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human microbiome project

Sandeep J Joseph, Ben Li, Robert A Petit Iii, Zhaohui S Qin, Lyndsey Darrow, Timothy D Read
In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S...
2016: PeerJ
Guoqin Yu, Steve Phillips, Mitchell H Gail, James J Goedert, Michael Humphrys, Jacques Ravel, Yanfang Ren, Neil E Caporaso
BACKGROUND: The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk. METHODS: We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA...
October 21, 2016: Cancer Epidemiology, Biomarkers & Prevention
Qichao Tu, Jiabao Li, Zhou Shi, Yanfei Chen, Lu Lin, Juan Li, Hongling Wang, Jianbo Yan, Qingming Zhou, Xiangzhen Li, Lanjuan Li, Jizhong Zhou, Zhili He
With the massive data generated by the Human Microbiome Project, how to transform such data into useful information and knowledge remains challenging. Here, with currently available sequencing information (reference genomes and metagenomes), we have developed a comprehensive microarray, HuMiChip2, for strain-level identification and functional characterization of human microbiomes. HuMiChip2 was composed of 29,467 strain-specific probes targeting 2063 microbial strains/species and 133,924 sequence- and group-specific probes targeting 157 key functional gene families involved in various metabolic pathways and host-microbiome interaction processes...
October 12, 2016: Applied Microbiology and Biotechnology
Thuy Do
Technological advances in high throughput DNA sequencing have revolutionised microbiology and changed the concept of the pathogenic functions of microbes that persisted for almost two centuries, and was shaped by the germ theory established by Koch and Pasteur. The decreasing costs of next-generation sequencing have allowed more rigorous investigations and improved insight into diverse and complex microbial communities with increasing resolution, particularly through the use of culture-independent approaches...
October 8, 2016: Oral Diseases
Elahe Kia, Brett Wagner Mackenzie, Danielle Middleton, Anna Lau, David W Waite, Gillian Lewis, Yih-Kai Chan, Marta Silvestre, Garth J S Cooper, Sally D Poppitt, Michael W Taylor
In studies of the human microbiome, faecal samples are frequently used as a non-invasive proxy for the study of the intestinal microbiota. To obtain reliable insights, the need for bacterial DNA of high quality and integrity following appropriate faecal sample collection and preservation steps is paramount. In a study of dietary mineral balance in the context of type 2 diabetes (T2D), faecal samples were collected from healthy and T2D individuals throughout a 13-day residential trial. These samples were freeze-dried, then stored mostly at -20°C from the trial date in 2000/2001 until the current research in 2014...
2016: PloS One
Rheinallt M Jones
The results generated from the NIH funded Human Microbiome Project (HMP) are necessarily tied to the overall mission of the agency, which is to foster scientific discoveries as a basis for protecting and improving health. The investment in the HMP phase 1 accomplished many of its goals including the preliminary characterization of the human microbiome and the identification of links between microbiome diversity and disease states. Going forward, the next step in these studies must involve the identification of the functional molecular elements that mediate the positive influence of a eubiotic microbiome on health and disease...
September 2016: Yale Journal of Biology and Medicine
Ji-Hoi Moon, Jae-Hyung Lee
Human oral cavity contains a highly personalized microbiome that is 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 ranges and diversity of both taxonomic compositions and functional potentials observed in the oral microbiome in healthy individuals...
September 29, 2016: BMB Reports
Ray K Boyapati, Rahul Kalla, Jack Satsangi, Gwo-Tzer Ho
The completion of the human genome project in 2003 represented a major scientific landmark, ushering in a new era with hopes and expectations of fresh insights into disease mechanisms and treatments. In inflammatory bowel disease (IBD), many important discoveries soon followed, notably the identification of >200 genetic susceptibility loci and characterization of the gut microbiome. As "big data", driven by advances in technology, becomes increasingly available and affordable, individuals with IBD and clinicians alike yearn for tangible outcomes from the promise of "precision medicine"-precise diagnosis, monitoring, and treatment...
September 27, 2016: American Journal of Gastroenterology
Michelle Beaumont, Julia K Goodrich, Matthew A Jackson, Idil Yet, Emily R Davenport, Sara Vieira-Silva, Justine Debelius, Tess Pallister, Massimo Mangino, Jeroen Raes, Rob Knight, Andrew G Clark, Ruth E Ley, Tim D Spector, Jordana T Bell
BACKGROUND: Variation in the human fecal microbiota has previously been associated with body mass index (BMI). Although obesity is a global health burden, the accumulation of abdominal visceral fat is the specific cardio-metabolic disease risk factor. Here, we explore links between the fecal microbiota and abdominal adiposity using body composition as measured by dual-energy X-ray absorptiometry in a large sample of twins from the TwinsUK cohort, comparing fecal 16S rRNA diversity profiles with six adiposity measures...
2016: Genome Biology
Claudio Donati, Moreno Zolfo, Davide Albanese, Duy Tin Truong, Francesco Asnicar, Valerio Iebba, Duccio Cavalieri, Olivier Jousson, Carlotta De Filippo, Curtis Huttenhower, Nicola Segata
Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes...
2016: Nature Microbiology
Lianwei Li, Zhanshan Sam Ma
The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health-the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general...
2016: Scientific Reports
Mark F Miller, William H Goodson, Masoud H Manjili, Nicole Kleinstreuer, William H Bisson, Leroy Lowe
BACKGROUND: The current "single chemical as carcinogen" risk assessment paradigm might underestimate or miss the cumulative effects of exposure to chemical mixtures, as highlighted in recent work from the Halifax Project. This is particularly important for chemical exposures in the low-dose range that may be affecting crucial cancer hallmark mechanisms that serve to enable carcinogenesis. OBJECTIVE: Could ongoing low-dose exposures to a mixture of commonly encountered environmental chemicals produce effects in concert that lead to carcinogenesis? A workshop held at the NIEHS in August, 2015, evaluated the scientific support for the Low-Dose Mixture Hypothesis of Carcinogenesis and developed a research agenda...
August 12, 2016: Environmental Health Perspectives
Homer L Twigg, George M Weinstock, Kenneth S Knox
The lung microbiome plays a significant role in normal lung function and disease. Because microbial colonization is likely influenced by immunodeficiency, one would speculate that infection with human immunodeficiency virus (HIV) alters the lung microbiome. Furthermore, how this alteration might impact pulmonary complications now seen in HIV-infected patients on antiretroviral therapy (ART), which has shifted from opportunistic infections to diseases associated with chronic inflammation, is not known. There have been limited publications on the lung microbiome in HIV infection, many of them emanating from the Lung HIV Microbiome Project...
July 18, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
Andrew Yeh, Matthew Brian Rogers, Brian Firek, Matthew D Neal, Brian S Zuckerbraun, Matthew J Morowitz
The microbiota of critically ill patients likely undergoes dramatic changes but has not been rigorously studied with a culture-independent high-throughput approach. The aim of this study was to characterize spatial and temporal variation in the microbiota of critically ill patients. Trauma and acute surgery patients admitted to the ICU were sampled at five body sites (stool, tongue, skin, trachea, urine) every 3 to 4 days. A mean of 10.8 samples were collected from 32 patients with a mean sampling period of 8...
July 21, 2016: Shock
Lita M Proctor
This overview describes the impetus for and the goals of the National Institutes of Health (NIH)'s Human Microbiome Project (HMP) and the research resources available through the HMP. As the HMP also serves as a catalyst for human microbiome research at the NIH, NIH Institutes and Centers support for this field is also briefly addressed.
June 24, 2016: Seminars in Fetal & Neonatal Medicine
Leho Tedersoo, Björn Lindahl
Fungi are the key players in ecosystems as well as in plant and human health. High-throughput molecular identification of fungi has greatly progressed our understanding about the diversity of mutualists, saprotrophs, and pathogens. We argue that the methods promoted by the microbiome consortia are suboptimal for detection of the most important fungal pathogens and ecologically important degraders. We recommend several sets of optimized primers for analysis of fungi or all eukaryote groups based on either short or long amplicons that cover the ITS region as well as part of 18S and 28S rDNA...
June 27, 2016: Environmental Microbiology Reports
Patricio Jeraldo, Alvaro Hernandez, Henrik B Nielsen, Xianfeng Chen, Bryan A White, Nigel Goldenfeld, Heidi Nelson, David Alhquist, Lisa Boardman, Nicholas Chia
The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of "most wanted" taxa: bacteria both prevalent among healthy volunteers and distantly related to any sequenced organisms. Unfortunately, the challenge of assembling high-quality genomes from a tangle of metagenomic reads has slowed progress in learning about these uncultured bacteria...
2016: Frontiers in Microbiology
Anthony M Cundell
This review article on the skin microbiota was written in response to recent advances that transitioned from culture methods to PCR amplification and sequencing of bacterial and fungal genes as a result of the Human Microbiome Project. This transition enables the investigation of the full diversity of microorganisms inhabiting human skin. The skin provides a range of habitats with different microbiota associated with the three major regions of the skin, namely the moist axilla, perineum, and toe webs; oily or sebaceous head, neck, and trunk; and dry forearms and legs...
May 31, 2016: Microbial Ecology
James J Ashton, R Mark Beattie, Sarah Ennis, David W Cleary
Microbiome research has experienced an unprecedented level of growth over the last decade. This is largely due to revolutionary developments in, and accessibility to, DNA sequencing technologies that have enabled laboratories with even modest budgets to undertake projects. Study of the human microbiome in particular has seen a surge in interest, and although a lot of time and money has been focused on health and disease, the clinical interpretation of these data and the ability of clinicians to understand these studies in the context of disease are less straightforward...
July 2016: Inflammatory Bowel Diseases
Krystal Thomas-White, Megan Brady, Alan J Wolfe, Elizabeth R Mueller
In the human body, there are 10 bacterial cells for every one human cell. This fact highlights the importance of the National institutes of Health's initiative to map the human microbiome. The Human Microbiome Project was the first large-scale mapping of the human microbiome of 5 body sites: GI tract, mouth, vagina, skin and nasal cavity using culture-independent methods. The bladder was not originally tested because it was considered to be sterile and there were complexities regarding sample collection. Over the last couple years our team along with other investigators have shown that a urinary microbiome exists and for most individuals it plays a protective role...
March 2016: Current Bladder Dysfunction Reports
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