scholarly journals The oral microbiome

2017 ◽  
Vol 1 (4) ◽  
pp. 287-296 ◽  
Author(s):  
Liam P. Shaw ◽  
Andrew M. Smith ◽  
Adam P. Roberts
Keyword(s):  
Human Microbiome ◽  
Oral Microbiome ◽  
Core Microbiome ◽  
Individual Level ◽  
Host Interactions ◽  
Paradoxical Situation ◽  
Health And Disease ◽  
Stable Core ◽  
The Individual ◽  
Conserved Core

The human microbiome is receiving a great deal of attention as its role in health and disease becomes ever more apparent. The oral microbiome, perhaps due to the ease with which we can obtain samples, is arguably the most well-studied human microbiome to date. It is obvious, however, that we have only just begun to scratch the surface of the complex bacterial and bacterial–host interactions within this complex community. Here, we describe the factors which are known to influence the development of the seemingly globally conserved, core, oral microbiome and those which are likely to be responsible for the observed differences at the individual level. We discuss the paradoxical situation of maintaining a stable core microbiome which is at the same time incredibly resilient and adaptable to many different stresses encountered in the open environment of the oral cavity. Finally, we explore the interactions of the oral microbiome with the host and discuss the interactions underlying human health and disease.

The Genetics and Genomics of Asthma

2018 ◽  
Vol 19 (1) ◽  
pp. 223-246 ◽  
Author(s):  
Saffron A.G. Willis-Owen ◽  
William O.C. Cookson ◽  
Miriam F. Moffatt
Keyword(s):  
Sequence Variation ◽  
Human Microbiome ◽  
Technological Advances ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range ◽  
Health And Disease ◽  
Wide Scale ◽  
Genetics And Genomics ◽  
The Individual

Asthma is a common, clinically heterogeneous disease with strong evidence of heritability. Progress in defining the genetic underpinnings of asthma, however, has been slow and hampered by issues of inconsistency. Recent advances in the tools available for analysis—assaying transcription, sequence variation, and epigenetic marks on a genome-wide scale—have substantially altered this landscape. Applications of such approaches are consistent with heterogeneity at the level of causation and specify patterns of commonality with a wide range of alternative disease traits. Looking beyond the individual as the unit of study, advances in technology have also fostered comprehensive analysis of the human microbiome and its varied roles in health and disease. In this article, we consider the implications of these technological advances for our current understanding of the genetics and genomics of asthma.

scholarly journals Nutraceutical Boom in Cancer: Inside the Labyrinth of Reactive Oxygen Species

2020 ◽  
Vol 21 (6) ◽  
pp. 1936 ◽  
Author(s):  
Maura Calvani ◽  
Amada Pasha ◽  
Claudio Favre
Keyword(s):  
Well Being ◽  
Epidemiological Studies ◽  
Long Term Results ◽  
Negative Effects ◽  
Cell Growth Arrest ◽  
Host Interactions ◽  
Health And Disease ◽  
Pros And Cons ◽  
The Individual

In recent years, epidemiological studies have shown that food is a very powerful means for maintaining a state of well-being and for health prevention. Many degenerative, autoimmune and neoplastic diseases are related to nutrition and the nutrient–organism interaction could define the balance between health and disease. Nutrients and dietary components influence epigenetic phenomena and modify drugs response; therefore, these food–host interactions can influence the individual predisposition to disease and its potential therapeutic response. Do nutraceuticals have positive or negative effects during chemotherapy? The use of nutraceutical supplements in cancer patients is a controversial debate without a definitive conclusion to date. During cancer treatment, patients take nutraceuticals to alleviate drug toxicity and improve long-term results. Some nutraceuticals may potentiate the effect of cytotoxic chemotherapy by inducing cell growth arrest, cell differentiation, and alteration of the redox state of cells, but in some cases, high levels of them may interfere with the effectiveness of chemotherapy, making cancer cells less reactive to chemotherapy. In this review, we highlighted the emerging opinions and data on the pros and cons on the use of nutraceutical supplements during chemotherapy.

scholarly journals Importance of Interkingdom Interactions Among Oral Microbiome Towards Caries Development – A Review

2021 ◽  
Vol 5 (2) ◽  
pp. 27-35
Author(s):  
Kalpana Balakrishnan ◽  
Divya Sivanesan ◽  
Gaanappriya Mohan ◽  
Sachin Gunthe ◽  
Rama Verma
Keyword(s):  
Human Microbiome ◽  
Oral Microbiome ◽  
Systemic Diseases ◽  
Holistic View ◽  
Host System ◽  
Bacterial Diseases ◽  
Microbial Network ◽  
Health And Disease ◽  
Ecological Shifts ◽  
Candidate Phyla Radiation

The human microbiome plays a crucial role in health and disease conditions. These microbiomes constitute a structured, coordinated microbial network throughout the human body. The oral cavity harbors one of the extensively diverse bacteria in the human system. Although many studies emphasize bacteriome and its interaction with the host system, very little attention is given to candidate phyla radiation (CPR), fungal components, and its interkingdom interaction in the oral microecology even with advanced techniques. The interkingdom interactions among caries causing microbes trigger the pathogenesis of bacterial diseases and cause ecological shifts and affect the host system. Studying the complex relations among the diverse oral microbiome and its host, especially CPR phyla and fungi, would give a holistic view of the caries etiology. This review provides evidence on the interkingdom interaction that establishes a complex community that could help predict future oral and systemic diseases.

scholarly journals The Oral Microbiome of Healthy Japanese People at the Age of 90

2020 ◽  
Vol 10 (18) ◽  
pp. 6450 ◽  
Author(s):  
Yoshiaki Nomura ◽  
Erika Kakuta ◽  
Noboru Kaneko ◽  
Kaname Nohno ◽  
Akihiro Yoshihara ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Hypervariable Regions ◽  
Study Population ◽  
Granulicatella Adiacens

For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. Pyrosequencing was performed using MiSeq. Operational taxonomic units (OTUs) were assigned on the basis of a 97% identity search in the EzTaxon-e database. Using the threshold of 100% detection on the species level, 13 species were detected: Streptococcus sinensis, Streptococcus pneumoniae, Streptococcus salivarius, KV831974_s, Streptococcus parasanguinis, Veillonella dispar, Granulicatella adiacens, Streptococcus_uc, Streptococcus peroris, KE952139_s, Veillonella parvula, Atopobium parvulum, and AFQU_vs. These species represent potential candidates for the core make-up of the human microbiome.

The Exposome: Molecules to Populations

2019 ◽  
Vol 59 (1) ◽  
pp. 107-127 ◽  
Author(s):  
Megan M. Niedzwiecki ◽  
Douglas I. Walker ◽  
Roel Vermeulen ◽  
Marc Chadeau-Hyam ◽  
Dean P. Jones ◽  
...  
Keyword(s):  
Population Level ◽  
Group Level ◽  
Individual Level ◽  
Biological Responses ◽  
Psychological Stressors ◽  
Health And Disease ◽  
Pharmacology And Toxicology ◽  
Scale Characterization ◽  
The Individual

Derived from the term exposure, the exposome is an omic-scale characterization of the nongenetic drivers of health and disease. With the genome, it defines the phenome of an individual. The measurement of complex environmental factors that exert pressure on our health has not kept pace with genomics and historically has not provided a similar level of resolution. Emerging technologies make it possible to obtain detailed information on drugs, toxicants, pollutants, nutrients, and physical and psychological stressors on an omic scale. These forces can also be assessed at systems and network levels, providing a framework for advances in pharmacology and toxicology. The exposome paradigm can improve the analysis of drug interactions and detection of adverse effects of drugs and toxicants and provide data on biological responses to exposures. The comprehensive model can provide data at the individual level for precision medicine, group level for clinical trials, and population level for public health.

scholarly journals Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Alejandra Hernandez-Agreda ◽  
William Leggat ◽  
Pim Bongaerts ◽  
César Herrera ◽  
Tracy D. Ainsworth
Keyword(s):  
Microbial Community ◽  
Core Microbiome ◽  
Functional Roles ◽  
Individual Level ◽  
Coral Microbiome ◽  
Coral Holobiont ◽  
Environmentally Responsive ◽  
The Individual ◽  
Species Specific ◽  
Responsive Community

ABSTRACTStudies of the coral microbiome predominantly characterize the microbial community of the host species as a collective, rather than that of the individual. This ecological perspective on the coral microbiome has led to the conclusion that the coral holobiont is the most diverse microbial biosphere studied thus far. However, investigating the microbiome of the individual, rather than that of the species, highlights common and conserved community attributes which can provide insights into the significance of microbial associations to the host. Here, we show there are consistent characteristics between individuals in the proposed three components of the coral microbiome (i.e., “environmentally responsive community,” “resident or individual microbiome,” and “core microbiome”). We found that the resident microbiome of a photoendosymbiotic coral harbored <3% (∼605 phylotypes) of the 16S rRNA phylotypes associated with all investigated individuals of that species (“species-specific microbiome”) (∼21,654 phylotypes; individuals fromPachyseris speciosa[n= 123],Mycedium elephantotus[n= 95], andAcropora aculeus[n= 91] from 10 reef locations). The remaining bacterial phylotypes (>96%) (environmentally responsive community) of the species-specific microbiome were in fact not found in association with the majority of individuals of the species. Only 0.1% (∼21 phylotypes) of the species-specific microbiome of each species was shared among all individuals of the species (core microbiome), equating to ∼3.4% of the resident microbiome. We found taxonomic redundancy and consistent patterns of composition, structure, and taxonomic breadth across individual microbiomes from the three coral species. Our results demonstrate that the coral microbiome is structured at the individual level.IMPORTANCEWe propose that the coral holobiont should be conceptualized as a diverse transient microbial community that is responsive to the surrounding environment and encompasses a simple, redundant, resident microbiome and a small conserved core microbiome. Most importantly, we show that the coral microbiome is comparable to the microbiomes of other organisms studied thus far. Accurately characterizing the coral-microbe interactions provides an important baseline from which the functional roles and the functional niches within which microbes reside can be deciphered.

scholarly journals Genome binning of viral entities from bulk metagenomics data

2021 ◽  
Author(s):  
Joachim Johansen ◽  
Damian R Plichta ◽  
Jakob Nybo Nissen ◽  
Marie Louise Jespersen ◽  
Shiraz A Shah ◽  
...  
Keyword(s):  
Deep Learning ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Gastrointestinal Diseases ◽  
Human Gut ◽  
Viral Genomes ◽  
Host Interactions ◽  
Metagenomics Data ◽  
Health And Disease ◽  
Viral Host Interactions

Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal are not well understood. In addition, a paucity of whole-virome datasets from subjects with gastrointestinal diseases is preventing a deeper understanding of the virome role in disease and in gastrointestinal ecology as a whole. By combining a deep-learning based metagenomics binning algorithm with paired metagenome and metavirome datasets we developed the Phages from Metagenomics Binning (PHAMB) approach for binning thousands of viral genomes directly from bulk metagenomics data. Simultaneously our methodology enables clustering of viral genomes into accurate taxonomic viral populations. We applied this methodology on the Human Microbiome Project 2 (HMP2) cohort and recovered 6,077 HQ genomes from 1,024 viral populations and explored viral-host interactions. We show that binning can be advantageously applied to existing and future metagenomes to illuminate viral ecological dynamics with other microbiome constituents.

scholarly journals The evolution and changing ecology of the African hominid oral microbiome

2021 ◽  
Vol 118 (20) ◽  
pp. e2021655118
Author(s):  
James A. Fellows Yates ◽  
Irina M. Velsko ◽  
Franziska Aron ◽  
Cosimo Posth ◽  
Courtney A. Hofman ◽  
...  
Keyword(s):  
Oral Bacteria ◽  
Oral Microbiome ◽  
Human Populations ◽  
Ancestral State ◽  
Oral Streptococci ◽  
Howler Monkeys ◽  
Modern Humans ◽  
Core Microbiome ◽  
Dental Biofilm ◽  
Health And Disease

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

scholarly journals Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

2021 ◽  
Vol 12 ◽  
Author(s):  
Bouchra Ezzamouri ◽  
Saeed Shoaie ◽  
Rodrigo Ledesma-Amaro
Keyword(s):  
Synthetic Biology ◽  
Microbial Communities ◽  
System Biology ◽  
Large Scale ◽  
Human Microbiome ◽  
Host Responses ◽  
Future Research ◽  
Host Interactions ◽  
Health And Disease ◽  
Genome Scale

A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next-generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays, and engineered bacteria can rewire the microbiome environment. In this article, we review the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models (GEMs) can advance our understanding of the microbe–microbe and microbe–host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields.

Differential Effects of Competence and Morality on Self-Esteem at the Individual and the Collective Level

2020 ◽  
Vol 51 (3) ◽  
pp. 183-198
Author(s):  
Wiktor Soral ◽  
Mirosław Kofta
Keyword(s):  
Self Esteem ◽  
Differential Effects ◽  
Individual Level ◽  
The Subject ◽  
The Individual

Abstract. The importance of various trait dimensions explaining positive global self-esteem has been the subject of numerous studies. While some have provided support for the importance of agency, others have highlighted the importance of communion. This discrepancy can be explained, if one takes into account that people define and value their self both in individual and in collective terms. Two studies ( N = 367 and N = 263) examined the extent to which competence (an aspect of agency), morality, and sociability (the aspects of communion) promote high self-esteem at the individual and the collective level. In both studies, competence was the strongest predictor of self-esteem at the individual level, whereas morality was the strongest predictor of self-esteem at the collective level.

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