Personal Microbiome Research Articles

Effective use of skin microbiome signatures for fingerprint identification.

Recent advances have increased the importance of the human microbiome, including the skin microbiome. Despite the hand microbiome research, the factors affecting the composition of the hand microbiome and their personal characteristics are incompletely known. Despite changing environmental factors and personal variation, we aimed to indicate the interpersonal distinction between skin microbiota using simple and rapid molecular methods. Over a non-consecutive 10-day period, samples were taken from 10 adult individuals, and ribotyping analysis of the 16S and 23S genes of S. epidermidis was performed on each skin sample. Additionally, EcoRI and HindIII enzyme reactions and variable number tandem repeat (VNTR) reactions of S. epidermidis obtained from DNA samples were performed. The skin microbiomes of individuals were evaluated along with the microbiome profiles left on the surfaces they touched. In the environmental samples taken, it has been observed that people preserve their core skin microbiota characters and carry them to their environment. It was determined that the highest similarity rate was 77.14%, and the lowest similarity rate was 31.74%. Our study showed that the core skin microbiota retains its characteristics and leaves traces in environments. The fact that the personal microbiome remains unchanged despite environmental differences and has characteristic features has shown that it can be used in forensic sciences to distinguish individuals from each other. These results with simple and rapid methods further increased the importance and significance of the study. The findings indicate that personal skin microbiota can provide a significant contribution to criminal investigations by increasing accuracy and reliability, especially in forensic analyses.

Using Gut Microbiome as A Tool in Dietary Intervention for Prevention and Management of Obesity

The gut microbiome has trillions of bacteria which play an important role in human health and disease. Several animal and human studies have shown that dysbiosis, microbial imbalance as the causative factor in obesity and metabolic syndrome. Significant research evidence demonstrates that changes in the proportion of Bacteroidetes and Firmicutes has been associated with obesity, but this has been recently challenged. Similar studies were carried out in several populations, however, there are no such studies, to date, among Asian Indians. We aimed to examine the usefulness of gut microbiome testing in developing personalized diet for managing obesity. In this study, we selected individuals, generally healthy, free- living adults, both men and women with BMI 25- 40 kg/m2 and with previous history of failures at weight loss who visited a Weight Loss Clinic, based in Coimbatore, India & were offered a gut microbiome test. We included 54 individuals in the intervention group who received personalized dietary advice for weight loss based on the gut microbiome test and another set of 52 individuals visiting the same clinic were included in the comparison group based on their age, height, weight and BMI who received generic diet. A statistically significant increase in the Bacteroidetes genus was observed in the personalized nutrition group (p = .04). The change (delta) values in gut microbiome composition in personalized nutrition group were significantly higher at the end of 120 days. Gut microbiome-based personalized microbiome modulation through diet significantly improves gut microbiome profiles among obese individuals. We would further need studies with larger sample size to validate these study findings and long-term follow-up are needed.

Distance-based linkage of personal microbiome records for identification and its privacy implications

Due to its high potential for analysis in clinical settings, research on the human microbiome has been flourishing for several years. As an increasing amount of data on the microbiome is gathered and stored, analysing the temporal and individual stability of microbiome readings, and the succeeding privacy risks, has gained importance. In 2015, Franzosa et al. demonstrated the feasibility of matching and linking individuals in microbiome-based datasets from the Human Microbiome Project, which could lead to re-identification of individuals, and thus poses privacy implications for microbiome study designs. Their technique is based on the construction of body site-specific metagenomic codes that maintain a certain stability over time.In this paper, we establish a distance-based technique for personal microbiome identification, which is combined with a solution for avoiding spurious, false positive matches. In a direct comparison with the approach from Franzosa et al., which assumes that information is available as microbial records, rather than at the more detailed (but less likely to be shared) nucleic acid level, our method improves upon the identification results on most of the considered datasets. Our main finding is an increase of the average percentage of true positive identifications of 30% on the widely studied microbiome of the gastrointestinal tract. While we particularly recommend our method for application on the gut microbiome, we also observed substantial identification success on other body sites. Our results demonstrate the potential of privacy threats in microbiome data gathering, storage, sharing, and analysis, and thus underline the need for solutions to protect the microbiome as personal and sensitive medical data. We also show that the method is robust to various hyper-parameter settings.Based on our observations, we further identify challenges in personal microbiome identification research, specifically, the scarcity of benchmark data and associated data analysis tasks. Based on our experience, we propose solutions for a more systematic and comparable evaluation, considering also aspects of costs entailed with applying privacy-preserving methods.

The Promise of Gut Microbiota

The Promise of Gut Microbiota

Is the pulmonary microbiome involved in lung cancer pathophysiology?

Abstract Bronchopulmonary cancer represents the neoplasms associated with the highest mortality rate, despite diagnostic and therapeutic advances in recent decades. Early diagnosis is often difficult due to the paucity of symptoms or superinfections. Screening subjects at risk of developing lung cancer include clinical, bacteriological, inflammatory status, and genetic profile assessment. The personal microbiome has an essential role in the physiology of the human body. The gut-lung axis plays an essential role in carcinogenesis, being involved in various pathways. The lung microbiome can contribute to the development of lung cancer either directly by acting on tumor cells or indirectly by modulating the tumor-associated immune response. The gut microbiome can directly affect the response to immunotherapy in patients with non-small cell lung cancer.

Gut Microbiota-Informed Precision Nutrition in the Generally Healthy Individual: Are We There Yet?

ABSTRACTSince next generation sequencing facilitated high-throughput and cost-efficient genomics analyses, the human gut metagenome has become an emerging frontier to explore toward precision nutrition. Significant progress has been made in identifying gut microbial features associated with a wide spectrum of human disease. However, other than a few microbiome-disease relations, there is a dearth of confirmed causal inferences, particularly in generally healthy populations. The relatively high unexplained variability in microbiome compositions in this group warrants caution in applying this complex biomarker toward precision nutrition, because our understanding of what constitutes a healthy microbiome is still rudimentary. Although gut microbiota harbor integrated environmental and host-specific information with the potential to facilitate personalized nutritional and lifestyle advice, these data cannot yet be confidently interpreted toward precise recommendations. Thus, nutritional advice for generally healthy individuals based on personal microbiome composition analysis might not yet be appropriate unless accompanied by established blood and physiological biomarkers.

Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification.

The highly personalized human skin microbiome may serve as a viable marker in personal identification. Amplicon sequencing resolution using 16S rRNA cannot identify bacterial communities sufficiently to discriminate between individuals. Thus, novel higher-resolution genetic markers are required for forensic purposes. The clustered regularly interspaced short palindromic repeats (CRISPRs) are prokaryotic genetic elements that can provide a history of infections encountered by the bacteria. The sequencing of CRISPR spacers may provide phylogenetic information with higher resolution than other markers. However, using spacer sequencing for discrimination of personal skin microbiome is difficult due to limited information on CRISPRs in human skin microbiomes. It remains unclear whether personal microbiome discrimination can be achieved using spacer diversity or which CRISPRs will be forensically relevant. We identified common CRISPRs in the human skin microbiome via metagenomic reconstruction and used amplicon sequencing for deep sequencing of spacers. We successfully reconstructed 24 putative CRISPR arrays using metagenomic data sets. A total of 1,223,462 reads from three CRISPR arrays revealed that spacers in the skin microbiome were highly personalized, and conserved repeats were commonly shared between individuals. These individual specificities observed using CRISPR typing were confirmed by comparing the CRISPR diversity to microbiome diversity assessed using 16S rRNA amplicon sequencing. CRISPR typing achieved 95.2% accuracy in personal classification, whereas 16S rRNA sequencing only achieved 52.6%. These results suggest that sequencing CRISPRs in the skin microbiome may be a more powerful approach for personal identification and ecological studies compared to conventional 16S rRNA sequencing.IMPORTANCE Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. In this study, we identified 24 putative CRISPR arrays using a shotgun metagenome data set of the human skin microbiome. The findings of this study expand our understanding of the nature of CRISPRs by identifying novel CRISPR candidates. We developed a method to efficiently determine the diversity of three CRISPR arrays. Our analysis revealed that the CRISPR spacer diversity in the human skin microbiome is highly personalized compared with the microbiome diversity assessed by 16S rRNA sequencing, providing a new perspective on the study of the skin microbiome.

Nutrition Factor and Evolutionary Genetic Development of Intestinal Microflora: Importance for Maintaining Immunityand Health

The article considers the microbiota of modern people and its changes in the course of evolution under the influence of external and internal environment factors. The researchers explain the diversity loss and lack of beneficial microorganisms by the lack of carbohydrates available to the microflora (CAM) in the man diet, including dietary fiber fermented into short chain fatty acids (SCFA) - the main source of energy and intestinal microflora metabolism regulator. The authors demonstrated the intestinal microflora connection with other organs and systems of the human body, including the immune and nervous systems, and determined its significance in the occurrence and development of common diseases. Special attention is paid to the analysis of pro-, pre-, metabiotics and their metabolites, which have individual differences in the metabolic processes of a healthy and sick organism. The mechanisms and ways of implementing these functions depend on specific microorganism strains, that determines the prospects for creating and applying new biotechnological products with directed functional properties. A man noted antagonistic contradictions between own and produced strains. The article demonstrates that the microorganism genome is able to evolve in the struggle for survival, responding to changing nutritional conditions by delegating a huge number of genes to the human genome, indicating the need for nutrient-metabolic support of the microbiome. The issues of “aging” microbiota and the possibility of its support, as well as the transfer of beneficial bacteria from the donor to the recipient’s intestines, carrying out the transfer of positive physiological characteristics are interesting. The researchers discussed decoding process prospects of sequencing the genes that make up the human genome, the mechanisms of forming a personal microbiome for understanding the diseases pathogenesis and developing highly effective therapies. The most effective way to restore and preserve healthy microflora is a scientifically based diet with the additional inclusion of specialized products, the active principles of which are the producers of various bacteria.

Challenges in Human Skin Microbial Profiling for Forensic Science: A Review.

The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a personal microbiome. This review highlights some important aspects of recent studies, many of which have revealed issues involving the effect of contamination of microbial samples from both technical and environmental sources and their impacts on microbiome research and the potential forensic applications of microbial profiling. It is imperative that these challenges be discussed and evaluated within a forensic context to better understand the future directions and potential applications of microbial profiling for human identification. It is necessary that the limitations identified be resolved prior to the adoption of microbial profiling, or, at a minimum, acknowledged by those applying this new approach.

GePMI: A statistical model for personal intestinal microbiome identification

Human gut microbiomes consist of a large number of microbial genomes, which vary by diet and health conditions and from individual to individual. In the present work, we asked whether such variation or similarity could be measured and, if so, whether the results could be used for personal microbiome identification (PMI). To address this question, we herein propose a method to estimate the significance of similarity among human gut metagenomic samples based on reference-free, long k-mer features. Using these features, we find that pairwise similarities between the metagenomes of any two individuals obey a beta distribution and that a p value derived accordingly well characterizes whether two samples are from the same individual or not. We develop a computational framework called GePMI (Generating inter-individual similarity distribution for Personal Microbiome Identification) and apply it to several human gut metagenomic datasets (>300 individuals and >600 samples in total). From the results of GePMI, most of the human gut microbiomes can be identified (auROC = 0.9470, auPRC = 0.8702). Even after antibiotic treatment or fecal microbiota transplantation, the individual k-mer signature still maintains a certain specificity.

CLOUD: a non-parametric detection test for microbiome outliers

BackgroundDysbiosis of the human gut microbiome is defined as a maladaptive or clinically relevant deviation of the community profile from the healthy or normal state. Dysbiosis has been implicated in an extensive set of metabolic, auto-immune, and infectious diseases, and yet there is substantial inter-individual variation in microbiome composition even within body sites of healthy humans. An individual’s microbiome varies over time in a high-dimensional space to form their personal microbiome cloud. This cloud may or may not be similar to that of other people, both in terms of the average microbiome profile (conformity) and the diameter of the cloud (stability). However, there is currently no robust non-parametric test that determines whether a patient’s microbiome cloud is an outlier with respect to a reference group of healthy individuals with widely varying microbiome profiles.MethodsHere, we propose a test for outliers’ detection in the human gut microbiome that accounts for the wide range of microbiome phenotypes observed in a typical set of healthy individuals and for intra-individual temporal variation. Our robust nonparametric outlier detection test, the CLOUD test, performs two assessments of a patient’s microbiome health: conformity, the extent to which the patient’s microbiome cloud is ecologically similar to a subset of healthy subjects; and stability, which compares the cloud diameter of a patient to those of healthy subjects. The CLOUD test is based on locally linear embedded ecological distances, allowing it to account for widely varying microbiome compositions among reference individuals. It also leverages temporal variability within patients and reference individuals to increase the robustness of the test.ResultsWe describe the CLOUD test, and we apply it to one novel and two previously published cohorts of patients receiving fecal microbiota transplantation for recurrent Clostridium difficile colitis, as well as to two known healthy cohorts, demonstrating high concordance of the CLOUD conformity and stability indices with clinical outcomes.ConclusionsAlthough the CLOUD test is not, on its own, a test for clinical dysbiosis, it nonetheless provides a framework for outlier testing that could be incorporated into evaluation of suspected dysbiosis, which may play a role in diagnosis and prognosis of numerous pediatric and adult diseases.

The microbiome and its publics: A participatory approach for engaging publics with the microbiome and its implications for health and hygiene.

EMBO Reports (2018) e45786 The past 20 years have seen a significant drop in the cost of DNA sequencing, which along with high‐throughput (or next‐generation) sequencing has helped to analyse the microbial diversity from environmental samples. Most of this research has focused on microbiomes of the human body and, although there is still much uncertainty about what constitutes a “normal” or “healthy” human microbiome, microbial “dysbiosis” has already been implicated in a range of non‐communicable diseases. > The growing affordability of DNA sequencing has facilitated a range of citizen science, crowd‐funded and DIY microbiome projects… This research is also challenging the common understandings of pathogens and the beneficial role of bacteria for human health [1], and increases awareness of how hygiene and antibiotics impact early‐life microbial colonisation and exposure, and their effects on human health and development [2]. There is both public health and commercial interest in translating this research that might lead to probiotic applications to improve human and animal health, domestic hygiene, waste management and agricultural productivity, amongst other potential benefits. As with the human genome, interest in the microbiome and its effect on health has begun to move beyond the laboratory. The growing affordability of DNA sequencing has facilitated a range of citizen science, crowd‐funded and DIY microbiome projects (http://robdunnlab.com/projects/wild-life-of-our-homes/; http://americangut.org/; www.ubiome.com; https://mapmygut.com/). Various publics have become involved by providing samples, through personalised sequencing and by designing their own experiments in personal microbiome management. Such health‐focused projects often reflect a growing anxiety about the “hygiene” or “microbiome depletion” hypotheses [3]: that the increase in the prevalence of autoimmune and inflammatory disease might be linked to dysbiosis caused by “missing microbes” [2], whose absence is caused by modern hygiene, diet and other lifestyle practices. Affordable sequencing offers new challenges …

Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses.

A critical area of emphasis for science educators is the identification of effective means of teaching and engaging undergraduate students. Personal microbiome analysis is a means of identifying the microbial communities found on or in our body. We hypothesized the use of personal microbiome analysis in the classroom could improve science education by making courses more applied and engaging for undergraduate students. We determined to test this prediction in three Brigham Young University undergraduate courses: Immunology, Advanced Molecular Biology Laboratory, and Genomics. These three courses have a two-week microbiome unit and students during the 2016 semester students could submit their own personal microbiome kit or use the demo data, whereas during the 2017 semester students were given access to microbiome data from an anonymous individual. The students were surveyed before, during, and after the human microbiome unit to determine whether analyzing their own personal microbiome data, compared to analyzing demo microbiome data, impacted student engagement and interest. We found that personal microbiome analysis significantly enhanced the engagement and interest of students while completing microbiome assignments, the self-reported time students spent researching the microbiome during the two week microbiome unit, and the attitudes of students regarding the course overall. Thus, we found that integrating personal microbiome analysis in the classroom was a powerful means of improving student engagement and interest in undergraduate science courses.

Language Ecosystem

Language Ecosystem Jen Coleman (bio) Entangled Bank James Sherry Chax Press www.chax.org/shop 85 Pages; Print, $17.00 "It is interesting to contemplate an entangled bank…"—so asserts Charles Darwin in his conclusion to Origin of the Species, and so begins James Sherry's 2016 book, Entangled Bank—a conceptual memoir of language ecosystems. What a canny gift the poet gives us: an invitation to contemplate each poem as a community of living language bits, co-evolving and interdependent, shaped by the environment—an environment in which the reader participates. As a memoir, Sherry acknowledges that each page recalls a language ecosystem as it was, now fixed on the page as a portrait. But when a reader takes up the invitation to contemplate how these pages are entangled ecosystems, the reader revivifies the poems with new sense, perception, and culture. We are vulnerable to, participating in, and culpable for this entangled bank. Calling it a conceptual work directs attention to the way systems work rather than the charismatic critters (e.g., poets) within those systems. Yet it is irresistible to read the book as a memoir of the poet himself. The works contemplate what it is to be a poet among poets, interdependent and in community, co-adapting the practice of language within a violent and destructive culture. Sherry suggests that change and adaptation in language ecosystems are ways to survive—yet the poet also places himself, mortal and vulnerable, as a critter among critters. Entangled. When the oar of your boat is tangled in a kelp forest, your physical presence becomes environment to sea urchins, otters, kelp, wolf eels, and myriad other creatures that provide food, shelter, competition, and more to one another. And in turn, as you free your oar, the kelp forest changes you. Your adrenaline sends inter-kingdom signals to the millions of critters in your personal microbiome, profoundly changing their environment. You are not simply ensnared by the forest, you are intricately interlaced with it. You set particles in motion. They in turn affect the position, spin, and momentum of other particles—even at a distance. That's the working of an ecosystem. And those are the relationships that Sherry encourages the reader to contemplate, as one style of writing tangles with another, each in turn affecting the way the other appears, read, and is written. The first nine pieces in the book include six "Beautiful Poems for My Friends" separated by poems with beautifully divergent language ecosystems. In the first two poems it is hard not to hear Joseph Kaplan's Kill List (2013) as part of the environment of the poems, as Rae Armantrout noted in her comment on the book (even though Sherry has said that the first of the "Beautiful Poems" were written in 2002). Like Kaplan's list, the poems categorize and sort poet-friends into a taxonomy. It's not passive; the taxonomy is charmingly conscious of the taxonomist. For Kim RosenfeldYou are beautifulI caught you lookingPitiless and forgivingFor thinking you beautiful These contemporary poets are part of the living ecosystem of the author. Their names, captured on the page, also become part of a taxonomical language ecosystem. Where Kaplan categorized by a concept of socioeconomic class, Sherry sorts by types of beauty. Present in the environment of these poems is the current culture: Beauty has been shirked by poets like Sherry for a generation. Yet these poems revive the value of the concept of beauty in nature and beauty in death—and even the critique of beauty—all concepts that postmodernism buried. And what of beauty in contemporary culture? By the third and fourth versions of "Beautiful Poems for My Friends," the phylum of friend extends beauty beyond romantic dominant culture expectations to include public figures (Barack Obama), civic figures (My Boss Frank), and corporate persons (Toyota Motors). A community of poets—immersed in contemporary culture—is classified by a poet dwelling in the same culture, according to a taxonomy reviving a romantic concept that, when read against Kaplan's poem, could be an antithesis to a socioeconomic concept. Entangled, indeed. How do these discrete poems tangle with other poems...

Probing the diversity of healthy oral microbiome with bioinformatics approaches

The human oral cavity contains a highly personalized microbiome essential to maintaining health, but capable of causing oral and systemic diseases. Thus, an in-depth definition of “healthy oral microbiome” is critical to understanding variations in disease states from preclinical conditions, and disease onset through progressive states of disease. With rapid advances in DNA sequencing and analytical technologies, population-based studies have documented the range and diversity of both taxonomic compositions and functional potentials observed in the oral microbiome in healthy individuals. Besides factors specific to the host, such as age and race/ethnicity, environmental factors also appear to contribute to the variability of the healthy oral microbiome. Here, we review bioinformatic techniques for metagenomic datasets, including their strengths and limitations. In addition, we summarize the interpersonal and intrapersonal diversity of the oral microbiome, taking into consideration the recent large-scale and longitudinal studies, including the Human Microbiome Project.

Mobile phones carry the personal microbiome of their owners.

Most people on the planet own mobile phones, and these devices are increasingly being utilized to gather data relevant to our personal health, behavior, and environment. During an educational workshop, we investigated the utility of mobile phones to gather data about the personal microbiome — the collection of microorganisms associated with the personal effects of an individual. We characterized microbial communities on smartphone touchscreens to determine whether there was significant overlap with the skin microbiome sampled directly from their owners. We found that about 22% of the bacterial taxa on participants’ fingers were also present on their own phones, as compared to 17% they shared on average with other people’s phones. When considered as a group, bacterial communities on men’s phones were significantly different from those on their fingers, while women’s were not. Yet when considered on an individual level, men and women both shared significantly more of their bacterial communities with their own phones than with anyone else’s. In fact, 82% of the OTUs were shared between a person’s index and phone when considering the dominant taxa (OTUs with more than 0.1% of the sequences in an individual’s dataset). Our results suggest that mobile phones hold untapped potential as personal microbiome sensors.

Maintaining health by balancing microbial exposure and prevention of infection: the hygiene hypothesis versus the hypothesis of early immune challenge

The human immune system is inseparably bonded to an individual's personal micro-biome from birth to death. Since the beginning of life, commensal relationships have ensured the survival of micro- and macro-organisms within complex relationships. However, technological advances and altered lifestyle imposed new rules for this interaction during recent decades. It has been observed that reduced exposure to micro-organisms and parasites results in decreased morbidity and mortality, but is also associated with a rising prevalence of atopic disorders and autoimmune diseases, mostly in industrialized countries. This inverse relationship is described by the 'hygiene hypothesis', put forward in 1989, yet this term only imperfectly describes these observations, as excessive hygiene or hygienic measures may not directly be the central cause. The lack of appropriate immune stimulation during early childhood with the consequence of disturbed alignment in the sequence of encountering self- or non-self-antigens might account in the rise of atopy and autoimmune disease. For this reason we propose the term 'early immune challenge hypothesis'. This concept highlights the importance of immune priming in early life in the context of genetic, social, geographic, cultural, and economic background. Moreover, it emphasizes the central role of 'training' of regulatory T-cells through sufficient microbial exposure, leading to a robust, healthy balance between inflammation and anti-inflammation or immune tolerance. Insufficient exposure might result in abnormal immune regulatory development. Finally, it incorporates the idea of encountering 'old friends' - organisms that shaped our immune system during human phylogeny. This article gives a comprehensive overview of the relationship between microbial exposure, and the incidence of asthma and hay fever is outlined. Although the outcomes of these studies originally were interpreted in the framework of the hygiene hypothesis, they may suit the concept of the hypothesis of early immune challenge even better. Moreover, recent studies have revealed that TH or TReg imbalances in disease may be partially corrected by the administration of helminthic or bacterial extracts.