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Human microbiome

Katsuhiko Hirota, Hiromichi Yumoto, Bayarmagnai Sapaar, Takashi Matsuo, Tetsuo Ichikawa, Yoichiro Miyake
Candida albicans is commonly found as a member of the human microflora and a major human opportunistic fungal pathogen. A perturbation of the microbiome can lead to infectious diseases caused by various microorganisms, including C. albicans. Moreover, the interactions between C. albicans and bacteria are considered to play critical roles in human health. The major biological feature of C. albicans, which impacts human health, resides in its ability to form biofilms. In particular, the extracellular matrix (ECM) of Candida biofilm plays a multifaceted role and therefore may be considered as a highly attractive target to combat biofilm-related infectious diseases...
October 21, 2016: Journal of Applied Microbiology
Ellen K Silbergeld
The microbiome is increasingly recognized as a critical component in human development, health, and disease. Its relevance to toxicology and pharmacology involves challenges to current concepts related to absorption, metabolism, gene:environment, and pathways of response. Framing testable hypotheses for experimental and epidemiological studies will require attention to study designs, biosampling, data analysis, and attention to confounders.
October 21, 2016: Toxicologic Pathology
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
Kensuke Yamamura, Yoshifumi Baba, Shigeki Nakagawa, Kosuke Mima, Keisuke Miyake, Kenichi Nakamura, Hiroshi Sawayama, Koichi Kinoshita, Takatsugu Ishimoto, Masaaki Iwatsuki, Yasuo Sakamoto, Yoichi Yamashita, Naoya Yoshida, Masayuki Watanabe, Hideo Baba
PURPOSE: Fusobacterium nucleatum (F. nucleatum) is a component of the human microbiome that primarily inhabits the oral cavity. It causes periodontal disease and has also been implicated in the development of human cancers. Although there are several reports of the relationship between F. nucleatum and the clinical outcome in human cancers, its prognostic significance in esophageal cancer remains unclear. EXPERIMENTAL DESIGN: We quantified F. nucleatum DNA in 325 resected esophageal cancer specimens by qPCR...
October 21, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
R Balfour Sartor, Gary D Wu
Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis, via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice...
October 18, 2016: Gastroenterology
Joan B Broderick, James D Moody
The human gut microbiome is the source of not only microbial diversity, but also of interesting chemical reactions and enzymology. An excellent example of this is CutC, an enzyme that makes trimethylamine (TMA). In this issue of Cell Chemical Biology, Bodea et al. (2016) show how CutC uses a glycyl radical to perform C-N bond cleavage needed for TMA production.
October 20, 2016: Cell Chemical Biology
Eric Banan-Mwine Daliri, Shuai Wei, Deog H Oh, Byong H Lee
The mammalian gastrointestinal tract has co-developed with a large number of microbes in a symbiotic relationship over millions of years. Recent studies indicate that indigenous bacteria are intimate with the intestine and play essential roles in health and disease. In the quest to maintain a stable niche, these prokaryotes influence multiple host metabolic pathways, resulting from an interactive host-microbiota metabolic signaling and impacting strongly on the metabolic phenotypes of the host. Since dysbiosis of the gut bacteria result in alteration in the levels of certain microbial and host co-metabolites, identifying these markers could enhance early detection of diseases...
October 21, 2016: Critical Reviews in Food Science and Nutrition
Matthias Willmann, Silke Peter
The increasing threat of antimicrobial resistance poses one of the greatest challenges to modern medicine. The collection of all antimicrobial resistance genes carried by various microorganisms in the human body is called the human resistome and represents the source of resistance in pathogens that can eventually cause life-threatening and untreatable infections. A deep understanding of the human resistome and its multilateral interaction with various environments is necessary for developing proper measures that can efficiently reduce the spread of resistance...
October 20, 2016: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
Shelby Calkins, M B Couger, Colin Jackson, Jordan Zandler, Garett C Hudgins, Radwa A Hanafy, Connie Budd, Donald P French, Wouter D Hoff, Noha Youssef
Staphylococcus hominis is a predominant member of the human skin microbiome. We here report on the genomic analysis of Staphylococcus hominis strain Hudgins that was isolated from the wrist area of human skin. The partial genome assembly of S. hominis Hudgins consists of 2,211,863 bp of DNA with 2174 protein-coding genes and 90 RNA genes. Based on the genomic analysis of KEGG pathways, the organism is expected to be a versatile heterotroph potentially capable of hydrolyzing the sugars glucose, fructose, mannose, and the amino acids alanine, aspartate, glutamate, glycine, threonine, cysteine, methionine, valine, isoleucine, leucine, lysine, arginine, phenylalanine, tyrosine, and tryptophan for energy production through aerobic respiration, with occasional lactate and acetate fermentation...
December 2016: Genomics Data
James J Cody, Wannaporn Ittiprasert, André N Miller, Lucie Henein, Margaret M Mentink-Kane, Michael H Hsieh
Schistosomiasis remains a health burden in many parts of the world. The complex life cycle of Schistosoma parasites and the economic and societal conditions present in endemic areas make the prospect of eradication unlikely in the foreseeable future. Continued and vigorous research efforts must therefore be directed at this disease, particularly since only a single World Health Organization (WHO)-approved drug is available for treatment. The National Institutes of Health (NIH)-National Institute of Allergy and Infectious Diseases (NIAID) Schistosomiasis Resource Center (SRC) at the Biomedical Research Institute provides investigators with the critical raw materials needed to carry out this important research...
October 2016: PLoS Neglected Tropical Diseases
Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
Walter H Moos, Carl A Pinkert, Michael H Irwin, Douglas V Faller, Krishna Kodukula, Ioannis P Glavas, Kosta Steliou
Preclinical Research Approximately 2,500 years ago, Hippocrates used the word herpes as a medical term to describe lesions that appeared to creep or crawl on the skin, advocating heat as a possible treatment. During the last 50 years, pharmaceutical research has made great strides, and therapeutic options have expanded to include small molecule antiviral agents, protease inhibitors, preventive vaccines for a handful of the papillomaviruses, and even cures for hepatitis C virus infections. However, effective treatments for persistent and recurrent viral infections, particularly the highly prevalent herpesviruses, continue to represent a significant unmet medical need, affecting the majority of the world's population...
October 20, 2016: Drug Development Research
Yushu Yin, Georgia Papavasiliou, Olga Y Zaborina, John C Alverdy, Fouad Teymour
The human gastrointestinal tract is the primary site of colonization of multidrug resistant pathogens and the major source of life-threatening complications in critically ill and immunocompromised patients. Eradication measures using antibiotics carry further risk of antibiotic resistance. Furthermore, antibiotic treatment can adversely shift the intestinal microbiome toward domination by resistant pathogens. Therefore, approaches directed to prevent replacement of health promoting microbiota with resistant pathogens should be developed...
October 19, 2016: Annals of Biomedical Engineering
Awa Diop, Saber Khelaifia, Nicholas Armstrong, Noémie Labas, Pierre-Edouard Fournier, Didier Raoult, Matthieu Million
BACKGROUND: Microbial culturomics represents an ongoing revolution in the characterization of environmental and human microbiome. METHODS: By using three media containing high salt concentration (100, 150, and 200 g/L), the halophilic microbial culturome of a commercial table salt was determined. RESULTS: Eighteen species belonging to the Terrabacteria group were isolated including eight moderate halophilic and 10 halotolerant bacteria. Gracilibacillus massiliensis sp...
2016: Microbial Ecology in Health and Disease
Justine Debelius, Se Jin Song, Yoshiki Vazquez-Baeza, Zhenjiang Zech Xu, Antonio Gonzalez, Rob Knight
Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect sizes of both biological and technical covariates can help improve study design and the quality of biological conclusions. Care must be taken to avoid technical bias that can lead to incorrect biological conclusions. The presentation of quantitative effect sizes in addition to P values will improve our ability to perform meta-analysis and to evaluate potentially relevant biological effects...
October 19, 2016: Genome Biology
Mária Džunková, Giuseppe D'Auria, Hua Xu, Jun Huang, Yinghua Duan, Andrés Moya, Ciarán P Kelly, Xinhua Chen
Antibiotics have significant and long-lasting impacts on the intestinal microbiota and consequently reduce colonization resistance against Clostridium difficile infection (CDI). Standard therapy using antibiotics is associated with a high rate of disease recurrence, highlighting the need for novel treatment strategies that target toxins, the major virulence factors, rather than the organism itself. Human monoclonal antibodies MK-3415A (actoxumab-bezlotoxumab) to C. difficile toxin A and toxin B, as an emerging non-antibiotic approach, significantly reduced the recurrence of CDI in animal models and human clinical trials...
2016: Frontiers in Cellular and Infection Microbiology
Kaleigh Giles, Benjamin Pluvinage, Alisdair B Boraston
The polysaccharide utilization locus in Bacteroides plebeius that confers the ability to catabolize porphyran contains a putative GH50 β-agarase (BACPLE_01683, BpGH50). BpGH50 did not show any clear activity on agarose or on the related algal galactans porphyran and carrageenan. However, the 1.4 Å resolution x-ray crystal structure of BpGH50 confirmed its possession of the core (α/β)8 barrel fold found in GH50 enzymes as well as the structural conservation of the catalytic residues and some substrate binding residues...
October 18, 2016: Proteins
Aran Singanayagam, Andrew I Ritchie, Sebastian L Johnston
PURPOSE OF REVIEW: The emergence of next-generation 16S rRNA sequencing techniques has facilitated a more detailed study of the body's microbiota and led to renewed interest in the association between microbial exposure and asthma inception. In this review, we evaluate the evidence that the respiratory tract and intestinal microbiota contribute to asthma pathogenesis and progression. RECENT FINDINGS: Human studies have revealed associations between the presence of potentially pathogenic bacteria in the respiratory tract in early life and subsequent risk of allergic sensitization and asthma...
October 15, 2016: Current Opinion in Pulmonary Medicine
Jay-Hyun Jo, Elizabeth A Kennedy, Heidi H Kong
Skin constantly encounters external elements, including microbes. Culture-based studies have identified fungi present on human skin and have linked some species with certain skin diseases. Moreover, modern medical treatments, especially immunosuppressants, have increased the population at risk for cutaneous and invasive fungal infections, emphasizing the need to understand skin fungal communities in health and disease. A major hurdle for studying fungal flora at a community level has been the heterogeneous culture conditions required by skin fungi...
October 18, 2016: Virulence
GwangPyo Ko
Recently, there were dramatically increased interests on human microbiome research worldwide. Human microbiome has been considered as the second genome in addition to our own genome and played very crucial roles in maintaining human health. Human microbiota typically reside on the surface of epithelial cells and play various biological roles ranging from metabolism, immune development, mental health, and to organ development. Since 2008, we have determined the diversity of Korean microbiome and determined the genes and pathways of gut microbiome using Korean Twin Cohort...
September 2016: Journal of Hypertension
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