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

Huang, Liyu; Wu, Xiaoling; Guo, Shaodong; Lv, Ying; Zhou, Peng; Huang, Guangrong; Duan, Zuzhen; Sun, Wen

doi:10.3389/fmicb.2022.951782

Cited by 9 publications

(7 citation statements)

References 60 publications

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“…Viruses are considered to be important components of the gut microbiome, and recent studies have identified the interactions between viruses and bacteria that affect the biological health of the host through functional annotation [ 56 , 57 , 58 ]. Through our functional annotation and enrichment of the six vOTUs change patterns, we found that, among the constantly increasing vOTUs groups, there are some enriched functions related to viruses’ adaptability to the environment, such as salt response and heat response.…”

Section: Discussionmentioning

confidence: 99%

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Luo,

Guan,

et al. 2024

Viruses

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Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai–Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

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Section: Discussionmentioning

confidence: 99%

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Luo,

Guan,

et al. 2024

Viruses

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“…In this study, we demonstrated that even alpha diversity indexes describing the characteristics of the microbiota of each individual patient provide information that makes it possible to distinguish the microbiome of a healthy person from a patient with a “classic” PCOS phenotype. Notably, in addition to the gut microbiome, other biotopes of patients with PCOS are being actively studied, for example, the oral cavity [ 48 , 49 ], vaginal microbiome [ 50 , 51 , 52 ], blood bacteria spectrum [ 53 ], and gut virome [ 54 ]. Undoubtedly, for a comprehensive characterization of the microbiome in PCOS, it is necessary to consider a complex of factors of bacterial origin.…”

Section: Discussionmentioning

confidence: 99%

Polycystic Ovary Syndrome and Gut Microbiota: Phenotype Matters

Suturina

Belkova

Igumnov

et al. 2022

Life

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Abnormalities in gut microbiota diversity are considered important mechanisms in metabolic disorders in polycystic ovarian syndrome (PCOS). However, the data on the association of these disorders with the PCOS phenotype remain controversial. The objectives of this study were to estimate the alpha diversity of the gut microbiota of healthy women and PCOS patients depending on phenotype. The study participants (184 premenopausal women: 63 with PCOS, 121 without PCOS) were recruited during the annual employment assessment in the Irkutsk Region and the Buryat Republic (Russia) in 2016–2019. For PCOS diagnosis, we used the Rotterdam (2003) criteria and definitions of PCOS phenotypes. Five indexes of alpha diversity (ASV, Shannon, Simpson, Chao, and ACE) were estimated for the gut microbiota in all participants using amplicon metasequencing. As a result, two out of five alpha diversity indexes showed a statistical difference between the non-PCOS and PCOS groups. We did not find a significant difference in the alpha diversity of gut microbiota in the subgroups of women with hyperandrogenic PCOS phenotypes vs non-androgenic phenotype D and the group of women with the presence of only one of the PCOS criteria. Nevertheless, “classic” PCOS phenotypes demonstrated the most significant decrease in alpha diversity compared with healthy women without any signs of PCOS.

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“…A gut virus catalog comprising over 67,000 nonredundant viral operational taxonomic units (vOTUs) was constructed from over 10,000 publicly available fecal metagenomes from the Chinese population ( 28 ). Protein-coding genes of the vOTUs were predicted using Prodigal ( 29 ) with the option “-p meta.” Taxonomic classification of vOTUs was performed based on protein sequence alignment to the combined database derived from the National Center for Biotechnology Information RefSeq database, the Virus‒Host database ( 30 ), the crAss-like protein sequences from Guerin’s study ( 31 ), and the viral protein sequences from Benler’s study ( 32 ).…”

Section: Methodsmentioning

confidence: 99%

Structural changes in the gut virome of patients with atherosclerotic cardiovascular disease

Li,

Ma,

Meng

et al. 2024

Microbiol Spectr

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The gut microbiota is an important risk factor and therapeutic target in atherosclerotic cardiovascular disease (ACVD), a leading cause of morbidity and mortality worldwide. However, alterations in the gut viral community and its contribution to ACVD have rarely been investigated. In this study, we characterized and compared the gut viromes from the fecal metagenomes of 214 patients with ACVD and 171 healthy individuals using a reference-dependent virome approach. We revealed that ACVD patients exhibited a significant increase in viral richness at the family level and a visible alteration in overall virome structure regardless of host sex, age, or body mass index. At the viral operational taxonomic unit (vOTU) level, we identified 105 vOTUs that significantly increased in abundance in ACVD patients and 60 vOTUs that increased in abundance in healthy controls. A majority (43.8%) of the ACVD-enriched vOTUs were predicted to infect Streptococcaceae , Lachnospiraceae , Ruminococcaceae , and Enterobacteriaceae , and Streptococcaceae had tight correlations with the corresponding gut bacterial species, whereas a considerable proportion (35.0%) of the control-enriched vOTUs were Bacteroidaceae , Burkholderiaceae , and Lachnospiraceae phages. Functional analyses revealed five viral auxiliary metabolic genes that differed in frequency between ACVD-enriched and control-enriched vOTUs. Moreover, we identified gut viral signatures for ACVD discrimination and achieved an optimal area under the receiver operator characteristic curve of 0.878 for distinguishing patients from healthy controls. Our results provide a comprehensive view of the ACVD gut virome, which may contribute to the development of novel diagnostic and therapeutic strategies for ACVD and additional relevant cardiovascular diseases. IMPORTANCE Existing studies have found that there is a close relationship between human virome and numerous diseases, and diseases may affect the diversity and composition of the virome; at the same time, changes in the virome will in turn affect the onset and progression of the disease. However, the composition and functional capabilities of the gut virome associated with atherosclerotic cardiovascular disease (ACVD) have not been systematically investigated. To our knowledge, this is the first study investigating the gut virome in patients with ACVD. We characterized the structural changes in the gut virome of ACVD patients, which may facilitate additional mechanistic, diagnostic, and interventional studies of ACVD and related diseases.

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

Cited by 9 publications

References 60 publications

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Polycystic Ovary Syndrome and Gut Microbiota: Phenotype Matters

Structural changes in the gut virome of patients with atherosclerotic cardiovascular disease

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