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https://www.readbyqxmd.com/read/28397264/population-densities-of-indigenous-acidobacteria-change-in-the-presence-of-plant-growth-promoting-rhizobacteria-pgpr-in-rhizosphere
#1
Sadaf Kalam, Subha Narayan Das, Anirban Basu, Appa Rao Podile
Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members...
April 11, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28363969/simulated-ribosomal-rna-dna-ratios-show-potential-to-misclassify-active-populations-as-dormant
#2
Blaire Steven, Cedar Hesse, John Soghigian, La Verne Gallegos-Graves, John Dunbar
The use of ribosomal RNA:DNA ratios derived from surveys of rRNA sequences in RNA and DNA extracts is an appealing but poorly validated approach to infer the activity status of environmental microbes. To improve interpretation of rRNA:DNA ratios, we performed simulations to investigate the effect of community structure, rRNA amplification, and sampling depth on the accuracy of rRNA:DNA ratios in classifying bacterial populations as "active" or "dormant". Community structure was an insignificant factor. In contrast, the extent of rRNA amplification that occurs as cells transition from dormant to growing had a significant effect (p < 0...
March 31, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28358811/alterations-in-airway-microbiota-in-patients-with-pao2-fio2-ratio-%C3%A2-300-after-burn-and-inhalation-injury
#3
Dana M Walsh, Shaun D McCullough, Scott Yourstone, Samuel W Jones, Bruce A Cairns, Corbin D Jones, Ilona Jaspers, David Diaz-Sanchez
BACKGROUND: Injury to the airways after smoke inhalation is a major mortality risk factor in victims of burn injuries, resulting in a 15-45% increase in patient deaths. Damage to the airways by smoke may induce acute respiratory distress syndrome (ARDS), which is partly characterized by hypoxemia in the airways. While ARDS has been associated with bacterial infection, the impact of hypoxemia on airway microbiota is unknown. Our objective was to identify differences in microbiota within the airways of burn patients who develop hypoxemia early after inhalation injury and those that do not using next-generation sequencing of bacterial 16S rRNA genes...
2017: PloS One
https://www.readbyqxmd.com/read/28347280/comparison-of-two-commercial-broad-range-pcr-and-sequencing-assays-for-identification-of-bacteria-in-culture-negative-clinical-samples
#4
Camilla Stavnsbjerg, Niels Frimodt-Møller, Claus Moser, Thomas Bjarnsholt
BACKGROUND: Culturing has long been the gold standard for detecting aetiologic agents in bacterial infections. In some cases, however, culturing fails to detect the infection. To further investigate culture-negative samples, amplification and subsequent sequencing of the 16S rRNA gene is often applied. The aim of the present study was to compare the current method used at our Department of Clinical Microbiology, based on the MicroSeq ID system (Applied Biosystems, USA) with the Universal Microbe Detection (UMD) SelectNA kit (Molzym, Germany)...
March 27, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28346925/microbiota-and-necrotizing-enterocolitis
#5
Sanjay Patole
Necrotizing enterocolitis (NEC) is an acquired gastrointestinal inflammatory condition with significant mortality and morbidity in preterm very low birth weight infants. The interplay between toll-like receptors, bacterial endotoxins, developmentally regulated excessive proinflammatory responses of the immature innate immune system, hypoxia, ischemia, reperfusion, free radicals, and the presence of substrates and bacterial endotoxins is thought to play an important role in the pathogenesis of NEC. The association (cause?) of various microbes (bacteria, viruses, and fungi) with NEC has intrigued researchers for many years...
2017: Nestlé Nutrition Institute Workshop Series
https://www.readbyqxmd.com/read/28330232/high-quality-metagenomic-dna-from-marine-sediment-samples-for-genomic-studies-through-a-preprocessing-approach
#6
Solly Solomon, Bhavya Kachiprath, G Jayanath, T P Sajeevan, I S Bright Singh, Rosamma Philip
Recent advances in culture-independent studies of microbes had proved to be more reliable and efficient than the conventional ones. The isolation of good quality and quantity of total community DNA are one of the major hurdles in this endeavour. Shearing of DNA during the extraction process and the co-extraction of inhibitory compounds reduce the quality of the isolated nucleic acids making it unsuitable for the construction of large insert metagenomic libraries. In the present study, a multi-level filtration step was brought in which efficiently isolated total bacterial DNA from three different environment samples...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28282386/strong-incidence-of-pseudomonas-aeruginosa-on-bacterial-rrs-and-its-genetic-structures-of-cystic-fibrosis-sputa
#7
Laurence Pages-Monteiro, Romain Marti, Carine Commun, Nolwenn Alliot, Claire Bardel, Helene Meugnier, Michele Perouse-de-Montclos, Philippe Reix, Isabelle Durieu, Stephane Durupt, Francois Vandenesch, Jean Freney, Benoit Cournoyer, Anne Doleans-Jordheim
Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P...
2017: PloS One
https://www.readbyqxmd.com/read/28177784/effects-of-several-in-feed-antibiotic-combinations-on-the-abundance-and-diversity-of-fecal-microbes-in-weaned-pigs
#8
Huizhi Li, Tingting Liang, Qingpo Chu, Feilong Xu, Yuan Li, Lingling Fu, Bo Zhou
To characterize the effects of several subtherapeutic antibiotic combinations on the abundance and diversity of fecal microbes, 400 weaned pigs were selected and randomly assigned to 8 groups, where they were continuously fed different antibiotic combinations for 28 days. Then, a total of 48 pigs were randomly selected to individually collect the feces for DNA extraction and 16S rRNA high-throughput sequencing. Compared with the pigs without antibiotic administration, the diversities of fecal microbes were decreased in the pigs fed chlortetracycline (CTC), olaquindox (OLA) and enramycin (ER)/ virginiamycin (VIR), where the relative abundance of the phymum Bacteroidetes and the genus Prevotella were increased...
January 24, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28174737/metagenomic-characterization-of-microbial-communities-in-situ-within-the-deeper-layers-of-the-ileum-in-crohn-s-disease
#9
Chandra Sekhar Pedamallu, Ami S Bhatt, Susan Bullman, Sharyle Fowler, Samuel S Freeman, Jacqueline Durand, Joonil Jung, Fujiko Duke, Veronica Manzo, Diana Cai, Ashwin Ananthakrishnan, Akinyemi I Ojesina, Aruna Ramachandran, Dirk Gevers, Ramnik J Xavier, Atul K Bhan, Matthew Meyerson, Vijay Yajnik
BACKGROUND & AIMS: Microbial dysbiosis and aberrant host-microbe interactions in the gut are believed to contribute to the development and progression of Crohn's disease (CD). Microbiome studies in CD typically have focused on microbiota in feces or superficial mucosal layers of the colon because accessing DNA from deeper layers of the bowel is challenging. In this study, we analyzed the deep tissue microbiome in patients who underwent surgical resection of the small intestine. METHODS: Paraffin blocks were obtained from 12 CD patients undergoing ileocecal resection, and healthy ileum samples (inflammatory bowel disease-free controls) were obtained from 12 patients undergoing surgery for right-sided colon cancer...
September 2016: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28161601/messages-from-the-first-international-conference-on-clinical-metagenomics-iccmg
#10
Etienne Ruppé, Gilbert Greub, Jacques Schrenzel
Metagenomics is recently entering in the clinical microbiology and an increasing number of diagnostic laboratories are now proposing the sequencing & annotation of bacterial genomes and/or the analysis of clinical samples by direct or PCR-based metagenomics with short time to results. In this context, the first International Conference on Clinical Metagenomics (ICCMg) was held in Geneva in October 2016 and several key aspects have been discussed including: i) the need for improved resolution, ii) the importance of interpretation given the common occurrence of sequence contaminants, iii) the need for improved bioinformatic pipelines, iv) the bottleneck of DNA extraction, v) the importance of gold standards, vi) the need to further reduce time to results, vii) how to improve data sharing, viii) the applications of bacterial genomics and clinical metagenomics in better adapting therapeutics and ix) the impact of metagenomics and new sequencing technologies in discovering new microbes...
February 1, 2017: Microbes and Infection
https://www.readbyqxmd.com/read/28125031/phylogenetic-heatmaps-highlight-composition-biases-in-sequenced-reads
#11
Sulbha Choudhari, Andrey Grigoriev
Due to advancements in sequencing technology, sequence data production is no longer a constraint in the field of microbiology and has made it possible to study uncultured microbes or whole environments using metagenomics. However, these new technologies introduce different biases in metagenomic sequencing, affecting the nucleotide distribution of resulting sequence reads. Here, we illustrate such biases using two methods. One is based on phylogenetic heatmaps (PGHMs), a novel approach for compact visualization of sequence composition differences between two groups of sequences containing the same phylogenetic groups...
January 24, 2017: Microorganisms
https://www.readbyqxmd.com/read/28070089/development-of-a-one-run-real-time-pcr-detection-system-for-pathogens-associated-with-bovine-respiratory-disease-complex
#12
Mai Kishimoto, Shinobu Tsuchiaka, Sayed Samim Rahpaya, Ayako Hasebe, Keiko Otsu, Satoshi Sugimura, Suguru Kobayashi, Natsumi Komatsu, Makoto Nagai, Tsutomu Omatsu, Yuki Naoi, Kaori Sano, Sachiko Okazaki-Terashima, Mami Oba, Yukie Katayama, Reiichiro Sato, Tetsuo Asai, Tetsuya Mizutani
Bovine respiratory disease complex (BRDC) is frequently found in cattle worldwide. The etiology of BRDC is complicated by infections with multiple pathogens, making identification of the causal pathogen difficult. Here, we developed a detection system by applying TaqMan real-time PCR (Dembo respiratory-PCR) to screen a broad range of microbes associated with BRDC in a single run. We selected 16 bovine respiratory pathogens (bovine viral diarrhea virus, bovine coronavirus, bovine parainfluenza virus 3, bovine respiratory syncytial virus, influenza D virus, bovine rhinitis A virus, bovine rhinitis B virus, bovine herpesvirus 1, bovine adenovirus 3, bovine adenovirus 7, Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, Trueperella pyogenes, Mycoplasma bovis and Ureaplasma diversum) as detection targets and designed novel specific primer-probe sets for nine of them...
March 18, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28005056/new-crispr-cas-systems-from-uncultivated-microbes
#13
David Burstein, Lucas B Harrington, Steven C Strutt, Alexander J Probst, Karthik Anantharaman, Brian C Thomas, Jennifer A Doudna, Jillian F Banfield
CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped...
February 9, 2017: Nature
https://www.readbyqxmd.com/read/28004217/lactobacillus-kefiri-shows-inter-strain-variations-in-the-amino-acid-sequence-of-the-s-layer-proteins
#14
Mariano Malamud, Paula Carasi, Sílvia Bronsoms, Sebastián A Trejo, María de Los Angeles Serradell
The S-layer is a proteinaceous envelope constituted by subunits that self-assemble to form a two-dimensional lattice that covers the surface of different species of Bacteria and Archaea, and it could be involved in cell recognition of microbes among other several distinct functions. In this work, both proteomic and genomic approaches were used to gain knowledge about the sequences of the S-layer protein (SLPs) encoding genes expressed by six aggregative and sixteen non-aggregative strains of potentially probiotic Lactobacillus kefiri...
April 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27988129/source-of-supplemental-dietary-copper-zinc-and-manganese-affects-fecal-microbial-relative-abundance-in-lactating-dairy-cows
#15
M J Faulkner, B A Wenner, L M Solden, W P Weiss
Appropriate trace mineral supplementation can improve immune response and hoof health in cattle and at much higher rates of supplementation to swine and poultry can alter microbial colonization of the gut, resulting in improved gut health. Diet can influence fecal microbial excretion in cattle, and the fecal microbiome may serve as a means for assessing gastrointestinal microbial changes. We hypothesized that feeding diets that differed in source of supplemental Cu, Zn, or Mn would alter the relative abundance of fecal microbes in lactating dairy cattle and that organic Zn would have the greatest effect...
February 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/27888152/an-improved-methodology-to-overcome-key-issues-in-human-fecal-metagenomic-dna-extraction
#16
Jitendra Kumar, Manoj Kumar, Shashank Gupta, Vasim Ahmed, Manu Bhambi, Rajesh Pandey, Nar Singh Chauhan
Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight (>23kb) metagenomic DNA (260/280 ratio >1...
December 2016: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/27829577/chronic-early-life-stress-in-rat-pups-alters-basal-corticosterone-intestinal-permeability-and-fecal-microbiota-at-weaning-influence-of-sex
#17
Nabila Moussaoui, Jonathan P Jacobs, Muriel Larauche, Mandy Biraud, Mulugeta Million, Emeran Mayer, Yvette Taché
Background/Aims: Wistar rat dams exposed to limited nesting stress (LNS) from post-natal days (PND) 2 to 10 display erratic maternal behavior, and their pups show delayed maturation of the hypothalamic-pituitary-adrenal axis and impaired epithelial barrier at PND10 and a visceral hypersensitivity at adulthood. Little is known about the impact of early life stress on the offspring before adulthood and the influence of sex. We investigated whether male and female rats previously exposed to LNS displays at weaning altered corticosterone, intestinal permeability, and microbiota...
January 30, 2017: Journal of Neurogastroenterology and Motility
https://www.readbyqxmd.com/read/27762069/an-introduction-to-microbiome-analysis-for-human-biology-applications
#18
Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
https://www.readbyqxmd.com/read/27754286/br-07-1-development-of-the-cell-microarray-for-high-throughput-analysis-of-gut-microbiota
#19
Seong-Tshool Hong
The human intestine contains a massive and complex microbial community called gut microbiota. A typical human carries 100 trillion microbes in his/her body which is 10 times greater than the number of their host cells, i.e. whole number of human cells. A combined microbial genome constituting gut microbiota is well excess our own human genome. The microbial composition of gut microbiotata and its role on diseases became a booming area of research, presenting a new paradigm of opportunities for modern medicines...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27720803/the-gut-microbiota-contributes-to-a-mouse-model-of-spontaneous-bile-duct-inflammation
#20
Elisabeth Schrumpf, Martin Kummen, Laura Valestrand, Thomas U Greiner, Kristian Holm, Velmurugesan Arulampalam, Henrik M Reims, John Baines, Fredrik Bäckhed, Tom H Karlsen, Richard S Blumberg, Johannes R Hov, Espen Melum
BACKGROUND & AIMS: A strong association between human inflammatory biliary diseases and gut inflammation has led to the hypothesis that gut microbes and lymphocytes activated in the intestine play a role in biliary inflammation. The NOD.c3c4 mouse model develops spontaneous biliary inflammation in extra- and intrahepatic bile ducts. We aimed to clarify the role of the gut microbiota in the biliary disease of NOD.c3c4 mice. METHODS: We sampled cecal content and mucosa from conventionally raised (CONV-R) NOD...
February 2017: Journal of Hepatology
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