Features of the gut prokaryotic virome of Japanese patients with Crohn’s disease

Imai, Toshio; Inoüe, Ryo; Nishida, Atsushi; Yokota, Yoshihiro; Morishima, So; Kawahara, Masahiro; Kusada, Hiroyuki; Tamaki, Hideyuki; Andoh, Akira

doi:10.1007/s00535-022-01882-8

Cited by 11 publications

(14 citation statements)

References 46 publications

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“…Simultaneously with disease development, the microbiota will shift towards an imbalanced microbial state. The gut virota is recognized to shift towards an imbalanced viral state as well, notwithstanding that studies revealed inconsistent results [ 11 , 64 , 79 , 131 , 132 , 133 , 134 , 135 , 136 ]. To accurately describe the consensus regarding the imbalanced IBD gut virome, methodological discrepancies between studies should be considered.…”

Section: The Pathophysiology Of Ibd Is Associated With a Disrupted Gu...mentioning

confidence: 99%

“…As mentioned earlier, several methods are known to affect the virome composition, including VLP enrichment, random amplification, type of assembler, tools used to identify the viral fraction, viral taxonomic rank of the analyses, and are summarized in Supplementary Table S1 for various IBD studies. Despite all the before-mentioned biases, the imbalanced IBD gut virome repeatedly revealed a higher relative abundance of Caudovirales , and a lower relative abundance of Microviridae phages [ 11 , 131 , 132 , 134 , 135 ] ( Supplementary Table S1 ). This imbalanced viral state was further characterized by a low prevalence and abundance of CrAss-like phages, although one single study performed by Takayuki and colleagues reported a higher relative abundance of CrAss-like phages in CD patients [ 64 , 79 , 134 ] ( Supplementary Table S1 ).…”

Section: The Pathophysiology Of Ibd Is Associated With a Disrupted Gu...mentioning

confidence: 99%

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The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

Jansen

Matthijnssens

2023

Viruses

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Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the “positive inflammatory feedback loop” that may play a role in the pathophysiology of IBD.

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Section: The Pathophysiology Of Ibd Is Associated With a Disrupted Gu...mentioning

confidence: 99%

Section: The Pathophysiology Of Ibd Is Associated With a Disrupted Gu...mentioning

confidence: 99%

The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

Jansen

Matthijnssens

2023

Viruses

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“…Bacteriophages consist of dsDNA Caudovirales order including Siphoviridae, Myoviridae, Podoviridae, Herelleviridae , Ackermannviridae as well as other unknown families, and Ligamenvirales order comprising Lipothrixviridae and ssDNA phage family Microviridae , whereas eukaryotic viruses are composed of Papillomaviridae, Picornaviridae, Coronaviridae, Orthomyxoviridae and Anelloviridae and Virgaviridae [ 31 , 32 ]. Compared with healthy people, IBD patients have increased abundance of Caudovirales , Lactococcus phages , Lactobacillus phages , Clostridium phages , Enterococcus phages and Streptococcus phages [ 32 ]. After long-term receipt of immunosuppressive therapy, high levels of Anelloviridae were found in the stool of IBD patients [ 33 ].…”

Section: Intestinal Flora and Ibdmentioning

confidence: 99%

“…In addition, human papilloma virus infection may also be a cause of IBD [ 34 ]. Moreover, there have been clues indicating an intimately interaction of viruses with other intestinal organisms [ 32 , 35 ].…”

Section: Intestinal Flora and Ibdmentioning

confidence: 99%

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Updated immunomodulatory roles of gut flora and microRNAs in inflammatory bowel diseases

2022

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Inflammatory bowel disease is a heterogeneous intestinal inflammatory disorder, including ulcerative colitis (UC) and Crohn's disease (CD). Existing studies have shown that the pathogenesis of IBD is closely related to the host's genetic susceptibility, intestinal flora disturbance and mucosal immune abnormalities, etc. It is generally believed that there are complicated interactions between host immunity and intestinal microflora/microRNAs during the occurrence and progression of IBD. Intestinal flora is mainly composed of bacteria, fungi, viruses and helminths. These commensals are highly implicated in the maintenance of intestinal microenvironment homeostasis alone or in combination. MiRNA is an endogenous non-coding small RNA with a length of 20 to 22 nucleotides, which can perform a variety of biological functions by silencing or activating target genes through complementary pairing bonds. A large quantity of miRNAs are involved in intestinal inflammation, mucosal barrier integrity, autophagy, vesicle transportation and other small RNA alterations in IBD circumstance. In this review, the immunomodulatory roles of gut flora and microRNAs are updated in the occurrence and progression of IBD. Meanwhile, the gut flora and microRNA targeted therapeutic strategies as well as other immunomodulatory approaches including TNF-α monoclonal antibodies are also emphasized in the treatment of IBD.

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Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases

Zeng,

Wan,

Guo

et al. 2024

Biomedicine & Pharmacotherapy

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Features of the gut prokaryotic virome of Japanese patients with Crohn’s disease

Cited by 11 publications

References 46 publications

The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance

Updated immunomodulatory roles of gut flora and microRNAs in inflammatory bowel diseases

Fecal virome transplantation: A promising strategy for the treatment of metabolic diseases

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