Viral Genome Isolation from Human Faeces for Succession Assessment of the Human Gut Virome

2018 ◽  
pp. 97-108 ◽  
Author(s):  
David Mayo-Muñoz
Keyword(s):  
Viral Genome ◽  
Human Gut ◽  
Human Faeces

scholarly journals A previously undescribed highly prevalent phage identified in a Danish enteric virome catalogue

2021 ◽  
Author(s):  
Lore Van Espen ◽  
Emilie Glad Bak ◽  
Leen Beller ◽  
Lila Close ◽  
Ward Deboutte ◽  
...  
Keyword(s):  
Viral Genome ◽  
De Novo ◽  
Human Gut ◽  
Host Genus ◽  
Faecal Samples ◽  
High Prevalence ◽  
Paediatric Cohort ◽  
Health And Disease ◽  
Wet Lab ◽  
Public Datasets

Abstract Background: Gut viruses are important players in the complex human gut microbial ecosystem. Recently, the number of human gut virome studies is steadily increasing, however we are still only scratching the surface of the immense viral diversity as many wet lab and bio-informatics challenges remain. In this study, 254 virus-enriched faecal metagenomes from 204 Danish subjects were used to generate a Danish Enteric Virome Catalogue (DEVoC) of 12,986 non-redundant viral genome sequences encoding 190,029 viral genes, which formed 67,921 orthologous groups. The DEVoC was used to characterize the composition of the healthy DEVoC gut viromes from 46 children and adolescents (6-18 years old) and 45 adults (40 -73 years old).Results: The majority of DEVoC viral sequences (67.3 %) and proteins (61.6 %) were not present in other (human gut) viral genome databases. Gut viromes of healthy Danish subjects mostly consisted of phages. While 39 phage genomes (PGs) were present in more than 10 healthy subjects, the degree of viral individuality was high. Among the 39 prevalent PGs, one was significantly more prevalent in the paediatric cohort, whereas two were more prevalent in adults. In 1,880 gut virome samples of 27 studies from across the world, the 39 prevalent PGs reveal several age-, geography- and disease-related prevalence patterns. Two PGs also showed a remarkably high prevalence worldwide – a crAss-like phage (20.6% prevalence), belonging to the tentative AlphacrAssvirinae subfamily, genus I; and a previously undescribed circular temperate phage (14.4% prevalence), named LoVEphage (because it encodes Lots of Viral Elements). A de novo assembly of selected public datasets generated an additional 18 circular LoVEphage-like genomes (67.9-72.4 kb). CRISPR spacer analysis suggested Bacteroides as a host genus for the LoVEphage, and a closely related prophage was identified in Bacteroides dorei, further confirming the host.Conclusions: The DEVoC, the largest human gut virome catalogue generated from consistently processed faecal samples, facilitated analysis of healthy Danish human gut viromes and we foresee that it will benefit future analysis on the roles of gut viruses in human health and disease. The identification of a previously undescribed prevalent phage illustrates the usefulness of developing a virome catalogue.

scholarly journals Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review

2021 ◽  
Vol 9 (3) ◽  
pp. 524
Author(s):  
Julie Callanan ◽  
Stephen R. Stockdale ◽  
Andrey Shkoporov ◽  
Lorraine A. Draper ◽  
R. Paul Ross ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Viral Metagenomics ◽  
Human Gut ◽  
Human Faeces ◽  
Vast Array ◽  
Viral Component ◽  
And Function ◽  
Bacterial Constituents

The human gut is colonised by a vast array of microbes that include bacteria, viruses, fungi, and archaea. While interest in these microbial entities has largely focused on the bacterial constituents, recently the viral component has attracted more attention. Metagenomic advances, compared to classical isolation procedures, have greatly enhanced our understanding of the composition, diversity, and function of viruses in the human microbiome (virome). We highlight that viral extraction methodologies are crucial in terms of identifying and characterising communities of viruses infecting eukaryotes and bacteria. Different viral extraction protocols, including those used in some of the most significant human virome publications to date, have introduced biases affecting their a overall conclusions. It is important that protocol variations should be clearly highlighted across studies, with the ultimate goal of identifying and acknowledging biases associated with different protocols and, perhaps, the generation of an unbiased and standardised method for examining this portion of the human microbiome.

An Electron Microscopic Study of an Avian Reovirus that Causes Arthritis

1971 ◽  
Vol 29 ◽  
pp. 254-255
Author(s):  
E, R. Walker ◽  
N. O. Olson ◽  
M. H. Friedman
Keyword(s):  
Electron Microscopy ◽  
Viral Genome ◽  
Inner Core ◽  
Avian Reovirus ◽  
Electron Microscopic ◽  
Outer Coat ◽  
Acid Type ◽  
Chicken Eggs ◽  
Icosahedral Particle ◽  
Mature Virus

An unidentified virus, responsible for an arthritic-like condition in chickens was studied by electron microscopy and other methods of viral investigation. It was characterized in chorio-allantoic membrane (CAM) lesions of embryonating chicken eggs and in tissue culture as to: 1) particle size; 2) structure; 3) mode of replication in the cell; and 4) nucleic acid type.The inoculated virus, coated and uncoated, is first seen in lysosomal-like inclusions near the nucleus; the virions appear to be uncoated in these electron dense inclusions (Figure 1), Although transfer of the viral genome from these inclusions is not observable, replicating virus and mature virus crystals are seen in the cytoplasm subsequent to the uncoating of the virions.The crystals are formed in association with a mass of fibrils 50 to 80 angstroms in diameter and a ribosome-studded structure that appears to be granular endoplasmic reticulum adapted to virus replication (Figure 2). The mature virion (Figure 3) is an icosahedral particle approximately 75 millimicrons in diameter. The inner core is 45 millimicrons, the outer coat 15 millimicrons, and the virion has no envelope.

In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
EM Pferschy-Wenzig ◽  
K Koskinen ◽  
C Moissl-Eichinger ◽  
R Bauer
Keyword(s):  
Gut Microbiota ◽  
In Vitro Study ◽  
Vitro Study ◽  
Bark Extract ◽  
Herbal Extracts ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Willow Bark

Combining LC-MS metabolomics and next generation sequencing to study the interactions between herbal medicines and human gut bacteria in-vitro

2017 ◽  
Author(s):  
EM Pferschy-Wenzig ◽  
K Koskinen ◽  
A Roßmann ◽  
K Ardjomand-Woelkart ◽  
C Moissl-Eichinger ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Herbal Medicines ◽  
Gut Bacteria ◽  
Next Generation ◽  
Human Gut ◽  
Generation Sequencing

Metabolization of the herbal combination STW-5 by human gut microbiota in vitro

2017 ◽  
Author(s):  
EM Pferschy-Wenzig ◽  
A Roßmann ◽  
K Koskinen ◽  
H Abdel-Aziz ◽  
C Moissl-Eichinger ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota

CHROMATOGRAPHIC STUDIES ON 131I-COMPOUNDS IN FAECES AND BILE

1964 ◽  
Vol 47 (2) ◽  
pp. 343-352
Author(s):  
B. Blomstedt ◽  
H. Y. Neujahr
Keyword(s):  
Intravenous Administration ◽  
Glucuronic Acid ◽  
Free Triiodothyronine ◽  
Considerable Part ◽  
Human Faeces ◽  
Total Excretion

ABSTRACT The occurrence of 131I-compounds in human faeces was studied after intravenous administration of 131I-thyroxine. The excretion of the radioactivity during 12 days ranged from 7.8 to 32.1 per cent of the dose administered with a mean of 16.0 (± 1.76). The radioactivity in the faeces was derived from free 131I-thyroxine. The total amount of faeces did not seem to influence the total excretion of the dose administered. After administration of 131I-triiodothyronine to rats and humans, triiodothyronine occurred in the bile mainly conjugated with glucuronic acid, but a considerable part of the radioactivity was found in diiodotyrosine. The radioacivity of human faeces after the administration of 131I-triiodothyronine was derived from free triiodothyronine. After injection of 131I-diiodotyrosine only labelled iodide was detected in the bile of rats. In the bile of humans most of the radioactivity was derived from iodide, and a small part of it was found in diiodotyrosine.

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