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Microbiome

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https://www.readbyqxmd.com/read/29776435/fecal-aliquot-straw-technique-fast-allows-for-easy-and-reproducible-subsampling-assessing-interpersonal-variation-in-trimethylamine-n-oxide-tmao-accumulation
#1
Kymberleigh A Romano, Kimberly A Dill-McFarland, Kazuyuki Kasahara, Robert L Kerby, Eugenio I Vivas, Daniel Amador-Noguez, Pamela Herd, Federico E Rey
BACKGROUND: Convenient, reproducible, and rapid preservation of unique biological specimens is pivotal to their use in microbiome analyses. As an increasing number of human studies incorporate the gut microbiome in their design, there is a high demand for streamlined sample collection and storage methods that are amenable to different settings and experimental needs. While several commercial kits address collection/shipping needs for sequence-based studies, these methods do not preserve samples properly for studies that require viable microbes...
May 18, 2018: Microbiome
https://www.readbyqxmd.com/read/29773078/optimizing-taxonomic-classification-of-marker-gene-amplicon-sequences-with-qiime-2-s-q2-feature-classifier-plugin
#2
Nicholas A Bokulich, Benjamin D Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A Huttley, J Gregory Caporaso
BACKGROUND: Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. RESULTS: We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly used classification methods implemented in QIIME 1 (RDP, BLAST, UCLUST, and SortMeRNA) and several new methods implemented in QIIME 2 (a scikit-learn naive Bayes machine-learning classifier, and alignment-based taxonomy consensus methods based on VSEARCH, and BLAST+) for classification of bacterial 16S rRNA and fungal ITS marker-gene amplicon sequence data...
May 17, 2018: Microbiome
https://www.readbyqxmd.com/read/29764499/gestational-diabetes-is-associated-with-change-in-the-gut-microbiota-composition-in-third-trimester-of-pregnancy-and-postpartum
#3
Mie Korslund Wiinblad Crusell, Tue Haldor Hansen, Trine Nielsen, Kristine Højgaard Allin, Malte C Rühlemann, Peter Damm, Henrik Vestergaard, Christina Rørbye, Niklas Rye Jørgensen, Ole Bjarne Christiansen, Femke-Anouska Heinsen, Andre Franke, Torben Hansen, Jeannet Lauenborg, Oluf Pedersen
BACKGROUND: Imbalances of gut microbiota composition are linked to a range of metabolic perturbations. In the present study, we examined the gut microbiota of women with gestational diabetes mellitus (GDM) and normoglycaemic pregnant women in late pregnancy and about 8 months postpartum. METHODS: Gut microbiota profiles of women with GDM (n = 50) and healthy (n = 157) pregnant women in the third trimester and 8 months postpartum were assessed by 16S rRNA gene amplicon sequencing of the V1-V2 region...
May 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29753324/the-effect-of-the-timing-of-exposure-to-campylobacter-jejuni-on-the-gut-microbiome-and-inflammatory-responses-of-broiler-chickens
#4
Phillippa L Connerton, Philip J Richards, Geraldine M Lafontaine, Peter M O'Kane, Nacheervan Ghaffar, Nicola J Cummings, Darren L Smith, Neville M Fish, Ian F Connerton
BACKGROUND: Campylobacters are an unwelcome member of the poultry gut microbiota in terms of food safety. The objective of this study was to compare the microbiota, inflammatory responses, and zootechnical parameters of broiler chickens not exposed to Campylobacter jejuni with those exposed either early at 6 days old or at the age commercial broiler chicken flocks are frequently observed to become colonized at 20 days old. RESULTS: Birds infected with Campylobacter at 20 days became cecal colonized within 2 days of exposure, whereas birds infected at 6 days of age did not show complete colonization of the sample cohort until 9 days post-infection...
May 12, 2018: Microbiome
https://www.readbyqxmd.com/read/29751830/amniotic-fluid-from-healthy-term-pregnancies-does-not-harbor-a-detectable-microbial-community
#5
Efrem S Lim, Cynthia Rodriguez, Lori R Holtz
Recent studies have conflicting data regarding the presence of intra-amniotic microbiota. Viral communities are increasingly recognized as important although overlooked components of the human microbiota. It is unknown if the developing fetus is exposed to a community of viruses (virome). Given the debate over the existence of an intra-amniotic microbial community and the importance of understanding how the infant gut is populated, we characterized the virome and bacterial microbiota of amniotic fluid from 24 uncomplicated term pregnancies using next-generation sequencing methods...
May 11, 2018: Microbiome
https://www.readbyqxmd.com/read/29747692/low-abundant-bacteria-drive-compositional-changes-in-the-gut-microbiota-after-dietary-alteration
#6
Jacquelynn Benjamino, Stephen Lincoln, Ranjan Srivastava, Joerg Graf
BACKGROUND: As the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions...
May 10, 2018: Microbiome
https://www.readbyqxmd.com/read/29739445/setting-the-pace-host-rhythmic-behaviour-and-gene-expression-patterns-in-the-facultatively-symbiotic-cnidarian-aiptasia-are-determined-largely-by-symbiodinium
#7
Michal Sorek, Yisrael Schnytzer, Hiba Waldman Ben-Asher, Vered Chalifa Caspi, Chii-Shiarng Chen, David J Miller, Oren Levy
BACKGROUND: All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the interpretation of rhythmic behaviours is complicated by the daily oscillations in tissue oxygen tension resulting from the photosynthetic and respiratory activities of the associated algal endosymbiont Symbiodinium. In order to better understand the integration of biological clocks in cnidarian hosts of Symbiodinium, daily rhythms of behaviour and gene expression were studied in symbiotic and aposymbiotic morphs of the sea-anemone Aiptasia diaphana...
May 9, 2018: Microbiome
https://www.readbyqxmd.com/read/29729671/multilevel-social-structure-and-diet-shape-the-gut-microbiota-of-the-gelada-monkey-the-only-grazing-primate
#8
Pål Trosvik, Eric J de Muinck, Eli K Rueness, Peter J Fashing, Evan C Beierschmitt, Kadie R Callingham, Jacob B Kraus, Thomas H Trew, Amera Moges, Addisu Mekonnen, Vivek V Venkataraman, Nga Nguyen
BACKGROUND: The gelada monkey (Theropithecus gelada), endemic to the Ethiopian highlands, is the only graminivorous primate, i.e., it feeds mainly on grasses and sedges. In spite of known dental, manual, and locomotor adaptations, the intestinal anatomy of geladas is similar to that of other primates. We currently lack a clear understanding of the adaptations in digestive physiology necessary for this species to subsist on a graminoid-based diet, but digestion in other graminivores, such as ruminants, relies heavily on the microbial community residing in the gastrointestinal (GI) system...
May 5, 2018: Microbiome
https://www.readbyqxmd.com/read/29729663/near-full-length-16s-rrna-gene-next-generation-sequencing-revealed-asaia-as-a-common-midgut-bacterium-of-wild-and-domesticated-queensland-fruit-fly-larvae
#9
Ania T Deutscher, Catherine M Burke, Aaron E Darling, Markus Riegler, Olivia L Reynolds, Toni A Chapman
BACKGROUND: Gut microbiota affects tephritid (Diptera: Tephritidae) fruit fly development, physiology, behavior, and thus the quality of flies mass-reared for the sterile insect technique (SIT), a target-specific, sustainable, environmentally benign form of pest management. The Queensland fruit fly, Bactrocera tryoni (Tephritidae), is a significant horticultural pest in Australia and can be managed with SIT. Little is known about the impacts that laboratory-adaptation (domestication) and mass-rearing have on the tephritid larval gut microbiome...
May 5, 2018: Microbiome
https://www.readbyqxmd.com/read/29720271/mind-the-gut-genomic-insights-to-population-divergence-and-gut-microbial-composition-of-two-marine-keystone-species
#10
Katharina Fietz, Christian Olaf Rye Hintze, Mikkel Skovrind, Tue Kjærgaard Nielsen, Morten T Limborg, Marcus A Krag, Per J Palsbøll, Lars Hestbjerg Hansen, Peter Rask Møller, M Thomas P Gilbert
BACKGROUND: Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ecological adaptive potential are classically viewed at the genetic level, it has recently been argued that their microbiomes may also contribute to population genetic divergence. We explored whether this might be plausible along the well-described environmental gradient of the Baltic Sea in two species of sand lance (Ammodytes tobianus and Hyperoplus lanceolatus)...
May 2, 2018: Microbiome
https://www.readbyqxmd.com/read/29716650/humans-as-holobionts-implications-for-prevention-and-therapy
#11
REVIEW
Maarten van de Guchte, Hervé M Blottière, Joël Doré
The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equilibrium, homeostasis, is maintained and serves health, but signs are that perturbation of this equilibrium beyond the limits of resilience can propel the system into an alternative stable state, a pre-disease state, more susceptible to the development of chronic diseases...
May 1, 2018: Microbiome
https://www.readbyqxmd.com/read/29703247/neutral-models-of-short-term-microbiome-dynamics-with-host-subpopulation-structure-and-migration-limitation
#12
Qinglong Zeng, Allen Rodrigo
BACKGROUND: Most empirical studies tend to focus on microbiome dynamics within hosts or microbiome compositional differences between hosts over short periods. However, there is still a dearth of formal models that allow us to investigate the observed short-term dynamics of microbiomes under a unified ecological and evolutionary framework. In our previous study, we developed a computational agent-based neutral framework that simulates microbiome dynamics spanning many host generations with the added dimension of a genealogy of hosts...
April 27, 2018: Microbiome
https://www.readbyqxmd.com/read/29695286/a-microorganisms-journey-between-plant-generations
#13
Nathan Vannier, Cendrine Mony, Anne-Kristel Bittebiere, Sophie Michon-Coudouel, Marine Biget, Philippe Vandenkoornhuyse
BACKGROUND: Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms...
April 26, 2018: Microbiome
https://www.readbyqxmd.com/read/29695307/use-of-dietary-indices-to-control-for-diet-in-human-gut-microbiota-studies
#14
Ruth C E Bowyer, Matthew A Jackson, Tess Pallister, Jane Skinner, Tim D Spector, Ailsa A Welch, Claire J Steves
BACKGROUND: Environmental factors have a large influence on the composition of the human gut microbiota. One of the most influential and well-studied is host diet. To assess and interpret the impact of non-dietary factors on the gut microbiota, we endeavoured to determine the most appropriate method to summarise community variation attributable to dietary effects. Dietary habits are multidimensional with internal correlations. This complexity can be simplified by using dietary indices that quantify dietary variance in a single measure and offer a means of controlling for diet in microbiota studies...
April 25, 2018: Microbiome
https://www.readbyqxmd.com/read/29695294/the-hologenome-concept-of-evolution-after-10-years
#15
REVIEW
Eugene Rosenberg, Ilana Zilber-Rosenberg
The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution...
April 25, 2018: Microbiome
https://www.readbyqxmd.com/read/29690931/modelling-upper-respiratory-tract-diseases-getting-grips-on-host-microbe-interactions-in-chronic-rhinosinusitis-using-in-vitro-technologies
#16
REVIEW
Charlotte De Rudder, Marta Calatayud Arroyo, Sarah Lebeer, Tom Van de Wiele
Chronic rhinosinusitis (CRS) is a chronic inflammation of the mucosa of the nose and paranasal sinuses affecting approximately 11% of the adult population in Europe. Inadequate immune responses, as well as a dysbiosis of the sinonasal microbiota, have been put forward as aetiological factors of the disease. However, despite the prevalence of this disease, there is no consensus on the aetiology and mechanisms of pathogenesis of CRS. Further research requires in vitro models mimicking the healthy and diseased host environment along with the sinonasal microbiota...
April 24, 2018: Microbiome
https://www.readbyqxmd.com/read/29690923/correction-to-cropping-practices-manipulate-abundance-patterns-of-root-and-soil-microbiome-members-paving-the-way-to-smart-farming
#17
Kyle Hartman, Marcel G A van der Heijden, Raphaël A Wittwer, Samiran Banerjee, Jean-Claude Walser, Klaus Schlaeppi
Following publication of the original article [1], the authors reported that while the ordination graphs are all correct, the symbols in the legend are wrong.
April 24, 2018: Microbiome
https://www.readbyqxmd.com/read/29690922/flexible-metagenome-analysis-using-the-mgx-framework
#18
Sebastian Jaenicke, Stefan P Albaum, Patrick Blumenkamp, Burkhard Linke, Jens Stoye, Alexander Goesmann
BACKGROUND: The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method...
April 24, 2018: Microbiome
https://www.readbyqxmd.com/read/29685174/drinking-alcohol-is-associated-with-variation-in-the-human-oral-microbiome-in-a-large-study-of-american-adults
#19
Xiaozhou Fan, Brandilyn A Peters, Eric J Jacobs, Susan M Gapstur, Mark P Purdue, Neal D Freedman, Alexander V Alekseyenko, Jing Wu, Liying Yang, Zhiheng Pei, Richard B Hayes, Jiyoung Ahn
BACKGROUND: Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance. RESULTS: We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa...
April 24, 2018: Microbiome
https://www.readbyqxmd.com/read/29678198/metabolic-retroconversion-of-trimethylamine-n-oxide-and-the-gut-microbiota
#20
Lesley Hoyles, Maria L Jiménez-Pranteda, Julien Chilloux, Francois Brial, Antonis Myridakis, Thomas Aranias, Christophe Magnan, Glenn R Gibson, Jeremy D Sanderson, Jeremy K Nicholson, Dominique Gauguier, Anne L McCartney, Marc-Emmanuel Dumas
BACKGROUND: The dietary methylamines choline, carnitine, and phosphatidylcholine are used by the gut microbiota to produce a range of metabolites, including trimethylamine (TMA). However, little is known about the use of trimethylamine N-oxide (TMAO) by this consortium of microbes. RESULTS: A feeding study using deuterated TMAO in C57BL6/J mice demonstrated microbial conversion of TMAO to TMA, with uptake of TMA into the bloodstream and its conversion to TMAO. Microbial activity necessary to convert TMAO to TMA was suppressed in antibiotic-treated mice, with deuterated TMAO being taken up directly into the bloodstream...
April 20, 2018: Microbiome
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