The oral microbiome: diversity, biogeography and human health

Nature Reviews Microbiology, Journal Year: 2023, Volume and Issue: 22(2), P. 89 - 104

Published: Sept. 12, 2023

Language: Английский

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A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(8), P. 2185 - 2200

Published: June 21, 2024

Abstract The human vagina harbours diverse microorganisms—bacteria, viruses and fungi—with profound implications for women’s health. Genome-level analysis of the vaginal microbiome across multiple kingdoms remains limited. Here we utilize metagenomic sequencing data fungal cultivation to establish Vaginal Microbial Genome Collection (VMGC), comprising 33,804 microbial genomes spanning 786 prokaryotic species, 11 species 4,263 viral operational taxonomic units. Notably, over 25% 85% units remain uncultured. This collection significantly enriches genomic diversity, especially prevalent pathogens such as BVAB1 (an uncultured bacterial vaginosis-associated bacterium) Amygdalobacter spp. (BVAB2 related species). Leveraging VMGC, characterize functional traits prokaryotes, notably Saccharofermentanales underexplored yet order), along with eukaryotic viruses, offering insights into their niche adaptation potential roles in vagina. VMGC serves a valuable resource studying microbiota its impact on

Language: Английский

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Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment

Journal of Advanced Research, Journal Year: 2022, Volume and Issue: 49, P. 103 - 114

Published: Oct. 2, 2022

Viruses have been reported as inducers of tumorigenesis. Little studies explored the impact gut virome on progression colorectal cancer. However, there is still a problem with repeatability viral signatures across multiple cohorts.The present study aimed to reveal repeatable vial cancer and adenoma patients decipher potential markers in disease risk assessment for diagnosis.1,282 available fecal metagenomes from 9 published were collected. A catalog was constructed via reference-independent approach. Viral identified by cross-cohort meta-analysis used build predictive models based machine learning algorithms. New samples collected validate generalization models.The composition drastically altered compared healthy, evidenced changes some Siphoviridae Myoviridae viruses enrichment Microviridae, whereas variation relatively low. Cross-cohort 405 differential cancer, including several phages Porphyromonas, Fusobacterium, Hungatella that enriched control-enriched Ruminococcaceae phages. In discovery cohorts, optimal model obtained an average area under curve 0.830 discriminating controls. This also showed consistently high accuracy 2 independent validation cohorts (optimal curve, 0.906). Gut analysis 88 achieved 0.772 controls.Our findings demonstrate characteristics highlight virus-bacterial synergy The may be new targets treatment. addition, power prediction suggest biomarkers non-invasive diagnostic tests adenoma.

Language: Английский

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Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 23, 2024

Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from palaeofaeces and human gut-content samples, identify an phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The damage patterns of the consistent with its origin and, despite 1300 years evolution, shares 97.7% nucleotide identity modern counterpart, indicating long-term relationship between prophage host. In addition, reconstruct authenticate 297 other genomes last 5300 years, including those belonging unknown families. Our findings demonstrate feasibility reconstructing sequences, thus expanding known virosphere offering insights into phage-bacteria interactions spanning several millennia.

Language: Английский

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Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: July 18, 2024

Abstract Background The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the IBD patients, especially across diverse geographic populations, is lacking. Results In this study, we conducted comprehensive virome-wide association study Chinese cohort 71 patients (15 with Crohn’s and 56 ulcerative colitis) 77 healthy controls via viral-like particle (VLP) bulk sequencing their feces. By utilizing an integrated virus catalog tailored to virome, revealed fundamental alterations patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted infect Escherichia , Klebsiella Enterococcus_B Streptococcus Veillonella species as well IBD-depleted targeting Prevotella Ruminococcus_E Bifidobacterium Blautia . Remarkably, these signatures demonstrated high consistency populations such those Europe USA, emphasizing significance broad relevance context. Furthermore, fecal transplantation experiments verified that colonization IBD-characterized viruses can modulate experimental colitis mouse models. Conclusions Building upon insights into identified potential biomarkers for prognosis therapy laying foundation further exploration viromes related conditions.

Language: Английский

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Alterations in the gut virome in patients with ankylosing spondylitis

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: March 30, 2023

Introduction Ankylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome. Methods To investigate characteristics of virome in AS, we profiled viral community 193 AS patients and 59 healthy subjects based on metagenome-wide analysis fecal metagenomes from two publicly available datasets. Results revealed significant decrease richness considerable alteration overall structure. At family level, had an increased abundance Gratiaviridae Quimbyviridae decreased Drexlerviridae Schitoviridae . We identified 1,004 differentially abundant operational taxonomic units (vOTUs) between controls, including higher proportion AS-enriched Myoviridae viruses control-enriched Siphoviridae viruses. Moreover, vOTUs were more likely infect bacteria such as Flavonifractor , Achromobacter Eggerthellaceae whereas be Blautia Ruminococcus Collinsella Prevotella Faecalibacterium bacteriophages. Additionally, some functional orthologs differed significantly frequency vOTUs, suggesting role these AS-associated trained classification models signatures discriminate with optimal area under receiver operator characteristic curve (AUC) up 0.936, clinical potential for diagnosing AS. Discussion This work provides novel insight into virome, findings may guide future mechanistic therapeutic studies other diseases.

Language: Английский

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Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: May 8, 2023

Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, further still, viruses these communities have been largely unexplored despite important roles related to host metabolism nutrient cycling. To begin address this, we present a large-scale viral catalog from rock microbial communities.We performed metagenomic analyses on rocks across Antarctica representing broad range environmental spatial conditions, which resulted predicted comprising > 75,000 operational taxonomic units (vOTUS). We found undescribed, highly diverse spatially structured virus had auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation biogeochemistry.This lays the foundation for expanding knowledge virosphere diversity, function, dynamics extreme environments. This work serves as step towards exploring adaptability face changing climate. Video Abstract.

Language: Английский

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Oral bacteriophages: metagenomic clues to interpret microbiomes

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e16947 - e16947

Published: Feb. 20, 2024

Bacteriophages are bacterial viruses that distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, dental plaque interact with microbiota can change biofilm formation. The interactions between bacteria be considered a portion of metagenomics. metagenomic profile microbiome indicates various bacteria. Indeed, there against these cavity. However, some other phages, like Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified This review gives an overview bacteriophage used for Metagenomics deals multi-drug-resistant plaques (biofilms) cavities infection. Hence, dentists pharmacologists should know this to cope predental infectious diseases.

Language: Английский

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The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures

Genome Medicine, Journal Year: 2025, Volume and Issue: 17(1)

Published: March 26, 2025

The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of genetic makeup, functional potential, disease associations remains incomplete. In this study, we collected 11,286 bulk or metagenomes from fecal samples across large-scale Chinese populations to establish a Gut Virus Catalogue (cnGVC) using de novo virus identification approach. We then examined the diversity compositional patterns virome relation common diseases by analyzing 6311 representing 28 unhealthy states. cnGVC contains 93,462 nonredundant genomes, with over 70% these being novel viruses not included existing databases. This resource enabled us characterize specificity virome. Using cnGVC, profiled populations, assessed sex- age-related variations, identified 4238 universal signatures diseases. A random forest classifier based on achieved high accuracy distinguishing diseased individuals controls (AUC = 0.698) high-risk patients 0.761), predictive ability was also validated external cohorts. Our resources findings significantly expand current provide comprehensive view between will pave way strategies treatment prevention

Language: Английский

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Unveiling the role of phages in shaping the periodontal microbial ecosystem

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

ABSTRACT The oral microbiome comprises various species and plays a crucial role in maintaining the ecosystem host health. Phages are an important component of periodontal microbiome, yet our understanding phages remains limited. Here, we investigated using advanced bioinformatics tools based on genomes key periodontitis pathogens. Prophages were found to encode auxiliary genes that potentially enhance survival pathogenicity, including involved carbohydrate metabolism, antibiotic resistance, immune modulation. We observed cross-species transmission among prophages with complex network phage-bacteria interactions. Our findings suggest play shaping microbial ecosystem, influencing community dynamics progression periodontitis. IMPORTANCE In context periodontitis, ecological largely driven by interactions between bacteria their phages. While impact regulating pathogens has been increasingly recognized, modulating disease underexplored. This study reveals within contribute significantly virulence factor dissemination, metabolism. By metabolic capabilities strategies bacterial hosts, may act as critical regulators communities cavity. Understanding these prophage-mediated is essential not only for unraveling mechanisms but also developing innovative therapeutic approaches target at genetic level. These insights emphasize need more comprehensive studies risks posed pathogenicity resistance.

Language: Английский

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