scholarly journals The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation

2016 ◽  
Vol 7 ◽  
Author(s):  
Christina Engels ◽  
Hans-Joachim Ruscheweyh ◽  
Niko Beerenwinkel ◽  
Christophe Lacroix ◽  
Clarissa Schwab
Keyword(s):  
Gut Microbe ◽  
The Common ◽  
Propionate Formation ◽  
Eubacterium Hallii

scholarly journals Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Francesco Beghini ◽  
Lauren J McIver ◽  
Aitor Blanco-Míguez ◽  
Leonard Dubois ◽  
Francesco Asnicar ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Strain Level ◽  
Community Studies ◽  
Shotgun Metagenomics ◽  
Taxonomic Profiling ◽  
Culture Independent ◽  
Gut Microbe ◽  
The Common ◽  
Phylogenetic Profiling ◽  
Improved Methods

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

The strict anaerobic gut microbe Eubacterium hallii transforms the carcinogenic dietary heterocyclic amine 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)

2016 ◽  
Vol 8 (2) ◽  
pp. 201-209 ◽  
Author(s):  
Mostafa I. Fekry ◽  
Christina Engels ◽  
Jianbo Zhang ◽  
Clarissa Schwab ◽  
Christophe Lacroix ◽  
...  
Keyword(s):  
Heterocyclic Amine ◽  
Gut Microbe ◽  
Eubacterium Hallii

scholarly journals Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

2020 ◽  
Author(s):  
Francesco Beghini ◽  
Lauren J. McIver ◽  
Aitor Blanco-Míguez ◽  
Leonard Dubois ◽  
Francesco Asnicar ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Strain Level ◽  
Community Studies ◽  
Shotgun Metagenomics ◽  
Taxonomic Profiling ◽  
Culture Independent ◽  
Gut Microbe ◽  
The Common ◽  
Phylogenetic Profiling ◽  
Improved Methods

AbstractCulture-independent analyses of microbial communities have advanced dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

scholarly journals A Novel Uropathogenic Escherichia Coli Genome (strain D3) and Comparative Analysis with Other Uropathogenic and Nonpathogenic Strains

2017 ◽  
Author(s):  
Brian B. Nadel ◽  
Shawn J. Cokus ◽  
Marco Morselli ◽  
Laura J. Marinelli ◽  
David Lopez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Uropathogenic Escherichia Coli ◽  
Cell Adherence ◽  
Male Adult ◽  
E Coli ◽  
Gut Microbe ◽  
The Common ◽  
Tract Infections ◽  
Multiple Antibiotics

AbstractBackgroundBacterial urinary tract infections are extremely prevalent, with half of women having at least one infection at some point in their lives. Most often the causative pathogen is the common gut microbe Escherichia coli. One such E. coli, strain D3, caused a bladder infection in a male adult, and was resistant to multiple antibiotics. We sequenced and assembled the genome of D3, and present it along with a comparative analysis against other pathogenic and nonpathogenic E. Coli strains.ResultsBy comparing the predicted proteins of D3 with those from 5 uropathogenic and 7 nonpathogenic E. Coli strains, we generated a list of 38 genes present in most (4-5) pathogenic strains, but absent in all nonpathogenic strains. Among these were 9 proteins of the Pap fimbrial operon, which has previously been associated with cell adherence and the formation of biofilms. Lastly, we analyzed the list of predicted genes uniquely present in D3 compared to all other strains, and identified multiple transposable elements.ConclusionsThe presence of fimbria in most pathogenic E. coli strains, and their absence in nonpathogenic ones, suggests that they play a role in pathogenicity, a notion supported by previous work. We also found that D3-specific genes are strongly enriched with transposases, recombinases, and integrase, suggesting that these mobile elements have been inserted or expanded in D3, relative to other strains in the study.

Catalogue reduction techniques

1978 ◽  
Vol 48 ◽  
pp. 389-390 ◽  
Author(s):  
Chr. de Vegt
Keyword(s):  
Adjustment Process ◽  
Proper Motions ◽  
Measuring Process ◽  
Aerial Photogrammetry ◽  
Reduction Techniques ◽  
Observational Technique ◽  
The Common ◽  
Astrometric Data

AbstractReduction techniques as applied to astrometric data material tend to split up traditionally into at least two different classes according to the observational technique used, namely transit circle observations and photographic observations. Although it is not realized fully in practice at present, the application of a blockadjustment technique for all kind of catalogue reductions is suggested. The term blockadjustment shall denote in this context the common adjustment of the principal unknowns which are the positions, proper motions and certain reduction parameters modelling the systematic properties of the observational process. Especially for old epoch catalogue data we frequently meet the situation that no independent detailed information on the telescope properties and other instrumental parameters, describing for example the measuring process, is available from special calibration observations or measurements; therefore the adjustment process should be highly self-calibrating, that means: all necessary information has to be extracted from the catalogue data themselves. Successful applications of this concept have been made already in the field of aerial photogrammetry.

Renilla Bioluminescence: A Morphologic Approach to the Location of Photocytes

1974 ◽  
Vol 32 ◽  
pp. 208-209
Author(s):  
Ben O. Spurlock ◽  
Milton J. Cormier
Keyword(s):  
Excited State ◽  
Ground State ◽  
Molecular Basis ◽  
Light Emission ◽  
Chemical Basis ◽  
Electronic Excited State ◽  
Colonial Form ◽  
The Common ◽  
Eighteenth And Nineteenth Centuries ◽  
Catalyzed Oxidation

The phenomenon of bioluminescence has fascinated layman and scientist alike for many centuries. During the eighteenth and nineteenth centuries a number of observations were reported on the physiology of bioluminescence in Renilla, the common sea pansy. More recently biochemists have directed their attention to the molecular basis of luminosity in this colonial form. These studies have centered primarily on defining the chemical basis for bioluminescence and its control. It is now established that bioluminescence in Renilla arises due to the luciferase-catalyzed oxidation of luciferin. This results in the creation of a product (oxyluciferin) in an electronic excited state. The transition of oxyluciferin from its excited state to the ground state leads to light emission.

Mammalian Bone Marrow Acetylcholinesterase

1982 ◽  
Vol 40 ◽  
pp. 44-45
Author(s):  
Ezzatollah Keyhani
Keyword(s):  
Central Nervous System ◽  
Bone Marrow ◽  
Nervous System ◽  
Common Property ◽  
Extracellular Medium ◽  
The Central Nervous System ◽  
The Common ◽  
Mammalian Bone

Acetylcholinesterase (EC 3.1.1.7) (ACHE) has been localized at cholinergic junctions both in the central nervous system and at the periphery and it functions in neurotransmission. ACHE was also found in other tissues without involvement in neurotransmission, but exhibiting the common property of transporting water and ions. This communication describes intracellular ACHE in mammalian bone marrow and its secretion into the extracellular medium.

Correlation analysis of radiation damage

1978 ◽  
Vol 36 (1) ◽  
pp. 214-215
Author(s):  
R. Hegerl ◽  
A. Feltynowski ◽  
B. Grill
Keyword(s):  
Electron Microscopy ◽  
Independent Random Variables ◽  
Optical Parameters ◽  
Bright Field Image ◽  
Bright Field ◽  
Expectation Value ◽  
All Optical ◽  
Image Element ◽  
Stochastic Series ◽  
The Common

Till now correlation functions have been used in electron microscopy for two purposes: a) to find the common origin of two micrographs representing the same object, b) to check the optical parameters e. g. the focus. There is a third possibility of application, if all optical parameters are constant during a series of exposures. In this case all differences between the micrographs can only be caused by different noise distributions and by modifications of the object induced by radiation.Because of the electron noise, a discrete bright field image can be considered as a stochastic series Pm,where i denotes the number of the image and m (m = 1,.., M) the image element. Assuming a stable object, the expectation value of Pm would be Ηm for all images. The electron noise can be introduced by addition of stationary, mutual independent random variables nm with zero expectation and the variance. It is possible to treat the modifications of the object as a noise, too.

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