scholarly journals Oral Microbiome and Cancer Therapy-Induced Oral Mucositis

2019 ◽  
Vol 2019 (53) ◽  
Author(s):  
Jean-Luc C Mougeot ◽  
Craig B Stevens ◽  
Darla S Morton ◽  
Michael T Brennan ◽  
Farah B Mougeot
Keyword(s):  
Cancer Therapy ◽  
Oral Mucositis ◽  
Human Microbiome ◽  
Holistic Approach ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Commensal Microbiota ◽  
Intestinal Mucositis

AbstractCharacterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients’ health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.

scholarly journals Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Daniel R. Utter ◽  
Gary G. Borisy ◽  
A. Murat Eren ◽  
Colleen M. Cavanaugh ◽  
Jessica L. Mark Welch
Keyword(s):  
Buccal Mucosa ◽  
Habitat Preferences ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Functional Enrichment ◽  
Habitat Adaptation ◽  
Haemophilus Parainfluenzae ◽  
Population Structures ◽  
Genome Content

Abstract Background The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. Results Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous. Conclusions Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

scholarly journals Peritoneal Microbiome in End-Stage Renal Disease Patients and the Impact of Peritoneal Dialysis Therapy

2020 ◽  
Vol 8 (2) ◽  
pp. 173
Author(s):  
Liliana Simões-Silva ◽  
Ricardo Araujo ◽  
Manuel Pestana ◽  
Isabel Soares-Silva ◽  
Benedita Sampaio-Maia
Keyword(s):  
Peritoneal Dialysis ◽  
Human Microbiome ◽  
Cross Sectional Study ◽  
Cross Sectional ◽  
Peritoneal Tissue ◽  
Stage Renal Disease ◽  
End Stage ◽  
The Impact

Factors influencing the occurrence of peritoneal dialysis (PD)-related infections are still far from fully understood. Recent studies described the existence of specific microbiomes in body sites previously considered microbiome-free, unravelling new microbial pathways in the human body. In the present study, we analyzed the peritoneum of end-stage kidney disease (ESKD) patients to determine if they harbored a specific microbiome and if it is altered in patients on PD therapy. We conducted a cross-sectional study where the peritoneal microbiomes from ESKD patients with intact peritoneal cavities (ESKD non-PD, n = 11) and ESKD patients undergoing PD therapy (ESKD PD, n = 9) were analyzed with a 16S rRNA approach. Peritoneal tissue of ESKD patients contained characteristically low-abundance microbiomes dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Patients undergoing PD therapy presented lower species richness, with dominance by the Pseudomonadaceae and Prevotelaceae families. This study provides the first characterization of the peritoneal microbiome in ESKD patients, bringing new insight to the human microbiome. Additionally, PD therapy may induce changes in this unique microbiome. The clinical relevance of these observations should be further explored to uncover the role of the peritoneal microbiome as a key element in the onset or aggravation of infection in ESKD patients, especially those undergoing PD.

scholarly journals Unity of bowel-lung axis and the role of beneficial microbiota in anti-infectious protection

2021 ◽  
Vol 4 (4) ◽  
pp. 355-361
Author(s):  
T.E. Taranushenko ◽  
Keyword(s):  
Immune Responses ◽  
Respiratory Infections ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Medical Community ◽  
Mucosal Inflammation ◽  
Potential Interactions ◽  
The Impact ◽  
And Child Health

NIH Human Microbiome Project determined particular attention of the worldwide medical community to the study of the human microbiome and the assessment of the impact of symbiont microorganisms in the development of various (not only gastrointestinal) disorders. Potential interactions between the bowel and lungs (bowel-lung axis) via microbiota that allow for the possible involvement of microorganisms in the development of respiratory diseases are actively debated. This paper reviews studies on the pattern of interactions between bowel and lungs in infectious diseases associated with mucosal inflammation. The association between gut microbiota and the protective barrier of the respiratory tract based on known mechanisms and novel data derived from recent studies on SARS-CoV-2 is discussed. The relevance of beneficial bacteria (symbionts) in local and systemic immune responses, their disease-modifying and, eventually, therapeutic strategymodifying properties, the ability to be a resource of preventive medicine and an orchestrating tool for infections are addressed. Practitioners’ difficulties with probiotics in preventive and treatment schedules for various conditions are highlighted. Finally, the use of probiotics in children with respiratory infections and COVID-19 is uncovered. KEYWORDS: microbiota, microbiome, probiotics, children, mucosal immunity, Bifidobacterium. FOR CITATION: Taranushenko T.E. Unity of bowel-lung axis and the role of beneficial microbiota in anti-infectious protection. Russian Journal of Woman and Child Health. 2021;4(4):355–361 (in Russ.). DOI: 10.32364/2618-8430-2021-4-4-355-361.

scholarly journals Forensic Human Identification for Cutaneous Microbiome, a Brief Review

2021 ◽  
Vol 10 (3) ◽  
pp. 244-251
Author(s):  
Natasha R.F. Novaes ◽  
Isabel C. M. Fensterseifer ◽  
José L. R. Martins ◽  
Osmar N. Silva
Keyword(s):  
Bacterial Genome ◽  
Human Microbiome ◽  
Human Identification ◽  
Human Microbiome Project ◽  
Forensic Identification ◽  
Skin Microbiome ◽  
Predictive Algorithms ◽  
Forensic Microbiology ◽  
The Relationship

Forensic Science compounds many study areas in context of solving crimes, one of which is the forensic microbiology. Combined with genomic approaches, microbiology has shown strong performance in studies regarding the relationship between microorganisms present on human skin and environment. The Human Microbiome Project (HMP) has contributed significantly to characterization of microbial complexity and their connection to human being. The purpose of this work consists of a historical overview of scientific articles, demonstrating the growth and possibility of using skin microbiome in forensic identification. Studies about use of cutaneous microbiome in human identification, as well its forensic approaches, were looked into for writing of this review. Comparisons among cutaneous microbial communities and manipulated objects have been tested using 16S rRNA, as well as a thorough sequencing of the bacterial genome. From use of ecological measures of distance to genetic markers with nucleotide variants and predictive algorithms, research has shown promising results for advances in field of forensic identification. The development of metagenomic microbial panel markers, named hidSkinPlax for targeted sequencing has been designed and tested with great results. Research results show satisfactory potential in human identification by cutaneous microbiome and the possibility for contributive use in elucidating crimes.

scholarly journals Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Si Xian Ho ◽  
Nyo Min ◽  
Emmerie Phaik Yen Wong ◽  
Chia Yin Chong ◽  
Justin Jang Hann Chu
Keyword(s):  
Wide Spectrum ◽  
Clinical Manifestations ◽  
Human Microbiome ◽  
Foot And Mouth Disease ◽  
Critical Factor ◽  
Mouth Disease ◽  
Oral Microbiome ◽  
Coxsackievirus A6 ◽  
Foot And Mouth

AbstractWhile the underlying determinants are unclear, hand, foot and mouth disease (HFMD) presents a wide spectrum of clinical manifestations with varying severity in different individuals. Recently, many studies identified the human microbiome as a critical factor in the pathogenesis of various diseases. Therefore, we here investigated the ecological dynamics of the oral microbiome changes during the HFMD infection. After targeted enrichment of all known vertebrate viruses, the virome profiles of symptomatic and asymptomatic HFMD patients were examined and revealed to be significantly altered from those of healthy individuals, with nine discriminative viruses detected. Further characterization of the prokaryotic microbiome revealed an elevated level of Streptococcus sp. as the most important signature of the symptomatic HFMD cohort, positively correlating to the level of enterovirus A RNA. In addition, we found that while coxsackievirus A5 is detected in saliva RNA of all asymptomatic cases, coxsackievirus A6 dominates the majority of the symptomatic cohort.

scholarly journals Improving characterization of understudied human microbiomes using targeted phylogenetics

2019 ◽  
Author(s):  
Bruce A Rosa ◽  
Kathie Mihindukulasuriya ◽  
Kymberlie Hallsworth-Pepin ◽  
Aye Wollam ◽  
John Martin ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Genomic Sequences ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Genomic Databases ◽  
Disease States ◽  
Health And Disease ◽  
Taxonomic Groups

AbstractWhole genome bacterial sequences are required to better understand microbial functions, niches-pecific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g. stool), as few as 13% of bacterial-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from under-represented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full length 16S rRNA sequences, clustered the sequences to ensure that no individual taxonomic group was over-selected for sequencing, prioritized bacteria from under-represented body sites (such as skin, respiratory and urinary tract), and sequenced and assembled genomes for 665 new bacterial strains. Here we show that addition of these genomes improved read mapping rates of HMP metagenomic samples by nearly 30% for the previously under-represented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and clinical perspective.ImportanceThe human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily stool), while other sites such as the skin, respiratory tract and urinary tracts are under-represented, resulting in as little as 13% of bacterial-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select under-represented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies.

scholarly journals Human Breast Milk Bacteriome in Health and Disease

Nutrients ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1643 ◽  
Author(s):  
Anna Ojo-Okunola ◽  
Mark Nicol ◽  
Elloise du Toit
Keyword(s):  
Breast Milk ◽  
Bacterial Diversity ◽  
Infant Health ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Human Breast Milk ◽  
Human Breast ◽  
Diseased State ◽  
Micro Organisms

It is well-known that, beyond nutritional components, human breast milk (HBM) contains a wide variety of non-nutritive bio-factors perfectly suited for the growing infant. In the pre-2000 era, HBM was considered sterile and devoid of micro-organisms. Though HBM was not included as part of the human microbiome project launched in 2007, great strides have been made in studying the bacterial diversity of HBM in both a healthy state and diseased state, and in understanding their role in infant health. HBM provides a vast array of beneficial micro-organisms that play a key role in colonizing the infant’s mucosal system, including that of the gut. They also have a role in priming the infant’s immune system and supporting its maturation. In this review, we provide an in-depth and updated insight into the immunomodulatory, metabolic, and anti-infective role of HBM bacteriome (bacterial community) and its effect on infant health. We also provide key information from the literature by exploring the possible origin of microbial communities in HBM, the bacterial diversity in this niche and the determinants influencing the HBM bacteriome. Lastly, we investigate the role of the HBM bacteriome in maternal infectious disease (human immunodeficiency virus (HIV) and mastitis)), and cancer. Key gaps in HBM bacterial research are also identified.

scholarly journals Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

2020 ◽  
Author(s):  
Daniel R. Utter ◽  
Gary G. Borisy ◽  
A. Murat Eren ◽  
Colleen M. Cavanaugh ◽  
Jessica L. Mark Welch
Keyword(s):  
Buccal Mucosa ◽  
Habitat Preferences ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
Functional Enrichment ◽  
Habitat Adaptation ◽  
Haemophilus Parainfluenzae ◽  
Population Structures ◽  
Genome Content

AbstractBackgroundThe increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.ResultsHere, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes revealed distinct genomic groups based on shared genome content. H. parainfluenzae genomes separated into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identified an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulated species-level taxonomy and habitat preferences. However, while most R. mucilaginosa were restricted to the tongue as expected, two genomes represented a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identified not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences were absent or ubiquitous.ConclusionsOur findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

scholarly journals The effect of the stress hormone cortisol on the metatranscriptome of the oral microbiome

2018 ◽  
Author(s):  
Ana E. Duran-Pinedo ◽  
Jose Solbiati ◽  
Jorge Frias-Lopez
Keyword(s):  
Expression Profiles ◽  
Biological Effects ◽  
Human Microbiome ◽  
Gene Expression Profiles ◽  
Oral Microbiome ◽  
Stress Hormone ◽  
Commensal Microbiota ◽  
Microbial Dysbiosis ◽  
Psychological Stressors ◽  
The Impact

ABSTRACTImbalances of the microbiome also referred to as microbial dysbiosis, could lead to a series of different diseases. One factor that has been shown to lead to dysbiosis of the microbiome is exposure to psychological stressors. Throughout evolution microorganisms of the human microbiome have developed systems for sensing host-associated signals such as hormones associated with those stressors, enabling them to recognize essential changes in its environment thus changing its expression gene profile to fit the needs of the new environment. The most widely accepted theory explaining the ability of hormones to affect the outcome of an infection involves the suppression of the immune system. Commensal microbiota is involved in stressor-induced immunomodulation, but other biological effects are not yet known. Here we present the impact that cortisol had on the community-wide transcriptome of the oral community. We used a metatranscriptomic approach to obtain first insights into the metabolic changes induced by this stress hormone as well as which members of the oral microbiome respond to the presence of cortisol in the environment. Our findings show that the stress hormone cortisol directly induces shifts in the gene expression profiles of the oral microbiome that reproduce results found in the profiles of expression of periodontal disease and its progression.

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