The gut virome in two indigenous populations from Malaysia

Lee, Chuen Zhang; Zoqratt, Muhammad Zarul Hanifah Md; Phipps, Maude E.; Barr, Jeremy J.; Lal, Sunil K.; Ayub, Qasim; Rahman, Sadequr

doi:10.1038/s41598-022-05656-3

Cited by 10 publications

(9 citation statements)

References 56 publications

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“…Siphoviridae, the most dominant viral family of the normal human gut viral community (Zuo et al, 2020;Tomofuji et al, 2021;Lee et al, 2022), was found to be less distributed in the gut virome of PCOS patients than in that of controls. Siphoviridae is a type of double-stranded DNA (dsDNA) virus that is known to be rich in temperate phages and infects a wide range of gut bacteria, such as Bacillus, Enterococcus, Clostridium, Streptococcus, Lactobacillus, and Escherichia (Sekulovic et al, 2014;Adriaenssens et al, 2015;Chehoud et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Huang

Guo

et al. 2022

Front. Microbiol.

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BackgroundPolycystic ovary syndrome (PCOS) is a complex disease that afflicts women of reproductive age, and its pathological mechanism has not been well explained. The gut microbiota is believed to be closely related to the development of PCOS. Although an important component of the gut microbiome, the role of the gut virome in the development of PCOS is still unclear.MethodsIn this study, we profiled and compared the gut viral community of 50 patients with PCOS and 43 healthy women based on the analysis of their fecal whole-metagenome dataset.ResultsThe gut virome of PCOS patients exhibited a significant decrease in within-sample viral diversity and a remarkable alteration of the overall virome composition compared with that of healthy controls. At the family level, Siphoviridae was significantly depleted in the gut virome of patients, while Quimbyviridae was enriched. We identified 1,089 viral operational taxonomic units (vOTUs) that differed in relative abundance between the two groups, of which 455 vOTUs were enriched in PCOS patients (including numerous Bacteroidaceae phages) and 634 were enriched in controls (including numerous viruses predicted to infect Oscillospiraceae, Prevotellaceae, and Ruminococcaceae). Functional comparison of the PCOS-enriched and control-enriched vOTUs uncovered the viral functional signatures associated with PCOS. Furthermore, we demonstrated gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.938, demonstrating the potential of the gut virome in the prediction of PCOS.ConclusionOur findings reveal specific alterations in viral diversity and taxonomic and functional compositions of the gut virome of PCOS patients. Further studies on the etiology of PCOS and the gut viral community will offer new prospects for treating and preventing PCOS and its related diseases.

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Section: Discussionmentioning

confidence: 99%

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Huang

Guo

et al. 2022

Front. Microbiol.

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“…Amplicon-based sequencing of the internal transcribed spacer or the 18S rRNA genes can be useful to characterize the eukaryotic members of the microbiome, but is also limited in terms of taxonomic resolution, is targeted to specific components of the microbiome, and has significant challenges given the evolutionary proximity of the eukaryotic components of the microbiome with the organisms harbouring the microbiome (Hu et al , 2015; Popovic et al , 2018; Campo et al , 2019). In the case of RNA and DNA viruses, non-amplicon-based metatranscriptomics and metagenomics are necessary, in particular for the genomic discovery and characterization of highly variable viruses in the microbiome (Dheilly et al , 2022; Lee et al , 2022).…”

Section: Where To Next?mentioning

confidence: 99%

Eco-evolutionary implications of helminth microbiomes

et al. 2023

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The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host–parasite interactions in light of new technological developments.

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“…As viruses are "our third genome", looming behind the bacterial "second genome", researchers turned to virome analyses in IBD to gain complementary insights into the pathogenesis of IBD beyond microbiota, genetics, immunological and environmental risk factors. A comprehensive study was published [35] . The researchers started with metagenome sequencing of stool filtrates for 18 Crohn's disease (CD) and 42 UC patients and compared them with stools from 12 non-IBD household controls.…”

Section: Virome Research In Ibdmentioning

confidence: 99%

The human microbiome project at ten years - some critical comments and reflections on “our third genome”, the human virome

Brüssow¹

2023

Microbiome Res Rep

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The Human Microbiome Project (HMP) has raised great expectations claiming the far-reaching influence of the microbiome on human health and disease ranging from obesity and malnutrition to effects going well beyond the gut. So far, with the notable exception of fecal microbiota transplantation in Clostridioides difficile infection, practical application of microbiome intervention has only achieved modest clinical effects. It is argued here that we need criteria for the link between microbiome and disease modelled on the links between pathogens and infectious disease in Koch’s postulates. The most important question is whether the microbiome change is a cause of the given disease or a consequence of a pathology leading to disease where the microbiome change is only a parallel event without a causal connection to the disease – in philosophical parlance, an epiphenomenon. Also discussed here is whether human virome research is a necessary complement to the microbiome project with a high potential for practical applications.

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The gut virome in two indigenous populations from Malaysia

Cited by 10 publications

References 56 publications

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome

Eco-evolutionary implications of helminth microbiomes

The human microbiome project at ten years - some critical comments and reflections on “our third genome”, the human virome

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