scholarly journals The Oral and Gut Bacterial Microbiomes: Similarities, Differences, and Connections

2020 ◽  
Vol 23 (1) ◽  
pp. 7-20
Author(s):  
Katherine A. Maki ◽  
Narjis Kazmi ◽  
Jennifer J. Barb ◽  
Nancy Ames
Keyword(s):  
Gut Microbiome ◽  
Alpha Diversity ◽  
Oral Microbiome ◽  
Taxonomic Resolution ◽  
Future Research ◽  
Sequencing Analysis ◽  
Systemic Diseases ◽  
Shotgun Metagenomics ◽  
Healthy Humans ◽  
Microbiome Research

Background: The oral cavity is associated with local and systemic diseases, although oral samples are not as commonly studied as fecal samples in microbiome research. There is a gap in understanding between the similarities and differences in oral and gut microbiomes and how they may influence each other. Methods: A scoping literature review was conducted comparing oral and gut microbiome communities in healthy humans. Results: Ten manuscripts met inclusion criteria and were examined. The oral microbiome sites demonstrated great variance in differential bacterial abundance and the oral microbiome had higher alpha diversity as compared to the gut microbiome. Studies using 16S rRNA sequencing analysis resulted in overall community differences between the oral and gut microbiomes when beta diversity was analyzed. Shotgun metagenomics sequencing increased taxonomic resolution to strain level (intraspecies) and demonstrated a greater percentage of shared taxonomy and oral bacterial translocation to the gut microbiome community. Discussion: The oral and gut microbiome bacterial communities may be more similar than earlier research has suggested, when species strain is analyzed through shotgun metagenomics sequencing. The association between oral health and systemic diseases has been widely reported but many mechanisms underlying this relationship are unknown. Although future research is needed, the oral microbiome may be a novel interventional target through its downstream effects on the gut microbiome. As nurse scientists are experts in symptom characterization and phenotyping of patients, they are also well posed to lead research on the connection of the oral microbiome to the gut microbiome in health and disease.

scholarly journals Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiangning Bai ◽  
Aswathy Narayanan ◽  
Piotr Nowak ◽  
Shilpa Ray ◽  
Ujjwal Neogi ◽  
...  
Keyword(s):  
Antiretroviral Therapy ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Human Gut ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Hiv 1

Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.

scholarly journals Evidence supporting the microbiota–gut–brain axis in a songbird

2020 ◽  
Vol 16 (11) ◽  
pp. 20200430
Author(s):  
Morgan C. Slevin ◽  
Jennifer L. Houtz ◽  
David J. Bradshaw ◽  
Rindy C. Anderson
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Cloacal Swab ◽  
Cognitive Tasks ◽  
Captive Population ◽  
Wild Populations ◽  
Alpha And Beta Diversity ◽  
Microbiome Research ◽  
Host Development

Recent research in mammals supports a link between cognitive ability and the gut microbiome, but little is known about this relationship in other taxa. In a captive population of 38 zebra finches ( Taeniopygia guttata ), we quantified performance on cognitive tasks measuring learning and memory. We sampled the gut microbiome via cloacal swab and quantified bacterial alpha and beta diversity. Performance on cognitive tasks related to beta diversity but not alpha diversity. We then identified differentially abundant genera influential in the beta diversity differences among cognitive performance categories. Though correlational, this study provides some of the first evidence of an avian microbiota–gut–brain axis, building foundations for future microbiome research in wild populations and during host development.

scholarly journals The Oral Microbiota: A Literature Review for Updating Professionals in Dentistry. Part I

2019 ◽  
pp. 143-152
Author(s):  
Cristina Barboza-Solís DDS, MSc, PhD ◽  
Luis Alberto Acuña-Amador PhD
Keyword(s):  
Oral Health ◽  
Scientific Evidence ◽  
Oral Microbiome ◽  
Current Evidence ◽  
Future Research ◽  
Oral Microbiota ◽  
Systemic Diseases ◽  
Conceptual Background ◽  
Keyword Searches

In recent decades, a body of literature examining the relationships between oral health and general health has rapidly developed. However, the biological mechanisms involved in explaining such relationships have not been fully described. Recent evidence has suggested that these relationships could be partially explained by the composition and interaction of the microbiome/microbiota between local and systemic body sites. For instance, it has been suggested that intestinal microbiota could have effects on non-communicable diseases, such as diabetes or cardiovascular diseases. The objective of this study is to explore current evidence of the link between oral and systemic diseases, to discuss whether oral microbiome/microbiota could represent an unexplored biological pathway partially explaining those relationships. A non-systematic review of the literature was carried out using keyword searches in Pubmed from February to May 2019. The ultimate goal was to present recent scientific evidence to update the general knowledge on this topic to professionals in dentistry. This review is divided in two parts for journal publication; however, it is intended to be used as one piece. In this first part, we will summarize the conceptual background of oral microbiome/microbiota, we will describe the main methods used in microbiology to characterize oral organisms, and will present the main composition of bacteria in oral microbiome/microbiota. The second part highlights the main evidence regarding the biological plausibility that links oral microbiome and systemic diseases and we will conclude with some future research recommendations. Taking into account the role of oral microbiota in the development of systemic diseases could change the main paradigm of how oral health is currently conceptualized by dental professionals.

scholarly journals Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Shi Huang ◽  
Niina Haiminen ◽  
Anna-Paola Carrieri ◽  
Rebecca Hu ◽  
Lingjing Jiang ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Prediction Models ◽  
The Body ◽  
Oral Microbiome ◽  
Chronological Age ◽  
Future Research ◽  
Skin Microbiome ◽  
Age Related ◽  
Relative Value

ABSTRACT Human gut microbiomes are known to change with age, yet the relative value of human microbiomes across the body as predictors of age, and prediction robustness across populations is unknown. In this study, we tested the ability of the oral, gut, and skin (hand and forehead) microbiomes to predict age in adults using random forest regression on data combined from multiple publicly available studies, evaluating the models in each cohort individually. Intriguingly, the skin microbiome provides the best prediction of age (mean ± standard deviation, 3.8 ± 0.45 years, versus 4.5 ± 0.14 years for the oral microbiome and 11.5 ± 0.12 years for the gut microbiome). This also agrees with forensic studies showing that the skin microbiome predicts postmortem interval better than microbiomes from other body sites. Age prediction models constructed from the hand microbiome generalized to the forehead and vice versa, across cohorts, and results from the gut microbiome generalized across multiple cohorts (United States, United Kingdom, and China). Interestingly, taxa enriched in young individuals (18 to 30 years) tend to be more abundant and more prevalent than taxa enriched in elderly individuals (>60 yrs), suggesting a model in which physiological aging occurs concomitantly with the loss of key taxa over a lifetime, enabling potential microbiome-targeted therapeutic strategies to prevent aging. IMPORTANCE Considerable evidence suggests that the gut microbiome changes with age or even accelerates aging in adults. Whether the age-related changes in the gut microbiome are more or less prominent than those for other body sites and whether predictions can be made about a person’s age from a microbiome sample remain unknown. We therefore combined several large studies from different countries to determine which body site’s microbiome could most accurately predict age. We found that the skin was the best, on average yielding predictions within 4 years of chronological age. This study sets the stage for future research on the role of the microbiome in accelerating or decelerating the aging process and in the susceptibility for age-related diseases.

scholarly journals Multi ‘Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway

2021 ◽  
Vol 12 ◽  
Author(s):  
Adam J. Berlinberg ◽  
Emilie H. Regner ◽  
Andrew Stahly ◽  
Ana Brar ◽  
Julie A. Reisz ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Intestinal Inflammation ◽  
Alpha Diversity ◽  
Distal Colon ◽  
Tryptophan Metabolism ◽  
Genetic Changes ◽  
Shotgun Metagenomics ◽  
Fecal Samples ◽  
Disease States ◽  
Microbial Dysbiosis

Intestinal microbial dysbiosis, intestinal inflammation, and Th17 immunity are all linked to the pathophysiology of spondyloarthritis (SpA); however, the mechanisms linking them remain unknown. One potential hypothesis suggests that the dysbiotic gut microbiome as a whole produces metabolites that influence human immune cells. To identify potential disease-relevant, microbiome-produced metabolites, we performed metabolomics screening and shotgun metagenomics on paired colon biopsies and fecal samples, respectively, from subjects with axial SpA (axSpA, N=21), Crohn’s disease (CD, N=27), and Crohn’s-axSpA overlap (CD-axSpA, N=12), as well as controls (HC, N=24). Using LC-MS based metabolomics of 4 non-inflamed pinch biopsies of the distal colon from subjects, we identified significant alterations in tryptophan pathway metabolites, including an expansion of indole-3-acetate (IAA) in axSpA and CD-axSpA compared to HC and CD and indole-3-acetaldehyde (I3Ald) in axSpA and CD-axSpA but not CD compared to HC, suggesting possible specificity to the development of axSpA. We then performed shotgun metagenomics of fecal samples to characterize gut microbial dysbiosis across these disease states. In spite of no significant differences in alpha-diversity among the 4 groups, our results confirmed differences in gene abundances of numerous enzymes involved in tryptophan metabolism. Specifically, gene abundance of indolepyruvate decarboxylase, which generates IAA and I3Ald, was significantly elevated in individuals with axSpA while gene abundances in HC demonstrated a propensity towards tryptophan synthesis. Such genetic changes were not observed in CD, again suggesting disease specificity for axSpA. Given the emerging role of tryptophan and its metabolites in immune function, altogether these data indicate that tryptophan metabolism into I3Ald and then IAA is one mechanism by which the gut microbiome potentially influences the development of axSpA.

scholarly journals Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Simone Rampelli ◽  
Matteo Soverini ◽  
Federica D’Amico ◽  
Monica Barone ◽  
Teresa Tavella ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Taxonomic Resolution ◽  
Human Beings ◽  
Human Gut ◽  
Shotgun Metagenomics ◽  
Human Gut Microbiome ◽  
Age Related ◽  
General Decline ◽  
Extreme Longevity ◽  
Xenobiotic Degradation

ABSTRACT The gut microbiome of long-lived people display an increasing abundance of subdominant species, as well as a rearrangement in health-associated bacteria, but less is known about microbiome functions. In order to disentangle the contribution of the gut microbiome to the complex trait of human longevity, we here describe the metagenomic change of the human gut microbiome along with aging in subjects with up to extreme longevity, including centenarians (aged 99 to 104 years) and semisupercentenarians (aged 105 to 109 years), i.e., demographically very uncommon subjects who reach the extreme limit of the human life span. According to our findings, the gut microbiome of centenarians and semisupercentenarians is more suited for xenobiotic degradation and shows a rearrangement in metabolic pathways related to carbohydrate, amino acid, and lipid metabolism. Collectively, our data go beyond the relationship between intestinal bacteria and physiological changes that occur with aging by detailing the shifts in the potential metagenomic functions of the gut microbiome of centenarians and semisupercentenarians as a response to progressive dietary and lifestyle modifications. IMPORTANCE The study of longevity may help us understand how human beings can delay or survive the most frequent age-related diseases and morbidities. In this scenario, the gut microbiome has been proposed as one of the variables to monitor and possibly support healthy aging. Indeed, the disruption of host-gut microbiome homeostasis has been associated with inflammation and intestinal permeability as well as a general decline in bone and cognitive health. Here, we performed a metagenomic assessment of fecal samples from semisupercentenarians, i.e., 105 to 109 years old, in comparison to young adults, the elderly, and centenarians, shedding light on the longest compositional and functional trajectory of the human gut microbiome with aging. In addition to providing a fine taxonomic resolution down to the species level, our study emphasizes the progressive age-related increase in degradation pathways of pervasive xenobiotics in Western societies, possibly as a result of a supportive process within the molecular continuum characterizing aging.

scholarly journals Practical considerations for large-scale gut microbiome studies

2017 ◽  
Vol 41 (Supplement_1) ◽  
pp. S154-S167 ◽  
Author(s):  
Doris Vandeputte ◽  
Raul Y. Tito ◽  
Rianne Vanleeuwen ◽  
Gwen Falony ◽  
Jeroen Raes
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Research Question ◽  
Cold Chain ◽  
Future Research ◽  
Cross Sectional ◽  
Sampling Studies ◽  
Relative Contribution ◽  
Small Effect Size ◽  
Microbiome Research

Abstract First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.

scholarly journals Is the Oral Microbiome Important in HIV-Associated Inflammation?

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Jennifer A. Fulcher
Keyword(s):  
Gastrointestinal Tract ◽  
Antiretroviral Therapy ◽  
Gut Microbiome ◽  
Inflammatory Markers ◽  
Oral Microbiome ◽  
Future Research ◽  
Soluble Cd14 ◽  
Microbiome Diversity ◽  
The Relationship

ABSTRACT Alterations in the gut microbiome during HIV infection have been implicated in chronic inflammation, but the role of the oral microbiome in this process is less clear. The article by M. K. Annavajhala, S. D. Khan, S. B. Sullivan, J. Shah, et al. (mSphere 5:e00798-19, 2020, https://doi.org/10.1128/mSphere.00798-19) investigated the relationship between oral and gut microbiome diversity and immune activation in patients with HIV on antiretroviral therapy. In this study, oral microbiome diversity was inversely associated with inflammatory markers such as soluble CD14 (sCD14), but surprisingly similar associations were not seen with gut microbiome diversity. Oral microbiome diversity was also associated with periodontitis in these patients. This study highlights the importance of continuing multisite examinations in studying the gastrointestinal tract microbiome and also stimulates important directions for future research defining the role of the oral-gut axis in HIV-associated inflammation.

scholarly journals Assessing saliva microbiome collection and processing methods

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Abigail J. S. Armstrong ◽  
Veenat Parmar ◽  
Martin J. Blaser
Keyword(s):  
Alpha Diversity ◽  
Shotgun Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Human Dna ◽  
Within Subjects ◽  
Saliva Collection ◽  
Lung Health ◽  
Over Time

AbstractThe oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.

scholarly journals Skin dysbiosis in the microbiome in atopic dermatitis is site-specific and involves bacteria, fungus and virus

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rie Dybboe Bjerre ◽  
Jacob Bak Holm ◽  
Albert Palleja ◽  
Julie Sølberg ◽  
Lone Skov ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Alpha Diversity ◽  
Future Research ◽  
Skin Microbiome ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Site Specific ◽  
Microbial Dysbiosis ◽  
Cutibacterium Acnes ◽  
The Individual

Abstract Background Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the microbial composition at other body sites have not been studied systematically. Objectives The aim of the study is to characterize the skin microbiome, including bacteria, fungi and virus, at different body sites in relation to AD, lesional state, and S. aureus colonization, and to test whether the nares could be a reservoir for S. aureus strain colonization. Methods Using shotgun metagenomics we characterized microbial compositions from 14 well defined skin sites from 10 patients with AD and 5 healthy controls. Results We found clear differences in microbial composition between AD and controls at multiple skin sites, most pronounced on the flexures and neck. The flexures exhibited lower alpha-diversity and were colonized by S. aureus, accompanied by S. epidermidis in lesions. Malassezia species were absent on the neck in AD. Virus mostly constituted Propionibacterium and Staphylococcusphages, with increased abundance of Propionibacterium phages PHL041 and PHL092 and Staphylococcus epidermidis phages CNPH82 and PH15 in AD. In lesional samples, both the genus Staphylococcus and Staphylococcus phages were more abundant. S. aureus abundance was higher across all skin sites except from the feet. In samples where S. aureus was highly abundant, lower abundances of S. hominis and Cutibacterium acnes were observed. M. osloensis and M. luteus were more abundant in AD. By single nucleotide variant analysis of S. aureus we found strains to be subject specific. On skin sites some S. aureus strains were similar and some dissimilar to the ones in the nares. Conclusions Our data indicate a global and site-specific dysbiosis in AD, involving both bacteria, fungus and virus. When defining targeted treatment clinicians should both consider the individual and skin site and future research into potential crosstalk between microbiota in AD yields high potential.

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