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Human microbiome

Zahra Jalili, Moein Saleh, Saeid Bouzari, Mohammad Pooya
BACKGROUND AND AIM: Urinary tract infection (UTI) is the second most frequent infection in human, and uropathogenic Escherichia coli is its most common cause. Although antibiotics are the standard treatment for UTI, they can cause harmful effects on gut microbiome and increase the rate of existing drug-resistant bacteria, which make the vaccine research reasonable. This study was conducted to construct a Killed but Metabolically Active (KBMA) E. coli strain, and to determine its characteristics as a possible vaccine candidate for UTI, which will be evaluated in further investigations...
June 20, 2018: Microbial Pathogenesis
Patrice D Cani
The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics...
June 22, 2018: Gut
Christa Kietz, Vilma Pollari, Annika Meinander
As several diseases have been linked to dysbiosis of the human intestinal microflora, manipulation of the microbiota has emerged as an exciting new strategy for potentially treating and preventing diseases. However, the human microbiota consists of a plethora of different species, and distinguishing the impact of a specific bacterial species on human health is challenging. In tackling this challenge, the fruit fly Drosophila melanogaster, with its far simpler microbial composition, has emerged as a powerful model for unraveling host-microbe interactions...
June 22, 2018: Current Protocols in Toxicology
Ömrüm Aydin, Max Nieuwdorp, Victor Gerdes
PURPOSE OF REVIEW: The objective of this review is to critically assess the contributing role of the gut microbiota in human obesity and type 2 diabetes (T2D). RECENT FINDINGS: Experiments in animal and human studies have produced growing evidence for the causality of the gut microbiome in developing obesity and T2D. The introduction of high-throughput sequencing technologies has provided novel insight into the interpersonal differences in microbiome composition and function...
June 21, 2018: Current Diabetes Reports
Clare Abreu, Anthony Ortiz Lopez, Jeff Gore
No abstract text is available yet for this article.
June 21, 2018: Molecular Systems Biology
Ophelia S Venturelli, Alex C Carr, Garth Fisher, Ryan H Hsu, Rebecca Lau, Benjamin P Bowen, Susan Hromada, Trent Northen, Adam P Arkin
The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions...
June 21, 2018: Molecular Systems Biology
Peilin Zheng, Zhixia Li, Zhiguang Zhou
Type 1 diabetes (T1D) is an autoimmune disease, which is characterized by the destruction of islet β cells in the pancreas triggered by genetic and environmental factors. In past decades, extensive familial and genome-wide association studies have revealed more than 50 risk loci in the genome. However, genetic susceptibility cannot explain the increased incidence of T1D worldwide, which is very likely attributed by the growing impact of environmental factors, especially gut microbiome. Recently, the role of gut microbiome in the pathogenesis of T1D have been uncovered by the increasing evidence from both human subjects and animal models, strongly indicating that gut microbiome might be a pivotal hub of T1D-triggering factors, especially environmental factors...
June 21, 2018: Diabetes/metabolism Research and Reviews
Sonja Bäumel, Hanne L P Tytgat, Birgit Nemec, Ruth Schmidt, Loo Wee Chia, Hauke Smidt
The Human Microbiome, as well as the exploration of the microorganisms inhabiting the human body, are not only integral to the field of microbiology but represent an intrinsic part of all human beings. Consequently, along with scientists, artists have been inspired by the microbiome: transforming it in to tangible artefacts in order to critically question, reflect on and break down the barrier between humans and their microcohabitants. By artistic means, artists help us to understand how microbial research topics are inevitably affected by societal influences, including (health) politics, economics and the arts...
July 2018: Microbial Biotechnology
Anna G Nilsson, Daniel Sundh, Fredrik Bäckhed, Mattias Lorentzon
The importance of the gut microbiome for bone metabolism in mice has recently been demonstrated, but no studies are available in humans. Lactobacillus reuteri ATCCPTA 6475 (L. reuteri 6475) has been reported to increase bone mineral density (BMD) in mice but its effect on the human skeleton is unknown. The objective of this trial was to investigate if L. reuteri 6475 affects bone loss in older women with low BMD. In this double-blind, placebo-controlled study, women from the population who were 75 to 80 years old and had low BMD were randomized to orally receive 1010 colony-forming units of L...
June 21, 2018: Journal of Internal Medicine
Tomohisa Takagi, Yuji Naito, Ryo Inoue, Saori Kashiwagi, Kazuhiko Uchiyama, Katsura Mizushima, Saeko Tsuchiya, Osamu Dohi, Naohisa Yoshida, Kazuhiro Kamada, Takeshi Ishikawa, Osamu Handa, Hideyuki Konishi, Kayo Okuda, Yoshimasa Tsujimoto, Hiromu Ohnogi, Yoshito Itoh
BACKGROUND: Human gut microbiota is involved in host health and disease development. Investigations of age-related and sex-related alterations in gut microbiota are limited, and the association between stool consistency and gut microbiota has not been fully investigated. We investigated gut microbiota differences related to age, sex, and stool consistency in healthy Japanese subjects. METHODS: Two-hundred and seventy-seven healthy Japanese subjects aged 20-89 years were enrolled...
June 20, 2018: Journal of Gastroenterology
Philip Burnham, Darshana Dadhania, Michael Heyang, Fanny Chen, Lars F Westblade, Manikkam Suthanthiran, John Richard Lee, Iwijn De Vlaminck
Urinary tract infections are one of the most common infections in humans. Here we tested the utility of urinary cell-free DNA (cfDNA) to comprehensively monitor host and pathogen dynamics in bacterial and viral urinary tract infections. We isolated cfDNA from 141 urine samples from a cohort of 82 kidney transplant recipients and performed next-generation sequencing. We found that urinary cfDNA is highly informative about bacterial and viral composition of the microbiome, antimicrobial susceptibility, bacterial growth dynamics, kidney allograft injury, and host response to infection...
June 20, 2018: Nature Communications
Neslihan Ucuncuoglu, Kurt Warncke
The adenosylcobalamin- (coenzyme B12 ) dependent ethanolamine ammonia-lyase (EAL) plays a key role in aminoethanol metabolism, associated with microbiome homeostasis and Salmonella- and Escherichia coli-induced disease conditions in the human gut. To gain molecular insight into these processes toward development of potential therapeutic targets, reactions of the cryotrapped (S)-2-aminopropanol substrate radical EAL from Salmonella typhimurium are addressed over a temperature (T) range of 220-250 K by using T-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy...
June 19, 2018: Biophysical Journal
Ravinder Nagpal, Carol A Shively, Susan A Appt, Thomas C Register, Kristofer T Michalson, Mara Z Vitolins, Hariom Yadav
The mammalian gastrointestinal tract harbors a highly diverse and dynamic community of bacteria. The array of this gut bacterial community, which functions collectively as a fully unified organ in the host metabolism, varies greatly among different host species and can be shaped by long-term nutritional interventions. Non-human primates, our close phylogenetic relatives and ancestors, provide an excellent model for studying diet-microbiome interaction; however, compared to clinical and rodent studies, research targeting primate gut microbiome has been limited...
2018: Frontiers in Nutrition
Emma Reece, Sean Doyle, Peter Greally, Julie Renwick, Siobhán McClean
Many cystic fibrosis (CF) airway infections are considered to be polymicrobial and microbe-microbe interactions may play an important role in disease pathology. Pseudomonas aeruginosa and Aspergillus fumigatus are the most prevalent bacterial and fungal pathogens isolated from the CF airway, respectively. We have previously shown that patients co-colonized with these pathogens had comparable outcomes to those chronically colonized with P. aeruginosa . Our objective was to examine the interactions between A...
2018: Frontiers in Microbiology
Hans-Frieder Schoett, Sabrina Krautbauer, Marcus Hoering, Gerhard Liebisch, Silke Matysik
There has been an increasing interest during recent years in the role of the gut microbiome on health and disease. Therefore, metabolites in human faeces related to microbial activity are attractive surrogate marker to track changes of microbiota induced by diet or disease. Such markers include 5α/β-stanols as microbiome-derived metabolites of sterols. Currently, reliable, robust, and fast methods to quantify faecal sterols and their related metabolites are missing. We developed a liquid chromatography-high resolution mass spectrometry (LC-MS/HRMS) method for the quantification of sterols and their 5α/β-stanols in human faecal samples...
June 19, 2018: Analytical Chemistry
Ekaterina Smirnova, Snehalata Huzurbazar, Farhad Jafari
The human microbiota composition is associated with a number of diseases including obesity, inflammatory bowel disease, and bacterial vaginosis. Thus, microbiome research has the potential to reshape clinical and therapeutic approaches. However, raw microbiome count data require careful pre-processing steps that take into account both the sparsity of counts and the large number of taxa that are being measured. Filtering is defined as removing taxa that are present in a small number of samples and have small counts in the samples where they are observed...
June 18, 2018: Biostatistics
Marc Noguera-Julian, Camila González-Beiras, Mariona Parera, August Kapa, Roger Paredes, Oriol Mitjà
Background: Treponema pallidum subsp. pertenue and Haemophilus ducreyi are causative agents of cutaneous ulcer (CU) in yaws endemic regions in the tropics. However, a significant proportion of CU patients remain PCR-negative for both bacterial agents. We aimed to identify potential additional aetiological agents of CU in a yaws-endemic region. Methods: This population-based cohort study included children in Lihir Island (Papua New Guinea) examined during a yaws eradication campaign in Oct 2013-Oct 2014...
June 16, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Mengyu Shen, Yuhui Yang, Wei Shen, Lujia Cen, Jeffrey S McLean, Wenyuan Shi, Shuai Le, Xuesong He
The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated an Actinomyces odontolyticus subsp. Actinosynbacte r strain XH001 from human oral cavity, and genomic analysis revealed the presence of an intact prophage, named xhp1. Here we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus Prophage xhp1 genome is 35 kb linear double-stranded DNA with 10 bp single-stranded cohesive ends at 3' of both ends...
June 18, 2018: Applied and Environmental Microbiology
Tariq Ismail, Nighat Fatima, Syed Aun Muhammad, Syed Saoud Zaidi, Nisar Rehman, Izhar Hussain, Najam Us Sahr Tariq, Imran Amirzada, Abdul Mannan
Candida albicans (Candida albicans) is one of the major sources of nosocomial infections in humans which may prove fatal in 30% of cases. The hospital acquired infection is very difficult to treat affectively due to the presence of drug resistant pathogenic strains, therefore there is a need to find alternative drug targets to cure this infection. In silico and computational level frame work was used to prioritize and establish antifungal drug targets of Candida albicans. The identification of putative drug targets was based on acquiring 5090 completely annotated genes of Candida albicans from available databases which were categorized into essential and non-essential genes...
2018: Acta Biochimica Polonica
Melanie Schirmer, Vinod Kumar, Mihai G Netea, Ramnik J Xavier
Cytokines are important cell-signaling molecules that activate and modulate immune responses. Major factors influencing cytokine variation in healthy individuals are host genetics, non-heritable factors and the microbiome. Genetic variation accounts for a significant part of heterogeneity in cytokine production by peripheral blood mononuclear cells. Variation in cytokines such as IL-6 and IL-6Ra is strongly influenced by heritability, suggesting an evolutionarily pressure for their genetic regulation that potentially contributes to differences in immune responsiveness between human populations...
June 15, 2018: Current Opinion in Immunology
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