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Microbiome

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https://www.readbyqxmd.com/read/28086968/microbiota-fingerprints-lose-individually-identifying-features-over-time
#1
David Wilkins, Marcus H Y Leung, Patrick K H Lee
BACKGROUND: Humans host individually unique skin microbiota, suggesting that microbiota traces transferred from skin to surfaces could serve as forensic markers analogous to fingerprints. While it is known that individuals leave identifiable microbiota traces on surfaces, it is not clear for how long these traces persist. Moreover, as skin and surface microbiota change with time, even persistent traces may lose their forensic potential as they would cease to resemble the microbiota of the person who left them...
January 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28038686/the-developing-hypopharyngeal-microbiota-in-early-life
#2
Martin Steen Mortensen, Asker Daniel Brejnrod, Michael Roggenbuck, Waleed Abu Al-Soud, Christina Balle, Karen Angeliki Krogfelt, Jakob Stokholm, Jonathan Thorsen, Johannes Waage, Morten Arendt Rasmussen, Hans Bisgaard, Søren Johannes Sørensen
BACKGROUND: The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a healthy airway microbiota in early life. Our goal was to understand the establishment of the airway microbiota within the first 3 months of life. We investigated the hypopharyngeal microbiota in the unselected COPSAC2010 cohort of 700 infants, using 16S rRNA gene sequencing of hypopharyngeal aspirates from 1 week, 1 month, and 3 months of age...
December 30, 2016: Microbiome
https://www.readbyqxmd.com/read/28038683/the-gut-microbiota-in-conventional-and-serrated-precursors-of-colorectal-cancer
#3
Brandilyn A Peters, Christine Dominianni, Jean A Shapiro, Timothy R Church, Jing Wu, George Miller, Elizabeth Yuen, Hal Freiman, Ian Lustbader, James Salik, Charles Friedlander, Richard B Hayes, Jiyoung Ahn
BACKGROUND: Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut microbiota and colorectal cancer; however, its relationship to the different early precursors of colorectal cancer is understudied. We tested, for the first time, the relationship of the gut microbiota to specific colorectal polyp types. RESULTS: Gut microbiota were assessed in 540 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples...
December 30, 2016: Microbiome
https://www.readbyqxmd.com/read/28034306/influence-of-maternal-breast-milk-ingestion-on-acquisition-of-the-intestinal-microbiome-in-preterm-infants
#4
Katherine E Gregory, Buck S Samuel, Pearl Houghteling, Guru Shan, Frederick M Ausubel, Ruslan I Sadreyev, W Allan Walker
BACKGROUND: The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and nutrition have all been shown to play a role in the assembly of the intestinal microbiome during early life. For preterm infants, who are disproportionately at risk of inflammatory intestinal disease (i.e., necrotizing enterocolitis), a unique set of clinical factors influence the establishment of the microbiome...
December 30, 2016: Microbiome
https://www.readbyqxmd.com/read/28034304/temporal-bacterial-and-metabolic-development-of-the-preterm-gut-reveals-specific-signatures-in-health-and-disease
#5
Christopher J Stewart, Nicholas D Embleton, Emma C L Marrs, Daniel P Smith, Andrew Nelson, Bashir Abdulkadir, Tom Skeath, Joseph F Petrosino, John D Perry, Janet E Berrington, Stephen P Cummings
BACKGROUND: The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <32 weeks gestation, we selected 7 infants who developed NEC (defined rigorously) and 28 matched controls. We performed detailed temporal bacterial (n = 641) and metabolomic (n = 75) profiling of the gut microbiome throughout the disease. RESULTS: A core community of Klebsiella, Escherichia, Staphyloccocus, and Enterococcus was present in all samples...
December 29, 2016: Microbiome
https://www.readbyqxmd.com/read/28034303/disruption-of-the-microbiota-across-multiple-body-sites-in-critically-ill-children
#6
Matthew B Rogers, Brian Firek, Min Shi, Andrew Yeh, Rachel Brower-Sinning, Victoria Aveson, Brittany L Kohl, Anthony Fabio, Joseph A Carcillo, Michael J Morowitz
BACKGROUND: Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets. RESULTS: Bacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs...
December 29, 2016: Microbiome
https://www.readbyqxmd.com/read/27998314/resilient-microorganisms-in-dust-samples-of-the-international-space-station-survival-of-the-adaptation-specialists
#7
Maximilian Mora, Alexandra Perras, Tatiana A Alekhova, Lisa Wink, Robert Krause, Alina Aleksandrova, Tatiana Novozhilova, Christine Moissl-Eichinger
BACKGROUND: The International Space Station (ISS) represents a unique biotope for the human crew but also for introduced microorganisms. Microbes experience selective pressures such as microgravity, desiccation, poor nutrient-availability due to cleaning, and an increased radiation level. We hypothesized that the microbial community inside the ISS is modified by adapting to these stresses. For this reason, we analyzed 8-12 years old dust samples from Russian ISS modules with major focus on the long-time surviving portion of the microbial community...
December 20, 2016: Microbiome
https://www.readbyqxmd.com/read/27912796/staphylococcal-species-heterogeneity-in-the-nasal-microbiome-following-antibiotic-prophylaxis-revealed-by-tuf-gene-deep-sequencing
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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