Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study

Manzoor, Muhammed; Leskelä, Jaakko; Pietiäinen, Milla; Martinez-Majander, Nicolas; Könönen, Eija; Niiranen, Teemu; Lahti, Leo; Sinisalo, Juha; Putaala, Jukka; Pussinen, Pirkko J.; Paju, Susanna

doi:10.1080/20002297.2024.2330867

Cited by 3 publications

(1 citation statement)

References 66 publications

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“…Sample processing, DNA extraction, metagenomic sequencing, and bioinformatics analysis are described in detail elsewhere [ 41 ]. Briefly, stimulated saliva samples were collected at the beginning of the oral examination into RNase/DNase-free tubes and stored at −70°C.…”

Section: Methodsmentioning

confidence: 99%

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

Manzoor,

Leskelä,

Pietiäinen

et al. 2024

ISME Communications

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Although knowledge of the role of the oral microbiome in ischemic stroke is steadily increasing, little is known about the multi-kingdom microbiota interactions and their consequences. We enrolled participants from a prospective multicentre case–control study and investigated multi-kingdom microbiome differences using saliva metagenomic datasets (n = 308) from young patients diagnosed with cryptogenic ischemic stroke (CIS) and age- and sex-matched stroke-free controls. Differentially abundant taxa were identified using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC2). Functional potential was inferred using HUMANn3. Our findings revealed significant differences in the composition and functional capacity of the oral microbiota associated with CIS. We identified 51 microbial species, including 47 bacterial, 3 viral, and one fungal species associated with CIS in the adjusted model. Co-abundance network analysis highlighted a more intricate microbial network in CIS patients, indicating potential interactions and co-occurrence patterns among microbial species across kingdoms. The results of our metagenomic analysis reflect the complexity of the oral microbiome, with high diversity and multi-kingdom interactions, which may play a role in health and disease.

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Section: Methodsmentioning

confidence: 99%

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

Manzoor,

Leskelä,

Pietiäinen

et al. 2024

ISME Communications

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Oral microbiome profiles of gingivitis and periodontitis by next-generation sequencing among a group of hospital patients in Korea: A cross-sectional study

Lee,

Park,

Jeong

et al. 2024

Journal of Oral Biosciences

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Multiomics Analysis Reveals Significant Disparities in the Oral Microbiota and Metabolites Between Pregnant Women with and without Periodontitis

Zhao,

Yang,

Zhu

et al. 2024

IDR

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Introduction Our study investigated the disparities and correlations between oral microbiota and metabolites in pregnant patients with and without periodontitis. Methods Subgingival plaque samples from all subjects were collected for shotgun metagenomic sequencing and broad-target metabolomics analysis. Results Forty pathogens, including Porphyromonas gingivalis , Fusobacterium nucleatum , Eubacterium saphenum , Gemella morbillorum , Tannerella forsythia , Streptococcus anginosus group, Selenomonas sputigena etc, were significantly enriched in pregnant patients with periodontitis (PPP). Conversely, symbiotic species such as Morococcus cerebrosus , Streptococcus vestibularis , S. salivarius , S. mitis , and S. pneumoniae were significantly more abundant in healthy controls (HCs). A total of 87 predicted functional modules (PFMs) exhibited significant differences between the two groups; eight PFMs showed high enrichment in PPP with involvement of PPP-enriched species within these pathways. The remaining 79 PFMs encompassing ribonucleotide biosynthesis, carbohydrate, and amino acid metabolism were highly abundant in HCs. For oral microbial metabolome, a total of 105 metabolites related to 150 KEGG pathways displayed significant differences between the two groups. Pathways such as pyruvate metabolism, folate biosynthesis, vascular smooth muscle contraction, and AMPK/mTOR signaling pathway along with their associated metabolites were found to be enriched in PPP, while carbohydrate metabolism predominated among HCs. Spearman’s rank correlation analysis revealed significant positive associations between species enriched in PPP and metabolites enriched in PPP, but significant negative associations between species enriched in PPP and metabolites enriched in HCs. Discussion Our findings provide potential biomarkers for distinguishing periodontitis during pregnancy while offering valuable insights into mechanisms exploration and clinical intervention.

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Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study

Cited by 3 publications

References 66 publications

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke

Oral microbiome profiles of gingivitis and periodontitis by next-generation sequencing among a group of hospital patients in Korea: A cross-sectional study

Multiomics Analysis Reveals Significant Disparities in the Oral Microbiota and Metabolites Between Pregnant Women with and without Periodontitis

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