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Bacterial distribution by body site. This figure shows the distribution by body site of bacteria that have been sequenced under the HMP or are in the sequencing pipelines.
Source publication
The Human Microbiome Project (HMP), funded as an initiative of the NIH Roadmap for Biomedical Research (http://nihroadmap.nih.gov), is a multi-component community resource. The goals of the HMP are: (1) to take advantage of new, high-throughput technologies to characterize the human microbiome more fully by studying samples from multiple body sites...
Context in source publication
Context 1
... of 500 new reference bacterial genomes (see Fig. 3 for distribution by body site). Developing a protocol for recruiting and sampling at five body sites (the gastrointestinal tract, the mouth, the vagina, the skin, and the nasal cavity) in a pilot with 250 ''normal'' volunteers made up of equal numbers of men and women recruited from a diverse population. Performing 16S rRNA gene ...
Similar publications
Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST...
With the advent of high-throughput DNA sequencing technology, the analysis and management of the increasing amount of biological sequence data has become a bottleneck for scientific progress. For example, MG-RAST, a metagenome annotation system serving a large scientific community world- wide, has experienced a sustained, exponential growth in data...
Citations
... For instance, in the literature concerning the oral microbiota, oral metagenomic data are collected to analyze the diversity and function of the oral microbiota only [15][16][17]. Similarly, data collected from the esophagus, stomach, and duodenum are used to study the characteristics and functions of the microbiota [18][19][20][21][22][23][24]. Few studies have collected mouth, esophagus, stomach, duodenum, and fecal samples [25] Thus, there an abundance of isolated metagenomic data concerning each part of the gastrointestinal tract but a lack of continuous data [26]. ...
The gastrointestinal (GI) tract harbors trillions of microorganisms known to influence human health and disease, and next-generation sequencing (NGS) now enables the in-depth analysis of their diversity and functions. Although a significant amount of research has been conducted on the GI microbiome, comprehensive metagenomic datasets covering the entire tract are scarce due to cost and technical challenges. Despite the widespread use of fecal samples, integrated datasets encompassing the entire digestive process, beginning at the mouth and ending with feces, are lacking. With this study, we aimed to fill this gap by analyzing the complete metagenome of the GI tract, providing insights into the dynamics of the microbiota and potential therapeutic avenues. In this study, we delved into the complex world of the GI microbiota, which we examined in five healthy Japanese subjects. While samples from the whole GI flora and fecal samples provided sufficient bacteria, samples obtained from the stomach and duodenum posed a challenge. Using a principal coordinate analysis (PCoA), clear clustering patterns were identified; these revealed significant diversity in the duodenum. Although this study was limited by its small sample size, the flora in the overall GI tract showed unwavering consistency, while the duodenum exhibited unprecedented phylogenetic diversity. A visual heat map illustrates the discrepancy in abundance, with Fusobacteria and Bacilli dominating the upper GI tract and Clostridia and Bacterioidia dominating the fecal samples. Negativicutes and Actinobacteria were found throughout the digestive tract. This study demonstrates that it is possible to continuously collect microbiome samples throughout the human digestive tract. These findings not only shed light on the complexity of GI microbiota but also provide a basis for future research.
... The microbiota with many residing on the skin and mucosal surfaces of the host body in a symbiotic relationship. In recent years, research has shown a significant link between microbiota and disease development, making the exploration of this relationship a key area of focus [1]. The unique structure of the ocular surface, constantly exposed to the external environment, results in the development of a stable symbiotic microbiota that plays a crucial role in maintaining the immune balance of the ocular surface. ...
Background
Dry eye is a chronic and multifactorial ocular surface disease caused by tear film instability or imbalance in the microenvironment of the ocular surface. It can lead to various discomforts such as inflammation of the ocular surface and visual issues. However, the mechanism of dry eye is not clear, which results in dry eye being only relieved but not cured in clinical practice. Finding multiple environmental pathways for dry eye and exploring the pathogenesis of dry eye have become the focus of research. Studies have found that changes in microbiota may be related to the occurrence and development of dry eye disease.
Methods
Entered the keywords “Dry eye”, “Microbiota”, “Bacteria” through PUBMED, summarised the articles that meet the inclusion criteria and then filtered them while the publication time range of the literature was defined in the past 5 years, with a deadline of 2023.A total of 13 clinical and 1 animal-related research articles were screened out and included in the summary.
Results
Study found that different components of bacteria can induce ocular immune responses through different receptors present on the ocular surface, thereby leading to an imbalance in the ocular surface microenvironment. Changes in the ocular surface microbiota and gut microbiota were also found when dry eye syndrome occurs, including changes in diversity, an increase in pro-inflammatory bacteria, and a decrease in short-chain fatty acid-related bacterial genera that produce anti-inflammatory effects. Fecal microbiota transplantation or probiotic intervention can alleviate signs of inflammation on the ocular surface of dry eye animal models.
Conclusions
By summarizing the changes in the ocular surface and intestinal microbiota when dry eye occurs, it is speculated and concluded that the intestine may affect the occurrence of eye diseases such as dry eye through several pathways and mechanisms, such as the occurrence of abnormal immune responses, microbiota metabolites- intervention of short-chain fatty acids, imbalance of pro-inflammatory and anti-inflammatory factors, and release of neurotransmitters, etc. Analyzing the correlation between the intestinal tract and the eyes from the perspective of microbiota can provide a theoretical basis and a new idea for relieving dry eyes in multiple ways in the future.
... The collection method was based on standard procedures of the Human Microbiology Project [19,20]. Sampling was performed between 9:00-11:00 am. ...
Background
Crohn’s disease (CD)-associated periodontitis is common. However, the role of periodontal pathogens in the Coexistence of CD and periodontal disease remains unclear.
Methods
To investigate the potential relationship mediated by periodontal pathogens between periodontitis and CD, we collected salivary samples from healthy participants (H group, n = 12), patients with CD (Ch group, n = 10), patients with periodontitis (Ps group, n = 12), and patients with Coexistence of CD and periodontal disease (Cp group, n = 12) and analyzed them by 16 S rRNA sequencing.
Results
Patients with Coexistence of CD and periodontal disease had increased levels of Fusobacterium, Actinomyces, Leptotrichia, and Prevotella, which correlated with the severity of periodontitis. Conversely, the levels of Streptococcus, Neisseria, Haemophilus, and Gemella, which decreased in Coexistence of CD and periodontal disease, were negatively correlated with the severity of periodontitis. To further investigate the role of periodontal pathogens in CD development, representative periodontal pathogens causing periodontitis, Porphyromonas gingivalis and Fusobacterium nucleatum, were administered to mice. These pathogens migrate to, and colonize, the gut, accelerating CD progression and aggravating colitis, and even systemic inflammation. In vitro experiments using a Caco-2/periodontal pathogen coculture revealed that P. gingivalis and F. nucleatum increased intestinal permeability by directly disrupting the tight junctions of intestinal epithelial cells.
Conclusion
Our findings strongly suggest that periodontal pathogens play a role in the relationship between periodontitis and CD. These results provide a basis for understanding the pathogenesis of Coexistence of CD and periodontal disease and may lead to the development of novel therapeutic strategies.
... The Human Microbiome project has revealed that approximately 9% of the total human microbiome is found in the female reproductive tract, and recent studies have proved the existence of the endometrial microbiome [12,13]. These bacterial communities play a crucial role in pregnancy maintenance, with disruptions potentially affecting in vitro fertilization (IVF) success through immune responses and metabolic fluctuations [14]. ...
This study investigates the association between body mass index (BMI) and the composition of the endometrial microbiota in infertile women of childbearing age. This is a retrospective clinical study comparing the endometrial microbiota across body weight in 132 patients presenting for care at an infertility clinic. The reason for infertility was recurrent pregnancy loss (RPL) or implantation failure with a prior IVF cycle. Microbe analysis was completed by Igenomix Laboratory (Valencia, Spain) using two comprehensive panels. Patients were separated into three groups based on their results: normal, dysbiotic, and pathogenic. Prevalence of these groups was compared across BMI categories and statistical analysis was used to determine significance. Of the 132 endometrial samples collected, 80 (60.6%) were normal, 16 (12.1%) were dysbiotic, and 36 (27.3%) were pathogenic. Patients with a BMI ≥ 30 showed a statistically significant increase in pathogenic endometrium compared to normal weight controls (p = 0.029). Our conclusion is that the prevalence of pathogenic endometrium was significantly higher in the obese group compared with normal weight controls. There is a possible association between obesity and the endometrial microbiome.
... In 2006, Steven R. Gill was the first to study human distal gut microbiome in his microbiology laboratory [15]. In the following year, the human microbiome project was initiated and published by Nature and National institute of Health [16] [17]. A bulk of recent evidence now supports the role of gut microbiome in the development of schizophrenia. ...
“... If anyone doubts the utility of a careful study of this subject, let him contemplate the feelings of the surgeon who has removed the only kidney a patient possessed, or of one who has explored the loin and found no kidney below the supra-renal capsule. Congenital errors in the development of the kidney occur with about the same frequency as do malformations elsewhere in the body. In 13,478 autopsies, one kidney was entirely absent in 4 cases, and atrophic in 59 cases.”
— Bayard Taylor Holmes, 1897
... The first phase of this project successfully revealed the microbial communities of the human body, while the second phase, Integrative HMP (iHMP), uncovered host-microbiome interactions using the "omics" approach. The findings from these studies highlight that microbial composition and diversity vary among individuals (7). ...
Host-microbe interactions are complex and ever-changing, especially during infections, which can significantly impact human physiology in both health and disease by influencing metabolic and immune functions. Infections caused by pathogens such as bacteria, viruses, fungi, and parasites are the leading cause of global mortality. Microbes have evolved various immune evasion strategies to survive within their hosts, which presents a multifaceted challenge for detection. Intracellular microbes, in particular, target specific cell types for survival and replication and are influenced by factors such as functional roles, nutrient availability, immune evasion, and replication opportunities. Identifying intracellular microbes can be difficult because of the limitations of traditional culture-based methods. However, advancements in integrated host microbiome single-cell genomics and transcriptomics provide a promising basis for personalized treatment strategies. Understanding host-microbiota interactions at the cellular level may elucidate disease mechanisms and microbial pathogenesis, leading to targeted therapies. This article focuses on how intracellular microbes reside in specific cell types, modulating functions through persistence strategies to evade host immunity and prolong colonization. An improved understanding of the persistent intracellular microbe-induced differential disease outcomes can enhance diagnostics, therapeutics, and preventive measures.
... In 2001, Joshua Lederberg introduced the concept of the human microbiome [1]. The primary focus of research revolves around the inheritance and metabolism of microorganisms in various human body sites, including the skin [2], oral cavity [3], vagina [4], and gastrointestinal tract. ...
... The objective is to comprehend their impact on host health and pathogenesis. The gut microbiome, a significant subject of human microbiome research, has garnered considerable attention since the proposal of the Human Intestinal Metagenome Initiative (HIMI) during the international conference in 2005 [1]. Over the past two decades, the rapid evolution of sequencing technology has led to an increasing number of reports on the gut microbiome [5]. ...
... (1) participants aged 18 years or older, both male and female, with female volunteers not being pregnant or lactating; (2) no history of severe diarrhea, severe constipation, or gastrointestinal disorders in the preceding month; (3) absence of antibiotic and probiotic use within the last three months; (4) absence of diabetes, hypertension, and hyperlipidemia; and (5) no major illnesses, cognitive impairment, or mental disorders. The excluded criteria were as follows: (1) does not conform to inclusion criteria. (2) poor compliance with the program. ...
(1) Background: Bifidobacterium plays a pivotal role within the gut microbiota, significantly affecting host health through its abundance and composition in the intestine. Factors such as age, gender, and living environment exert considerable influence on the gut microbiota, yet scant attention has been directed towards understanding the specific effects of these factors on the Bifidobacterium population. Therefore, this study focused on 98 adult fecal samples to conduct absolute and relative quantitative analyses of bifidobacteria. (2) Methods: Using droplet digital PCR and the PacBio Sequel II sequencing platform, this study sought to determine the influence of various factors, including living environment, age, and BMI, on the absolute content and biodiversity of intestinal bifidobacteria. (3) Results: Quantitative results indicated that the bifidobacteria content in the intestinal tract ranged from 106 to 109 CFU/g. Notably, the number of bifidobacteria in the intestinal tract of the school population surpassed that of the off-campus population significantly (p = 0.003). Additionally, the group of young people exhibited a significantly higher count of bifidobacteria than the middle-aged and elderly groups (p = 0.041). The normal-weight group displayed a significantly higher bifidobacteria count than the obese group (p = 0.027). Further analysis of the relative abundance of bifidobacteria under different influencing factors revealed that the living environment emerged as the primary factor affecting the intestinal bifidobacteria structure (p = 0.046, R2 = 2.411). Moreover, the diversity of bifidobacteria in the intestinal tract of college students surpassed that in the out-of-school population (p = 0.034). This was characterized by a notable increase in 11 strains, including B. longum, B. bifidum, and B. pseudolongum, in the intestinal tract of college students, forming a more intricate intestinal bifidobacteria interaction network. (4) Conclusions: In summary, this study elucidated the principal factors affecting intestinal bifidobacteria and delineated their characteristics of intestinal bifidobacteria in diverse populations. By enriching the theory surrounding gut microbiota and health, this study provides essential data support for further investigations into the intricate dynamics of the gut microbiota.
... The development of the Human Microbiome project, proposed as an initiative of the National Institutes of Health (NIH) Roadmap for Biomedical Research, made it possible to characterize the microbiome associated with various parts of the body [10]. It has also allowed us to determine if there are associations between microbiome changes and human health to evaluate the opportunities to ameliorate health through the monitoring and/or manipulation of the human microbiome [11,12]. Among the several niches where microbiota reside, of special interest is the human gut microbiota, which is considered the most important regarding health maintenance [8]. ...
The human microbiome has a crucial role in the homeostasis and health of the host. These microorganisms along with their genes are involved in various processes, among these are neurological signaling, the maturation of the immune system, and the inhibition of opportunistic pathogens. In this sense, it has been shown that a healthy ocular microbiota acts as a barrier against the entry of pathogens, contributing to the prevention of infections. In recent years, a relationship has been suggested between microbiota dysbiosis and the development of neurodegenerative diseases. In patients with glaucoma, it has been observed that the microbiota of the ocular surface, intraocular cavity, oral cavity, stomach, and gut differ from those observed in healthy patients, which may suggest a role in pathology development, although the evidence remains limited. The mechanisms involved in the relationship of the human microbiome and this neurodegenerative disease remain largely unknown. For this reason, the present review aims to show a broad overview of the influence of the structure and composition of the human oral and gut microbiota and relate its dysbiosis to neurodegenerative diseases, especially glaucoma.
... The Human Microbiome Project has identi ed that approximately 9% of the human microbiome resides in the female genital tract (FGT) [5] . This microbiome plays a pivotal role in maintaining homeostasis, defending against pathogens, and potentially in uencing fertility [6] . ...
Background: Infertility rates are on the rise, presenting a complex array of causative factors. Recent advancements in human microbiome and associated techniques have shed light on the potential impact of vaginal microbiota disruptions on female fertility. Our study aims to investigate differences in vaginal microbiome between fertile women and those experiencing infertility. Additionally, we aim to investigate how microbial composition in infertile population may affect the success of assisted reproduction technology (ART).
Methods: We enrolled 194 women diagnosed with infertility at the Reproductive Medicine Center of Shanghai Changzheng Hospital between November 2018 and November 2021, along with 102 healthy women undergoing routine physical examinations at the hospital’s Physical Examination Center. Vaginal secretions were collected from both groups, and polymerase chain reaction (PCR) was used to amplify the bacterial 16S rRNA V4-V6 conserved region for microbial analysis. A machine learning model was built based on the genus abundances to predict infertility. Additionally, we employed the PICRUSt algorithm to predict the metabolic pathway activities, providing insights into potential molecular mechanisms underlying female infertility and ART outcomes.
Results: Women with infertility exhibited a significantly different vaginal microbial composition compared to healthy women, with the infertility group showing higher microbial diversity. Burkholderia, Pseudomonas, and Prevotella levels were significantly elevated in the vaginal microbiota of the infertility group, while Bifidobacterium and Lactobacillus abundances were reduced. Recurrent implantation failure (RIF) within the infertile population showed even higher diversity of vaginal microbiota, with specific genera such as Mobiluncus, Peptoniphilus, Prevotella, and Varibaculum being more abundant. Overgrowth of Mobiluncus and Varibaculum emerged as independent risk factors affecting ART outcomes. Eleven metabolic pathways were associated with both RIF and infertility, with Prevotella demonstrating stronger correlations.
Conclusions: The present study provides insights into the differences in vaginal mircobiome between healthy and infertile women, offering a new understanding of how vaginal microbiota may impact infertility and ART outcomes. Our findings underscore the significance of specific microbial taxa in women with recurrent implantation failure, suggesting avenues for targeted interventions to enhance embryo transplantation success rates.
... Overall, the microbiota in the urine track is less diverse and less abundant than in other body parts. Analysis of bacterial distribution throughout the human body by The Human Microbiome Project [40] found that only 9% of symbiotic microorganisms can be found in the genitourinary tract, a small proportion compared to 29% in the digestive tract and 26% in the mouth. This lack of similarity between the genera of bacteria reported in different studies depends on many factors, such as gender, age, microbial niche, the size of the urine sample and how it was collected, and the techniques used in the study [17,38,39]. ...
There is a growing focus on understanding the role of the male microbiome in fertility issues. Although research on the bacterial communities within the male reproductive system is in its initial phases, recent discoveries highlight notable variations in the microbiome's composition and abundance across distinct anatomical regions like the skin, foreskin, urethra, and coronary sulcus. To assess the relationship between male genitourinary microbiome and reproduction, we queried various databases, including MEDLINE (available via PubMed), SCOPUS, and Web of Science to obtain evidence-based data. The literature search was conducted using the following terms "gut/intestines microbiome," "genitourinary system microbiome," "microbiome and female/male infertility," "external genital tract microbiome," "internal genital tract microbiome," and "semen microbiome." Fifty-one relevant papers were analyzed, and eleven were strictly semen quality or male fertility related. The male microbiome, especially in the accessory glands like the prostate, seminal vesicles, and bulbourethral glands, has garnered significant interest because of its potential link to male fertility and reproduction. Studies have also found differences in bacterial diversity present in the testicular tissue of normozoospermic men compared to azoospermic suggesting a possible role of bacterial dysbiosis and reproduction. Correlation between the bacterial taxa in the genital microbiota of sexual partners has also been found, and sexual activity can influence the composition of the urogenital microbiota. Exploring the microbial world within the male reproductive system and its influence on fertility opens doors to developing ways to prevent, diagnose, and treat infertility. The present work emphasizes the importance of using consistent methods, conducting long-term studies, and deepening our understanding of how the reproductive tract microbiome works. This helps make research comparable, pinpoint potential interventions, and smoothly apply microbiome insights to real-world clinical practices.
