Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

Butcher, James; Mack, David; Stintzi, Alain

doi:10.3389/fcimb.2020.582187

Cited by 14 publications

(18 citation statements)

References 77 publications

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“…Pregnant women with diabetes mellitus type 1 had a different composition of the virome as healthy pregnant women [ 291 ]. Most data of the virome exist from fecal samples, but studies with mucosal biopsies have recently been investigated for IBD [ 272 , 292 , 293 ]. Zuo et al found dysbiosis in IBD patients with increase of Caudovirales bacteriophages and was able to correlate dysbiosis with intestinal inflammation and functional impairment [ 292 ].…”

Section: Gut Viromementioning

confidence: 99%

The Gut-Liver Axis in Cholestatic Liver Diseases

Blesl

Stadlbauer

2021

Nutrients

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The gut-liver axis describes the physiological interplay between the gut and the liver and has important implications for the maintenance of health. Disruptions of this equilibrium are an important factor in the evolution and progression of many liver diseases. The composition of the gut microbiome, the gut barrier, bacterial translocation, and bile acid metabolism are the key features of this cycle. Chronic cholestatic liver diseases include primary sclerosing cholangitis, the generic term secondary sclerosing cholangitis implying the disease secondary sclerosing cholangitis in critically ill patients and primary biliary cirrhosis. Pathophysiology of these diseases is not fully understood but seems to be multifactorial. Knowledge about the alterations of the gut-liver axis influencing the pathogenesis and the outcome of these diseases has considerably increased. Therefore, this review aims to describe the function of the healthy gut-liver axis and to sum up the pathological changes in these cholestatic liver diseases. The review compromises the actual level of knowledge about the gut microbiome (including the mycobiome and the virome), the gut barrier and the consequences of increased gut permeability, the effects of bacterial translocation, and the influence of bile acid composition and pool size in chronic cholestatic liver diseases. Furthermore, therapeutic implications and future scientific objectives are outlined.

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Section: Gut Viromementioning

confidence: 99%

The Gut-Liver Axis in Cholestatic Liver Diseases

Blesl

Stadlbauer

2021

Nutrients

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“…They have been classified into 4 subfamilies and 10 genera. 23,27 Using similar methods, we were able to classify only 30 % of our crAss-like phages, with genera VI, VII and VIII being the most represented. In the Western population, the most common genus is I and in the Malawian cohorts, they are genera VIII and IX.…”

Section: Discussionmentioning

confidence: 99%

Insights into the Human Gut Virome by Sampling a Population from the Indian Subcontinent

Bhardwaj

Garg

Pandey

et al. 2022

Preprint

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Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (< 20%) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VII, VIII and VI. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analyzed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10% of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.

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“…The detrimental effects of CsCl should be avoided to maintain diversity and integrity as much as possible. Additionally, even though sequencing has introduced a wealth of information regarding phage constituents within the microbiome [ 39 , 40 , 41 , 42 , 43 ], it has become apparent that there is a need to move into research that investigates the activity of said phage populations in relation to health and dysbiosis. As such, it is even more important to retain not only the community structure, but the activity.…”

Section: Discussionmentioning

confidence: 99%

Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity

Carroll‐Portillo

Coffman

Varga

et al. 2021

Viruses

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For decades, bacteriophage purification has followed structured protocols focused on generating high concentrations of phage in manageable volumes. As research moves toward understanding complex phage populations, purification needs have shifted to maximize the amount of phage while maintaining diversity and activity. The effects of standard phage purification procedures such as polyethylene glycol (PEG) precipitation and cesium chloride (CsCl) density gradients on both diversity and activity of a phage population are not known. We have examined the effects of PEG precipitation and CsCl density gradients on a number of known phage (M13, T4, and ΦX 174) of varying structure and size, individually and as mixed sample. Measurement of phage numbers and activity throughout the purification process was performed. We demonstrate that these methods, used routinely to generate “pure” phage samples, are in fact detrimental to retention of phage number and activity; even more so in mixed phage samples. As such, minimal amounts of processing are recommended to introduce less bias and maintain more of a phage population.

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Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface

Cited by 14 publications

References 77 publications

The Gut-Liver Axis in Cholestatic Liver Diseases

The Gut-Liver Axis in Cholestatic Liver Diseases

Insights into the Human Gut Virome by Sampling a Population from the Indian Subcontinent

Standard Bacteriophage Purification Procedures Cause Loss in Numbers and Activity

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