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Whole genome sequence microbiome

Philippe Chouvarine, Lutz Wiehlmann, Patricia Moran Losada, David S DeLuca, Burkhard Tümmler
Ever-increasing affordability of next-generation sequencing makes whole-metagenome sequencing an attractive alternative to traditional 16S rDNA, RFLP, or culturing approaches for the analysis of microbiome samples. The advantage of whole-metagenome sequencing is that it allows direct inference of the metabolic capacity and physiological features of the studied metagenome without reliance on the knowledge of genotypes and phenotypes of the members of the bacterial community. It also makes it possible to overcome problems of 16S rDNA sequencing, such as unknown copy number of the 16S gene and lack of sufficient sequence similarity of the "universal" 16S primers to some of the target 16S genes...
2016: PloS One
Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here we addressed these questions in the rumen microbiome ecosystem - a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes...
October 1, 2016: Environmental Microbiology
Ericka L Anderson, Weizhong Li, Niels Klitgord, Sarah K Highlander, Mark Dayrit, Victor Seguritan, Shibu Yooseph, William Biggs, J Craig Venter, Karen E Nelson, Marcus B Jones
As reports on possible associations between microbes and the host increase in number, more meaningful interpretations of this information require an ability to compare data sets across studies. This is dependent upon standardization of workflows to ensure comparability both within and between studies. Here we propose the standard use of an alternate collection and stabilization method that would facilitate such comparisons. The DNA Genotek OMNIgene∙Gut Stool Microbiome Kit was compared to the currently accepted community standard of freezing to store human stool samples prior to whole genome sequencing (WGS) for microbiome studies...
2016: Scientific Reports
Liyi Xu, Ilana L Brito, Eric J Alm, Paul C Blainey
We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial cells and human microbiome samples in the virtual microfluidics system, and demonstrated whole-genome sequencing of single-cell MDA products with excellent coverage uniformity and markedly reduced chimerism compared with products of liquid MDA reactions...
September 2016: Nature Methods
Khemraj Budachetri, Daniel Gaillard, Jaclyn Williams, Nabanita Mukherjee, Shahid Karim
The gopher tortoise tick, Amblyomma tuberculatum, has a unique relationship with the gopher tortoise, Gopherus polyphemus, found in sandy habitats across the southeastern United States. We aimed to understand the overall bacterial community associated with A. tuberculatum while also focusing on spotted fever group Rickettsia. These tortoises in the Southern Mississippi region are a federally threatened species; therefore, we have carefully trapped the tortoises and removed the species-specific ticks attached to them...
October 2016: Ticks and Tick-borne Diseases
Sagar M Utturkar, W Nathan Cude, Michael S Robeson, Zamin K Yang, Dawn M Klingeman, Miriam L Land, Steve L Allman, Tse-Yuan S Lu, Steven D Brown, Christopher W Schadt, Mircea Podar, Mitchel J Doktycz, Dale A Pelletier
UNLABELLED: Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots...
September 15, 2016: Applied and Environmental Microbiology
Mitchell J Brittnacher, Sonya L Heltshe, Hillary S Hayden, Matthew C Radey, Eli J Weiss, Christopher J Damman, Timothy L Zisman, David L Suskind, Samuel I Miller
BACKGROUND: Comparative analysis of gut microbiomes in clinical studies of human diseases typically rely on identification and quantification of species or genes. In addition to exploring specific functional characteristics of the microbiome and potential significance of species diversity or expansion, microbiome similarity is also calculated to study change in response to therapies directed at altering the microbiome. Established ecological measures of similarity can be constructed from species abundances, however methods for calculating these commonly used ecological measures of similarity directly from whole genome shotgun (WGS) metagenomic sequence are lacking...
2016: PloS One
Moran Yassour, Tommi Vatanen, Heli Siljander, Anu-Maaria Hämäläinen, Taina Härkönen, Samppa J Ryhänen, Eric A Franzosa, Hera Vlamakis, Curtis Huttenhower, Dirk Gevers, Eric S Lander, Mikael Knip, Ramnik J Xavier
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life...
June 15, 2016: Science Translational Medicine
M Malone, I B Gosbell, H G Dickson, K Vickery, B A Espedido, S O Jensen
Diabetes foot infections (DFI) are a common condition and a major causal pathway to lower extremity amputation. Identification of causative pathogens is vital in directing antimicrobial therapy. Historically, clinicians have relied upon culture-dependent techniques that are now acknowledged as both being selective for microorganisms that thrive under the physiological and nutritional constraints of the microbiology laboratory, and that grossly underestimate the microbial diversity of a sample. The amplification and sequence analysis of the 16S rRNA gene has revealed a diversity of microorganisms in DFIs, extending the view of the diabetic foot microbiome...
June 12, 2016: Diabetes/metabolism Research and Reviews
Matthew Thoendel, Patricio R Jeraldo, Kerryl E Greenwood-Quaintance, Janet Z Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel
Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus...
August 2016: Journal of Microbiological Methods
David W Collins, Harini V Gudiseva, Benjamin Trachtman, Anita S Bowman, Anna Sagaser, Prithvi Sankar, Eydie Miller-Ellis, Amanda Lehman, Victoria Addis, Joan M O'Brien
PURPOSE: To estimate the population frequencies of all common mitochondrial variants and ancestral haplogroups among 1,999 subjects recruited for the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study, including 1,217 primary open-angle glaucoma (POAG) cases and 782 controls, and to identify ancestral subpopulations and mitochondrial mutations as potential risk factors for POAG susceptibility. METHODS: Subject classification by characteristic glaucomatous optic nerve findings and corresponding visual field defects, as defined by enrolling glaucoma specialists, stereo disc photography, phlebotomy, extraction of total DNA from peripheral blood or saliva, DNA quantification and normalization, PCR amplification of whole mitochondrial genomes, Ion Torrent deep semiconductor DNA sequencing on DNA pools ("Pool-seq"), Sanger sequencing of 3,479 individual mitochondrial DNAs, and bioinformatic analysis...
2016: Molecular Vision
Emily Vogtmann, Xing Hua, Georg Zeller, Shinichi Sunagawa, Anita Y Voigt, Rajna Hercog, James J Goedert, Jianxin Shi, Peer Bork, Rashmi Sinha
Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population...
2016: PloS One
Hilary P Browne, Samuel C Forster, Blessing O Anonye, Nitin Kumar, B Anne Neville, Mark D Stares, David Goulding, Trevor D Lawley
Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown...
May 26, 2016: Nature
Dominick J Lemas, Bridget E Young, Peter R Baker, Angela C Tomczik, Taylor K Soderborg, Teri L Hernandez, Becky A de la Houssaye, Charles E Robertson, Michael C Rudolph, Diana Ir, Zachary W Patinkin, Nancy F Krebs, Stephanie A Santorico, Tiffany Weir, Linda A Barbour, Daniel N Frank, Jacob E Friedman
BACKGROUND: Increased maternal body mass index (BMI) is a robust risk factor for later pediatric obesity. Accumulating evidence suggests that human milk (HM) may attenuate the transfer of obesity from mother to offspring, potentially through its effects on early development of the infant microbiome. OBJECTIVES: Our objective was to identify early differences in intestinal microbiota in a cohort of breastfeeding infants born to obese compared with normal-weight (NW) mothers...
May 2016: American Journal of Clinical Nutrition
Heidi H Kong
The use of genomic sequencing to investigate microbes has expanded, yet it has also raised questions regarding optimal approaches to studying the skin microbiome. Meisel et al. show that while whole genome shotgun metagenomic sequences were most similar to expected microbial profiles, sequencing of the hypervariable regions V1-V3 of the 16S ribosomal RNA gene had greater accuracy than sequencing of the hypervariable region V4 in determining genus and species level classifications of prominent skin bacteria...
May 2016: Journal of Investigative Dermatology
Valeria D'Argenio, Giorgio Casaburi, Vincenza Precone, Chiara Pagliuca, Roberta Colicchio, Daniela Sarnataro, Valentina Discepolo, Sangman M Kim, Ilaria Russo, Giovanna Del Vecchio Blanco, David S Horner, Matteo Chiara, Graziano Pesole, Paola Salvatore, Giovanni Monteleone, Carolina Ciacci, Gregory J Caporaso, Bana Jabrì, Francesco Salvatore, Lucia Sacchetti
OBJECTIVES: Celiac disease (CD)-associated duodenal dysbiosis has not yet been clearly defined, and the mechanisms by which CD-associated dysbiosis could concur to CD development or exacerbation are unknown. In this study, we analyzed the duodenal microbiome of CD patients. METHODS: The microbiome was evaluated in duodenal biopsy samples of 20 adult patients with active CD, 6 CD patients on a gluten-free diet, and 15 controls by DNA sequencing of 16S ribosomal RNA libraries...
June 2016: American Journal of Gastroenterology
Christian Schulz, Kerstin Schütte, Peter Malfertheiner
The discovery of Helicobacter pylori changed the traditional view of the stomach as a hostile organ to bacterial survival. H. pylori induces chronic gastritis, which has the potential to progress to severe complications such as peptic ulcer disease and gastric neoplasia. The development of modern nucleotide sequencing techniques and new biocomputational tools allow the possibility of studying the diversity and complexity of the microbiome in the whole gastrointestinal (GI) tract and overcome the limitations of culturing techniques...
2016: Digestive Diseases
Daniel E Ross, Christopher W Marshall, Harold D May, R Sean Norman
Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance...
2016: PloS One
Maria J Soto-Giron, Luis M Rodriguez-R, Chengwei Luo, Michael Elk, Hodon Ryu, Jill Hoelle, Jorge W Santo Domingo, Konstantinos T Konstantinidis
Although the source of drinking water (DW) used in hospitals is commonly disinfected, biofilms forming on water pipelines are a refuge for bacteria, including possible pathogens that survive different disinfection strategies. These biofilm communities are only beginning to be explored by culture-independent techniques that circumvent the limitations of conventional monitoring efforts. Hence, theories regarding the frequency of opportunistic pathogens in DW biofilms and how biofilm members withstand high doses of disinfectants and/or chlorine residuals in the water supply remain speculative...
May 2016: Applied and Environmental Microbiology
Amanda L Prince, Jun Ma, Paranthaman S Kannan, Manuel Alvarez, Tate Gisslen, R Alan Harris, Emma L Sweeney, Christine L Knox, Donna S Lambers, Alan H Jobe, Claire A Chougnet, Suhas G Kallapur, Kjersti M Aagaard
BACKGROUND: Preterm birth (PTB) is a leading cause of neonatal morbidity and mortality and is not uncommonly associated with chorioamnionitis. We recently have demonstrated that the placenta harbors a unique microbiome with similar flora to the oral community. We also have shown an association of these placental microbiota with PTB, history of antenatal infection, and excess maternal weight gain. On the basis of these previous observations, we hypothesized that the placental membranes would retain a microbiome community that would vary in association with preterm birth and chorioamnionitis...
May 2016: American Journal of Obstetrics and Gynecology
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