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Microbiome

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https://www.readbyqxmd.com/read/27912796/staphylococcal-species-heterogeneity-in-the-nasal-microbiome-following-antibiotic-prophylaxis-revealed-by-tuf-gene-deep-sequencing
#1
Claire L McMurray, Katherine J Hardy, Szymon T Calus, Nicholas J Loman, Peter M Hawkey
BACKGROUND: Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient's risk of postoperative infection. The impact of surgical prophylaxis on the nasal staphylococcal microbiome is largely unknown. Here, we report the species present in the nasal staphylococcal microbiome and the impact of surgical prophylaxis revealed by a novel culture independent technique...
December 2, 2016: Microbiome
https://www.readbyqxmd.com/read/27912785/transmission-of-viruses-via-our-microbiomes
#2
Melissa Ly, Marcus B Jones, Shira R Abeles, Tasha M Santiago-Rodriguez, Jonathan Gao, Ivan C Chan, Chandrabali Ghose, David T Pride
BACKGROUND: Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the human body, but their ecology suggests they may be shared between close contacts. RESULTS: Here, we report the ecology of viruses in the guts and mouths of a cohort and demonstrate that substantial numbers of gut and oral viruses were shared amongst genetically unrelated, cohabitating individuals...
December 2, 2016: Microbiome
https://www.readbyqxmd.com/read/27884206/large-scale-benchmarking-reveals-false-discoveries-and-count-transformation-sensitivity-in-16s-rrna-gene-amplicon-data-analysis-methods-used-in-microbiome-studies
#3
Jonathan Thorsen, Asker Brejnrod, Martin Mortensen, Morten A Rasmussen, Jakob Stokholm, Waleed Abu Al-Soud, Søren Sørensen, Hans Bisgaard, Johannes Waage
BACKGROUND: There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of 16S rRNA gene hypervariable regions, aggregating sequence-similar amplicons into operational taxonomic units (OTUs). Strategies for detecting differential relative abundance of OTUs between sample conditions include classical statistical approaches as well as a plethora of newer methods, many borrowing from the related field of RNA-seq analysis...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27884202/extending-colonic-mucosal-microbiome-analysis-assessment-of-colonic-lavage-as-a-proxy-for-endoscopic-colonic-biopsies
#4
Euan Watt, Matthew R Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I Murray, Emad El-Omar, Georgina L Hold
BACKGROUND: Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27855721/the-lung-microbiota-in-early-rheumatoid-arthritis-and-autoimmunity
#5
Jose U Scher, Vijay Joshua, Alejandro Artacho, Shahla Abdollahi-Roodsaz, Johan Öckinger, Susanna Kullberg, Magnus Sköld, Anders Eklund, Johan Grunewald, Jose C Clemente, Carles Ubeda, Leopoldo N Segal, Anca I Catrina
BACKGROUND: Airway abnormalities and lung tissue citrullination are found in both rheumatoid arthritis (RA) patients and individuals at-risk for disease development. This suggests the possibility that the lung could be a site of autoimmunity generation in RA, perhaps in response to microbiota changes. We therefore sought to test whether the RA lung microbiome contains distinct taxonomic features associated with local and/or systemic autoimmunity. METHODS: 16S rRNA gene high-throughput sequencing was utilized to compare the bacterial community composition of bronchoalveolar lavage fluid (BAL) in patients with early, disease-modifying anti-rheumatic drugs (DMARD)-naïve RA, patients with lung sarcoidosis, and healthy control subjects...
November 17, 2016: Microbiome
https://www.readbyqxmd.com/read/27842559/dna-from-fecal-immunochemical-test-can-replace-stool-for-detection-of-colonic-lesions-using-a-microbiota-based-model
#6
Nielson T Baxter, Charles C Koumpouras, Mary A M Rogers, Mack T Ruffin, Patrick D Schloss
BACKGROUND: There is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the gut microbiota can complement the fecal occult blood test and fecal immunochemical test (FIT). However, a barrier to microbiota-based screening is the need to collect and store a patient's stool sample. RESULTS: Using stool samples collected from 404 patients, we tested whether the residual buffer containing resuspended feces in FIT cartridges could be used in place of intact stool samples...
November 14, 2016: Microbiome
https://www.readbyqxmd.com/read/27802830/the-vaginal-microbiota-human-papillomavirus-infection-and-cervical-intraepithelial-neoplasia-what-do-we-know-and-where-are-we-going-next
#7
REVIEW
Anita Mitra, David A MacIntyre, Julian R Marchesi, Yun S Lee, Phillip R Bennett, Maria Kyrgiou
The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth study of vaginal microbial community structure to a level of detail not possible with standard culture-based microbiological techniques. The human papillomavirus (HPV) causes both cervical intraepithelial neoplasia (CIN) and cervical cancer. Although the virus is highly prevalent, only a small number of women have a persistent HPV infection and subsequently develop clinically significant disease...
November 1, 2016: Microbiome
https://www.readbyqxmd.com/read/27769291/unusual-sub-genus-associations-of-faecal-prevotella-and-bacteroides-with-specific-dietary-patterns
#8
Francesca De Filippis, Nicoletta Pellegrini, Luca Laghi, Marco Gobbetti, Danilo Ercolini
BACKGROUND: Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and protein-rich diets. Nevertheless, closely related species and strains may harbour different genetic pools; therefore, further studies should aim to understand whether species of the same genus are consistently linked to dietary patterns or equally responsive to diet variations...
October 21, 2016: Microbiome
https://www.readbyqxmd.com/read/27760570/rumen-metagenome-and-metatranscriptome-analyses-of-low-methane-yield-sheep-reveals-a-sharpea-enriched-microbiome-characterised-by-lactic-acid-formation-and-utilisation
#9
Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H Janssen, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and is a heritable trait that can be used to select animals that yield less methane per unit of feed eaten. We previously demonstrated elevated expression of hydrogenotrophic methanogenesis pathway genes of methanogenic archaea in the rumens of high methane yield (HMY) sheep compared to their low methane yield (LMY) counterparts...
October 19, 2016: Microbiome
https://www.readbyqxmd.com/read/27756413/fat-and-vitamin-intakes-during-pregnancy-have-stronger-relations-with-a-pro-inflammatory-maternal-microbiota-than-does-carbohydrate-intake
#10
Siddhartha Mandal, Keith M Godfrey, Daniel McDonald, Will V Treuren, Jørgen V Bjørnholt, Tore Midtvedt, Birgitte Moen, Knut Rudi, Rob Knight, Anne Lise Brantsæter, Shyamal D Peddada, Merete Eggesbø
BACKGROUND: Although diet is known to have a major modulatory influence on gut microbiota, knowledge of the specific roles of particular vitamins, minerals, and other nutrients is limited. Modulation of the composition of the microbiota in pregnant women is especially important as maternal microbes are transferred during delivery and initiate the colonization process in the infant. We studied the associations between intake of specific dietary nutrients during pregnancy and gut microbiota composition...
October 19, 2016: Microbiome
https://www.readbyqxmd.com/read/27717408/the-structure-and-diversity-of-human-animal-and-environmental-resistomes
#11
Chandan Pal, Johan Bengtsson-Palme, Erik Kristiansson, D G Joakim Larsson
BACKGROUND: Antibiotic resistance genes (ARGs) are widespread but cause problems only when present in pathogens. Environments where selection and transmission of antibiotic resistance frequently take place are likely to be characterized by high abundance and diversity of horizontally transferable ARGs. Large-scale quantitative data on ARGs is, however, lacking for most types of environments, including humans and animals, as is data on resistance genes to potential co-selective agents, such as biocides and metals...
October 7, 2016: Microbiome
https://www.readbyqxmd.com/read/27717398/rapid-change-of-fecal-microbiome-and-disappearance-of-clostridium-difficile-in-a-colonized-infant-after-transition-from-breast-milk-to-cow-milk
#12
Manli Y Davis, Husen Zhang, Lera E Brannan, Robert J Carman, James H Boone
BACKGROUND: Clostridium difficile is the most common known cause of antibiotic-associated diarrhea. Upon the disturbance of gut microbiota by antibiotics, C. difficile establishes growth and releases toxins A and B, which cause tissue damage in the host. The symptoms of C. difficile infection disease range from mild diarrhea to pseudomembranous colitis and toxic megacolon. Interestingly, 10-50 % of infants are asymptomatic carriers of C. difficile. This longitudinal study of the C. difficile colonization in an infant revealed the dynamics of C...
October 7, 2016: Microbiome
https://www.readbyqxmd.com/read/27716450/picodroplet-partitioned-whole-genome-amplification-of-low-biomass-samples-preserves-genomic-diversity-for-metagenomic-analysis
#13
Maria Hammond, Felix Homa, Helene Andersson-Svahn, Thijs J G Ettema, Haakan N Joensson
BACKGROUND: Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet...
October 6, 2016: Microbiome
https://www.readbyqxmd.com/read/27671352/the-impact-of-sequence-database-choice-on-metaproteomic-results-in-gut-microbiota-studies
#14
Alessandro Tanca, Antonio Palomba, Cristina Fraumene, Daniela Pagnozzi, Valeria Manghina, Massimo Deligios, Thilo Muth, Erdmann Rapp, Lennart Martens, Maria Filippa Addis, Sergio Uzzau
BACKGROUND: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification...
September 27, 2016: Microbiome
https://www.readbyqxmd.com/read/27640125/intestinal-microbiota-in-pediatric-patients-with-end-stage-renal-disease-a-midwest-pediatric-nephrology-consortium-study
#15
Janice Crespo-Salgado, V Matti Vehaskari, Tyrus Stewart, Michael Ferris, Qiang Zhang, Guangdi Wang, Eugene E Blanchard, Christopher M Taylor, Mahmoud Kallash, Larry A Greenbaum, Diego H Aviles
BACKGROUND: End-stage renal disease (ESRD) is associated with uremia and increased systemic inflammation. Alteration of the intestinal microbiota may facilitate translocation of endotoxins into the systemic circulation leading to inflammation. We hypothesized that children with ESRD have an altered intestinal microbiota and increased serum levels of bacterially derived uremic toxins. METHODS: Four groups of subjects were recruited: peritoneal dialysis (PD), hemodialysis (HD), post-kidney transplant and healthy controls...
September 17, 2016: Microbiome
https://www.readbyqxmd.com/read/27044504/colitis-susceptibility-in-p47-phox-mice-is-mediated-by-the-microbiome
#16
E Liana Falcone, Loreto Abusleme, Muthulekha Swamydas, Michail S Lionakis, Li Ding, Amy P Hsu, Adrian M Zelazny, Niki M Moutsopoulos, Douglas B Kuhns, Clay Deming, Mariam Quiñones, Julia A Segre, Clare E Bryant, Steven M Holland
BACKGROUND: Chronic granulomatous disease (CGD) is caused by defects in nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) complex subunits (gp91(phox) (a.k.a. Nox2), p47(phox), p67(phox), p22(phox), p40(phox)) leading to reduced phagocyte-derived reactive oxygen species production. Almost half of patients with CGD develop inflammatory bowel disease, and the involvement of the intestinal microbiome in relation to this predisposing immunodeficiency has not been explored. RESULTS: Although CGD mice do not spontaneously develop colitis, we demonstrate that p47(phox-/-) mice have increased susceptibility to dextran sodium sulfate colitis in association with a distinct colonic transcript and microbiome signature...
April 5, 2016: Microbiome
https://www.readbyqxmd.com/read/26792212/correlation-of-the-lung-microbiota-with-metabolic-profiles-in-bronchoalveolar-lavage-fluid-in-hiv-infection
#17
Sushma K Cribbs, Karan Uppal, Shuzhao Li, Dean P Jones, Laurence Huang, Laura Tipton, Adam Fitch, Ruth M Greenblatt, Lawrence Kingsley, David M Guidot, Elodie Ghedin, Alison Morris
BACKGROUND: While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung's bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information on bacterial function and impact on the host. Metabolic profiles can provide functional information on host-microbe interactions in the lungs. We investigated the relationship between the respiratory microbiota and metabolic profiles in the bronchoalveolar lavage fluid of HIV-infected and HIV-uninfected outpatients...
January 20, 2016: Microbiome
https://www.readbyqxmd.com/read/26757703/metatranscriptomic-analysis-of-diverse-microbial-communities-reveals-core-metabolic-pathways-and-microbiome-specific-functionality
#18
Yue Jiang, Xuejian Xiong, Jayne Danska, John Parkinson
BACKGROUND: Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function...
January 12, 2016: Microbiome
https://www.readbyqxmd.com/read/27600525/post-translational-modifications-are-enriched-within-protein-functional-groups-important-to-bacterial-adaptation-within-a-deep-sea-hydrothermal-vent-environment
#19
Weipeng Zhang, Jin Sun, Huiluo Cao, Renmao Tian, Lin Cai, Wei Ding, Pei-Yuan Qian
BACKGROUND: Post-translational modification (PTM) of proteins is one important strategy employed by bacteria for environmental adaptation. However, PTM profiles in deep-sea microbes remain largely unexplored. RESULTS: We provide here insight into PTMs in a hydrothermal vent microbial community through integration of metagenomics and metaproteomics. In total, 2919 unique proteins and 1306 unique PTMs were identified, whereas the latter included acetylation, deamination, hydroxylation, methylation, nitrosylation, oxidation, and phosphorylation...
2016: Microbiome
https://www.readbyqxmd.com/read/27600392/mungo-bean-sprout-microbiome-and-changes-associated-with-culture-based-enrichment-protocols-used-in-detection-of-gram-negative-foodborne-pathogens
#20
Heike Margot, Roger Stephan, Taurai Tasara
BACKGROUND: Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. However, the high number of commensal bacteria found on sprouted seeds hampers the detection of these pathogens. Knowledge about the composition of the sprout microbiome is limited. In this study, the microbiome of mungo bean sprouts and the impact of buffered peptone water (BPW) and Enterobacteriaceae enrichment broth (EE-broth)-based enrichment protocols on this microbiome were investigated...
2016: Microbiome
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