Abstract:Pathogenesis of Crohn's disease (CD) relates to gut microbiome dysbiosis. However, less is known about the viral microbiome, consisting of bacteriophages and eukaryotic viruses, in CD. Here, we profiled the stool virome, viral functions, and viral-bacterial correlations that involved in CD pathogenesis. Metagenomics and metaviromics with novel viral identification and data analysis workflow were performed on stool of non-CD household controls, CD flare and remission patients.Both bacteriome and DNA/RNA virome … Show more
“…Notably, some functions related to viral replication and integration, phage lysis of bacteria host, virus-host biology, and bacterial susceptibility were decreased in T2D subjects, including ABC transporter, integrase core domain, DNA replication, transcription DNA-templated, translation, ribosome, beta-lactamase superfamily domain, glutamine metabolic process, and glutamine amidotransferase domain ( Figure 6 ). 20 , 21 Figure 6. Differential viral functions between (a) T2D subjects and healthy controls and (b) T2D-Ne subjects and healthy controls against GO and Pfam protein family databases.…”
Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we characterized the gut virome alterations in T2D and its complications diabetic nephropathy (DN) by metagenomic sequencing of fecal viral-like particles. Compared with controls, T2D subjects, especially those with DN, had significantly lower viral richness and diversity. 81 viral species were identified to be significantly altered in T2D subjects, including a decrease in some phages (e.g.
Flavobacterium phage
and
Cellulophaga phaga
). DN subjects were depleted of 12 viral species, including
Bacteroides phage
,
Anoxybacillus virus
and
Brevibacillus phage
, and enriched in 2 phages (
Shigella phage
and
Xylella phage
). Multiple viral functions, particularly those of phage lysing host bacteria, were markedly reduced in T2D and DN. Strong viral-bacterial interactions in healthy controls were disrupted in both T2D and DN. Moreover, the combined use of gut viral and bacterial markers achieved a powerful diagnostic performance for T2D and DN, with AUC of 99.03% and 98.19%, respectively. Our results suggest that T2D and its complication DN are characterized by a significant decrease in gut viral diversity, changes in specific virus species, loss of multiple viral functions, and disruption of viral-bacterial correlations. The combined gut viral and bacterial markers have diagnostic potential for T2D and DN.
“…Notably, some functions related to viral replication and integration, phage lysis of bacteria host, virus-host biology, and bacterial susceptibility were decreased in T2D subjects, including ABC transporter, integrase core domain, DNA replication, transcription DNA-templated, translation, ribosome, beta-lactamase superfamily domain, glutamine metabolic process, and glutamine amidotransferase domain ( Figure 6 ). 20 , 21 Figure 6. Differential viral functions between (a) T2D subjects and healthy controls and (b) T2D-Ne subjects and healthy controls against GO and Pfam protein family databases.…”
Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we characterized the gut virome alterations in T2D and its complications diabetic nephropathy (DN) by metagenomic sequencing of fecal viral-like particles. Compared with controls, T2D subjects, especially those with DN, had significantly lower viral richness and diversity. 81 viral species were identified to be significantly altered in T2D subjects, including a decrease in some phages (e.g.
Flavobacterium phage
and
Cellulophaga phaga
). DN subjects were depleted of 12 viral species, including
Bacteroides phage
,
Anoxybacillus virus
and
Brevibacillus phage
, and enriched in 2 phages (
Shigella phage
and
Xylella phage
). Multiple viral functions, particularly those of phage lysing host bacteria, were markedly reduced in T2D and DN. Strong viral-bacterial interactions in healthy controls were disrupted in both T2D and DN. Moreover, the combined use of gut viral and bacterial markers achieved a powerful diagnostic performance for T2D and DN, with AUC of 99.03% and 98.19%, respectively. Our results suggest that T2D and its complication DN are characterized by a significant decrease in gut viral diversity, changes in specific virus species, loss of multiple viral functions, and disruption of viral-bacterial correlations. The combined gut viral and bacterial markers have diagnostic potential for T2D and DN.
“… 29 , 30 Therefore, the higher relative abundance of lytic Faecalibacterium phages in cognitively impaired patients and correlation of these phages with poor cognitive testing could be due to their lytic action against Faecalibacterium . 31 On the other hand, Lactobacillus phages had a complicated relationship with bacteria and cognitive function longitudinally and cross-sectionally. 32 .…”
Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (
n
= 138) and longitudinal analyses (
n
= 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with
Streptococcus
,
Faecalibacterium
, and
Lactobacillus
, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with
Streptococcus
,
Faecalibacterium
, and
Lactobacillus
were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.
“…An increase in anellovirus sequences has been observed in patients with IBD, strengthening the hypothesis that they may indirectly contribute to the progression of the disease [ 143 ]. In patients with CD, it was observed that TTV is related to inflammation in this disease, and relationships were found with complications and treatment approaches [ 144 ]. AVs are elevated in patients with IBD before initiation of therapeutic approaches.…”
Anelloviruses (AVs) that infect the human population are members of the Anelloviridae family. They are widely distributed in human populations worldwide. Torque teno virus (TTV) was the first virus of this family to be identified and is estimated to be found in the serum of 80–90% of the human population. Sometime after the identification of TTV, Torque teno mini virus (TTMV) and Torque teno midi virus (TTMDV) were also identified and classified in this family. Since identifying these viruses, have been detected in various types of biological fluids of the human body, including blood and urine, as well as vital organs such as the liver and kidney. They can be transmitted from person to person through blood transfusions, fecal-oral contact, and possibly sexual intercourse. Recent studies on these newly introduced viruses show that although they are not directly related to human disease, they may be indirectly involved in initiating or exacerbating some human population-related diseases and viral infections. Among these diseases, we can mention various types of cancers, immune system diseases, viral infections, hepatitis, and AIDS. Also, they likely use the microRNAs (miRNAs) they encode to fulfill this cooperative role. Also, in recent years, the role of proliferation and their viral load, especially TTV, has been highlighted to indicate the immune system status of immunocompromised people or people who undergo organ transplants. Here, we review the possible role of these viruses in diseases that target humans and highlight them as important viruses that require further study. This review can provide new insights to researchers.
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