova, Dina R Yarullina, Ilgiz G Gataullin
Current studies of human gut microbiome usually do not consider the special functional role of transient microbiota, although some of its members remain in the host for a long time and produce broad spectrum of biologically active substances. Getting into the gastrointestinal tract (GIT) with food, water and probiotic preparations, two representatives of Bacilli class, genera Bacillus and Lactobacillus, colonize epithelium blurring the boundaries between resident and transient microbiota. Despite their minor proportion in the microbiome composition, these bacteria can significantly affect both the intestinal microbiota and the entire body thanks to a wide range of secreted compounds...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28917182/analysis-of-functional-genomes-from-metagenomes-revealing-the-accelerated-electron-transfer-in-microbial-fuel-cell-with-rhamnolipid-addition
#18
Yunshu Zhang, Junqiu Jiang, Qingliang Zhao, Kun Wang, Hang Yu
Extracellular electron transfer is the predominant electricity generation process in microbial fuel cells (MFCs). Our pervious study have proved that the anodic adsorption of rhamnolipid resulted in the Frumkin effect, which enhanced anodic microorganism attachment and accelerated anodic electron transfer. In this study, an in-depth research on the influence of rhamnolipid on functional genes of anodic biofilms metagenomes was carried out to explain its mechanism at the gene level. The result showed that the composition and distribution of functional genes in each dominant genus were different...
September 11, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28917117/anaerobic-granular-sludge-for-simultaneous-biomethanation-of-synthetic-wastewater-and-co-with-focus-on-the-identification-of-co-converting-microorganisms
#19
Yuhang Jing, Stefano Campanaro, Panagiotis Kougias, Laura Treu, Irini Angelidaki, Shicheng Zhang, Gang Luo
CO is a main component of syngas, which can be produced from the gasification of organic wastes and biomass. CO can be converted to methane by anaerobic digestion (AD), however, it is still challenging due to its toxicity to microorganisms and limited knowledge about CO converting microorganisms. In the present study, anaerobic granular sludge (AGS) was used for the simultaneous biomethanation of wastewater and CO. Batch experiments showed that AGS tolerated CO partial pressure as high as 0.5 atm without affecting its ability for synthetic wastewater degradation, which had higher tolerance of CO compared to suspended sludge (less than 0...
September 9, 2017: Water Research
https://www.readbyqxmd.com/read/28912952/noncontiguous-finished-genome-sequences-and-descriptions-of-paenibacillus-bouchesdurhonensis-paenibacillus-rubinfantis-paenibacillus-senegalimassiliensis-and-paenibacillus-tuaregi-identified-by-culturomics
#20
T-P-T Pham, M Tidjani Alou, S I Traore, S Brah, B Ali Diallo, A Diallo, C Sokhna, E Baptiste, A Levasseur, P-E Fournier, F Cadoret, D Raoult
Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: 'Paenibacillus bouchesdurhonensis' strain Marseille-P3071(T), 'Paenibacillus rubinfantis' strain MT18(T), 'Paenibacillus senegalimassiliensis' strain SIT18(T) and 'Paenibacillus tuaregi' strain Marseille-P2472(T), which are all facultatively aerobic and Gram-positive bacilli...
November 2017: New Microbes and New Infections
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