Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization

Zuo, Tao; Sun, Yuhao; Wan, Yating; Yeoh, Yun Kit; Zhang, Fen; Cheung, Chun Pan; Chen, Nan; Luo, Juan; Wen, Wang; Sung, Joseph J.Y.; Chan, Paul Kay Sheung; Wang, Kunhua; Chan, Francis K.L.; Miao, Yi; Ng, Siew C.

doi:10.1016/j.chom.2020.08.005

Cited by 119 publications

(117 citation statements)

References 61 publications

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“…Indeed, data point towards an individual but stable and very diverse virome in every human [278]. Composition of the gut virome is dependent on age, geography, ethnicity, urbanization, and diet [279][280][281]. In addition to the interplay between VLPs and the bacterial microbiome, the virome also exerts influence on immune responses [223].…”

Section: Gut Virome 71 Introductionmentioning

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 Virome 71 Introductionmentioning

confidence: 99%

The Gut-Liver Axis in Cholestatic Liver Diseases

Blesl

Stadlbauer

2021

Nutrients

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“…In contrast, PMMoV is much more prevalent in our cohort (~67%) and another US cohort [26]. Human gut virome is know to vary substantially across population, geography and lifestyle [27], and highly individual-speci c [13]. Therefore the observed differences in gut virome con guration between studies might be accounted for by the host and environmental factors in conjunction with population characteristics.…”

Section: Discussionmentioning

confidence: 60%

“…Such virome compositional features might be a consequence of SARS-CoV-2 infection along with its impact on the host immunity and the holistic ecology of the host gut microbiota [8,15,16]. The gut virome changes in COVID-19 were modest, given that COVID-19 is an acute respiratory disease primarily in icting the respiratory tract with miniscule enteric involvement [2][3][4][5] and that human gut virome is substantially diverse across healthy individuals [27]. We also observed persistently discrepant viromes in COVID-19 patients with that of healthy controls over time, both during disease course and after disease resolution.…”

Section: Discussionmentioning

confidence: 99%

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

Zuo

Liu

Zhang

et al. 2020

Preprint

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Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had faecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Results: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, Pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.Conclusions: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.

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“…Medication can also alter the gut virome [ 14 ], which is highly correlated with the bacterial community [ 15 ]. This is because the gut virome is dominated by bacteriophages [ 16 ] (phages): viruses that infect and lyse bacteria.…”

Section: Introductionmentioning

confidence: 99%

Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut

Sutcliffe

Shamash

Hynes

et al. 2021

Viruses

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Many bacteria carry bacteriophages (bacterial viruses) integrated in their genomes in the form of prophages, which replicate passively alongside their bacterial host. Environmental conditions can lead to prophage induction; the switching from prophage replication to lytic replication, that results in new bacteriophage progeny and the lysis of the bacterial host. Despite their abundance in the gut, little is known about what could be inducing these prophages. We show that several medications, at concentrations predicted in the gut, lead to prophage induction of bacterial isolates from the human gut. We tested five medication classes (non-steroidal anti-inflammatory, chemotherapy, mild analgesic, cardiac, and antibiotic) for antimicrobial activity against eight prophage-carrying human gut bacterial representative isolates in vitro. Seven out of eight bacteria showed signs of growth inhibition in response to at least one medication. All medications led to growth inhibition of at least one bacterial isolate. Prophage induction was confirmed in half of the treatments showing antimicrobial activity. Unlike antibiotics, host-targeted medications led to a species-specific induction of Clostridium beijerinckii, Bacteroides caccae, and to a lesser extent Bacteroides eggerthii. These results show how common medication consumption can lead to phage-mediated effects, which in turn would alter the human gut microbiome through increased prophage induction.

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Human-Gut-DNA Virome Variations across Geography, Ethnicity, and Urbanization

Cited by 119 publications

References 61 publications

The Gut-Liver Axis in Cholestatic Liver Diseases

The Gut-Liver Axis in Cholestatic Liver Diseases

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity

Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut

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