Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis

Heng, Weiwei; Wang, Wenmei; Dai, Tingting; Jiang, Ping; Lu, Yong; Li, Ruowei; Zhang, Miaomiao; Xie, Ruiqi; Zhou, Yifan; Zhao, Ming; Duan, Ning; Ye, Zhengqin; Yan, Fuhua; Wang, Xiang

doi:10.1128/spectrum.02737-22

Cited by 21 publications

(18 citation statements)

References 75 publications

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“…This highlights the utility of amplicon sequencing in sufficient and rather deep capture of the sparsely abundant members of the rare biosphere (in this case fungi), which could be missed by a data demanding WGS. Members of Penicillium and Wallemia have also previously been known to be observed in a handful of human oral microbiome (14,20,33,55). Given the understudied and under characterized nature of the human mycobiota due to the limited available reports, along with a relatively nascent stage of fungal classification-databases and algorithms, it is expected that new members may further be identified through future technical advancements.…”

Section: Discussionmentioning

confidence: 99%

“…Human microbiome is predominantly composed of the bacterial cells (e.g., ∼10 11 -10 12 CFU/g of cultivable bacteria in the faeces or 10 9 -10 10 CFU/ml of saliva in the oral cavity) (1, 32). A sparse content of other microorganisms, also called as the rare biosphere, is also observed in the human microflora (e.g., fungi, comparably forming ∼10 3 -10 6 CFU/g of faeces or 10 1 -10 4 CFU/ml of saliva) (1, 4, 32, 33). This inherent sparsity of non-bacteriome populations in the total microbiome can perhaps offer an advantage in concomitantly sequencing a fraction of their (few kilobase long) marker amplicons (∼ 0.6 kb ITS region) along with the major proportion of the bacterial amplicons (∼ 1.5 kb 16S gene) without prejudicing the coverage of the either.…”

Section: Introductionmentioning

confidence: 99%

“…A few recent reports, though using short reads and a small number of samples, have in fact provided encouraging evidence towards potential to concomitantly capture both bacteriome and mycobiome using amplicon sequencing (31, 34). Current literature evidence however seems to indicate that a majority of non-bacteriome (primarily mycobiota) studies are done in silos (e.g., only mycobiome profiling of oral cavity) (5, 14, 20, 22, 35, 36) with a handful of short read microbiome studies attempting both bacterial and fungal amplicon sequencing for the targeted samples, often as independent libraries or even independently sequenced bioprojects (31, 33, 37–39). Studies showcasing the success (and even failures) of the multi-kingdom amplicon sequencing approach, with clearly outlined protocols may add to the currently very limited evidence and encourage the (resource constrained) researchers to expand the scope of their microbiome research.…”

Section: Introductionmentioning

confidence: 99%

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EnsembleSeq: A workflow towards real-time, rapid and simultaneous multi-kingdom amplicon sequencing for holistic and cost-effective microbiome research at scale

Nagpal,

Mande,

Hooda

et al. 2023

Preprint

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BackgroundBacterial communities are often concomitantly present with numerous microorganisms in the human body and other natural environments. Amplicon based microbiome studies have generally paid a skewed attention, that too at a rather shallow genus level resolution, to the highly abundant bacteriome, with interest now forking towards the other microorganisms, particularly fungi. Given the generally sparse abundance of other microbes in the total microbiome, simultaneous sequencing of amplicons targeting multiple microbial kingdoms could be possible even with full multiplexing. Guiding studies are currently needed for performing and monitoring multi-kingdom-amplicon sequencing and data capture at scale.MethodFull length bacterial 16S rRNA gene and entire fungal ITS region amplification was performed for human saliva samples (n=96, including negative and positive controls). Combined amplicon DNA libraries were prepared for nanopore sequencing using a major fraction of 16S molecules and a minor fraction of ITS amplicons. Sequencing was performed in a single run of an R10.4.1 flowcell employing the latest V14 chemistry. An approach for real time monitoring of the species saturation using dynamic rarefaction was designed as a guiding determinant of optimal run time.ResultsReal-time saturation monitoring for both bacterial and fungal species enabled the completion of sequencing within 30 hours, utilizing less than 60% of the total nanopores. ∼5 million HQ taxonomically assigned reads were generated (∼4.2 million bacterial and 0.7 million fungal), providing a wider (beyond bacteriome) snapshot of human oral microbiota at species level resolution. Among the more than 400 bacterial and 240 fungal species identified in the studied samples, the species of Streptococcus (e.g.S. mitis, S. oralis) and Candida (e.g.C. albicans, C. tropicalis) were observed to be the dominating microbes in the oral cavity, respectively. This conformed well with the previous reports of the human oral microbiota.ConclusionEnsembleseq provides a proof-of-concept towards identification of both fungal and bacterial species simultaneously in a single fully multiplexed nanopore sequencing run in a time and resource effective manner. Details of this workflow are provided to enable large scale application for a holistic species level microbiome study.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

EnsembleSeq: A workflow towards real-time, rapid and simultaneous multi-kingdom amplicon sequencing for holistic and cost-effective microbiome research at scale

Nagpal,

Mande,

Hooda

et al. 2023

Preprint

View full text Add to dashboard Cite

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“…One additional limitation applies to phage therapeutics in a microbiome setting, namely the vital emerging roles of non-bacterial drivers of dysbiosis. These include viruses other than phages, which are increasingly recognized as important in maintaining gut ecological balance and contributors to dysbiosis in disease [ 109 , 110 , 111 , 112 ], as well as fungi and protozoa [ 113 , 114 , 115 , 116 , 117 ]. Phages targeting bacteria exclusively are unable to directly affect these organisms of emerging importance.…”

Section: Targeted Microbiome Therapeutics: Opportunities and Challengesmentioning

confidence: 99%

A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics—Leveraging Principles of Systems Biology

et al. 2023

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The study of human microbiomes has yielded insights into basic science, and applied therapeutics are emerging. However, conflicting definitions of what microbiomes are and how they affect the health of the “host” are less understood. A major impediment towards systematic design, discovery, and implementation of targeted microbiome therapeutics is the continued reliance on taxonomic indicators to define microbiomes in health and disease. Such reliance often confounds analyses, potentially suggesting associations where there are none, and conversely failing to identify significant, causal relationships. This review article discusses recent discoveries pointing towards a molecular understanding of microbiome “dysbiosis” and away from a purely taxonomic approach. We highlight the growing role of systems biological principles in the complex interrelationships between the gut microbiome and host cells, and review current approaches commonly used in targeted microbiome therapeutics, including fecal microbial transplant, bacteriophage therapies, and the use of metabolic toxins to selectively eliminate specific taxa from dysbiotic microbiomes. These approaches, however, remain wholly or partially dependent on the bacterial taxa involved in dysbiosis, and therefore may not capitalize fully on many therapeutic opportunities presented at the bioactive molecular level. New technologies capable of addressing microbiome-associated diseases as molecular problems, if solved, will open possibilities of new classes and categories of targeted microbiome therapeutics aimed, in principle, at all dysbiosis-driven disorders.

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“…In turn, this would lead to an inflammatory response in patients with MAFLD. Most studies have focused on gut bacteria, with little attention given to fungal alterations( Heng et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease

Niu

Jin

et al. 2023

Front. Cell. Infect. Microbiol.

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Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed “oral-gut-liver axis” concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible “oral-gut-liver” axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.

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Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis

Cited by 21 publications

References 75 publications

EnsembleSeq: A workflow towards real-time, rapid and simultaneous multi-kingdom amplicon sequencing for holistic and cost-effective microbiome research at scale

EnsembleSeq: A workflow towards real-time, rapid and simultaneous multi-kingdom amplicon sequencing for holistic and cost-effective microbiome research at scale

A Taxonomy-Agnostic Approach to Targeted Microbiome Therapeutics—Leveraging Principles of Systems Biology

Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease

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