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Human microbiome

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https://www.readbyqxmd.com/read/28448493/variable-habitat-conditions-drive-species-covariation-in-the-human-microbiota
#1
Charles K Fisher, Thierry Mora, Aleksandra M Walczak
Two species with similar resource requirements respond in a characteristic way to variations in their habitat-their abundances rise and fall in concert. We use this idea to learn how bacterial populations in the microbiota respond to habitat conditions that vary from person-to-person across the human population. Our mathematical framework shows that habitat fluctuations are sufficient for explaining intra-bodysite correlations in relative species abundances from the Human Microbiome Project. We explicitly show that the relative abundances of closely related species are positively correlated and can be predicted from taxonomic relationships...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28447406/the-prenatal-gut-microbiome-are-we-colonized-with-bacteria-in-utero
#2
REVIEW
R W Walker, J C Clemente, I Peter, R J F Loos
The colonization of the gut with microbes in early life is critical to the developing newborn immune system, metabolic function and potentially future health. Maternal microbes are transmitted to offspring during childbirth, representing a key step in the colonization of the infant gut. Studies of infant meconium suggest that bacteria are present in the foetal gut prior to birth, meaning that colonization could occur prenatally. Animal studies have shown that prenatal transmission of microbes to the foetus is possible, and physiological changes observed in pregnant mothers indicate that in utero transfer is likely in humans as well...
April 26, 2017: Pediatric Obesity
https://www.readbyqxmd.com/read/28446062/metabolite-sensing-g-protein-coupled-receptors-facilitators-of-diet-related-immune-regulation
#3
Jian K Tan, Craig McKenzie, Eliana Mariño, Laurence Macia, Charles R Mackay
Nutrition and the gut microbiome regulate many systems, including the immune, metabolic, and nervous systems. We propose that the host responds to deficiency (or sufficiency) of dietary and bacterial metabolites in a dynamic way, to optimize responses and survival. A family of G protein-coupled receptors (GPCRs) termed the metabolite-sensing GPCRs bind to various metabolites and transmit signals that are important for proper immune and metabolic functions. Members of this family include GPR43, GPR41, GPR109A, GPR120, GPR40, GPR84, GPR35, and GPR91...
April 26, 2017: Annual Review of Immunology
https://www.readbyqxmd.com/read/28444712/the-urinary-microbiome-and-its-contribution-to-lower-urinary-tract-symptoms-ici-rs-2015
#4
REVIEW
Marcus J Drake, Nicola Morris, Apostolos Apostolidis, Mohammad S Rahnama'i, Julian R Marchesi
AIMS: The microbiome is the term used for the symbiotic microbial colonisation of healthy organs. Studies have found bacterial identifiers within voided urine which is apparently sterile on conventional laboratory culture, and accordingly there may be health and disease implications. METHODS: The International Consultation on Incontinence Research Society (ICI-RS) established a literature review and expert consensus discussion focussed on the increasing awareness of the urinary microbiome, and potential research priorities...
April 2017: Neurourology and Urodynamics
https://www.readbyqxmd.com/read/28444239/the-influence-of-social-conditions-across-the-life-course-on-the-human-gut-microbiota-a-pilot-project-with-the-wisconsin-longitudinal-study
#5
Pamela Herd, Nora Cate Schaeffer, Kerryann DiLoreto, Karen Jacques, John Stevenson, Federico Rey, Carol Roan
Objective: To test the feasibility of collecting and integrating data on the gut microbiome into one of the most comprehensive longitudinal studies of aging and health, the Wisconsin Longitudinal Study (WLS). The long-term goal of this integration is to clarify the contribution of social conditions in shaping the composition of the gut microbiota late in life. Research on the microbiome, which is considered to be of parallel importance to human health as the human genome, has been hindered by human studies with nonrandomly selected samples and with limited data on social conditions over the life course...
April 25, 2017: Journals of Gerontology. Series B, Psychological Sciences and Social Sciences
https://www.readbyqxmd.com/read/28443082/inbred-mouse-populations-exhibit-intergenerational-changes-in-intestinal-microbiota-composition-and-function-following-introduction-to-a-facility
#6
Jocelyn M Choo, Paul J Trim, Lex E X Leong, Guy C J Abell, Carly Brune, Nicole Jeffries, Steve Wesselingh, T N Dear, Marten F Snel, Geraint B Rogers
Inbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3, and 6), following their introduction to a stringently controlled facility...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28441565/gut-microbiota-small-molecules-modulate-host-cellular-functions
#7
Jacob M Luber, Aleksandar D Kostic
The human gut metagenome was recently discovered to encode vast collections of biosynthetic gene clusters with diverse chemical potential, almost none of which are yet functionally validated. Recent work elucidates common microbiome-derived biosynthetic gene clusters encoding peptide aldehydes that inhibit human proteases.
April 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28440278/an-insider-s-perspective-bacteroides-as-a-window-into-the-microbiome
#8
REVIEW
Aaron G Wexler, Andrew L Goodman
Over the last decade, our appreciation for the contribution of resident gut microorganisms-the gut microbiota-to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium...
April 25, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28439499/tick-pathogen-interactions-and-vector-competence-identification-of-molecular-drivers-for-tick-borne-diseases
#9
REVIEW
José de la Fuente, Sandra Antunes, Sarah Bonnet, Alejandro Cabezas-Cruz, Ana G Domingos, Agustín Estrada-Peña, Nicholas Johnson, Katherine M Kocan, Karen L Mansfield, Ard M Nijhof, Anna Papa, Nataliia Rudenko, Margarita Villar, Pilar Alberdi, Alessandra Torina, Nieves Ayllón, Marie Vancova, Maryna Golovchenko, Libor Grubhoffer, Santo Caracappa, Anthony R Fooks, Christian Gortazar, Ryan O M Rego
Ticks and the pathogens they transmit constitute a growing burden for human and animal health worldwide. Vector competence is a component of vectorial capacity and depends on genetic determinants affecting the ability of a vector to transmit a pathogen. These determinants affect traits such as tick-host-pathogen and susceptibility to pathogen infection. Therefore, the elucidation of the mechanisms involved in tick-pathogen interactions that affect vector competence is essential for the identification of molecular drivers for tick-borne diseases...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28438217/a-powerful-microbiome-based-association-test-and-a-microbial-taxa-discovery-framework-for-comprehensive-association-mapping
#10
Hyunwook Koh, Martin J Blaser, Huilin Li
BACKGROUND: The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. METHODS: Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT)...
April 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28437450/esprit-forest-parallel-clustering-of-massive-amplicon-sequence-data-in-subquadratic-time
#11
Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun
The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analy- sis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437060/high-throughput-and-quantitative-measurement-of-microbial-metabolome-by-gas-chromatography-mass-spectrometry-using-automated-alkyl-chloroformate-derivatization
#12
Linjing Zhao, Yan Ni, Mingming Su, Hongsen Li, Fangcong Dong, Wenlian Chen, Runmin Wei, Lulu Zhang, Seu-Ping Guiraud, François-Pierre J Martin, Cynthia Rajani, Guoxiang Xie, Wei Jia
The ability to identify and quantify small molecule metabolites derived from gut microbial-mammalian co-metabolism is essential for the understanding of the distinct metabolic functions of the microbiome. To date, analytical protocols that quantitatively measure a complete panel of microbial metabolites in biological samples have not been established, but urgently needed by the microbiome research community. Here, we report an automated high-throughput quantitative method using a gas chromatography/time-of-flight mass spectrometry (GC/TOFMS) platform to simultaneously measure over one hundred microbial metabolites in human serum, urine, feces and Escherichia coli cell samples within 15 minutes per sample...
April 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28436097/the-vaginal-microbiome-and-gynaecological-cancer-exercise-caution-when-considering-causation
#13
Neal C Ramchander, Emma J Crosbie
Genital infection with high-risk human papillomavirus (HPV) is extremely common in young, sexually active women, but most infections are transient and clear without ever causing disease. Persistent infection causes premalignant cervical intraepithelial neoplasia (CIN), which, if left untreated, can undergo malignant transformation and become invasive cancer. Cervical cancer is thus considered a late, rare consequence of persistent high-risk HPV infection (Crosbie et al. Lancet 2013; 382:889-99). Factors that influence the acquisition of genital HPV and the rate of its natural clearance are therefore important in the pathogenesis of cervical cancer...
April 24, 2017: BJOG: An International Journal of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28435856/dynamic-microbiome-evolution-in-social-bees
#14
Waldan K Kwong, Luis A Medina, Hauke Koch, Kong-Wah Sing, Eunice Jia Yu Soh, John S Ascher, Rodolfo Jaffé, Nancy A Moran
The highly social (eusocial) corbiculate bees, comprising the honey bees, bumble bees, and stingless bees, are ubiquitous insect pollinators that fulfill critical roles in ecosystem services and human agriculture. Here, we conduct wide sampling across the phylogeny of these corbiculate bees and reveal a dynamic evolutionary history behind their microbiota, marked by multiple gains and losses of gut associates, the presence of generalist as well as host-specific strains, and patterns of diversification driven, in part, by host ecology (for example, colony size)...
March 2017: Science Advances
https://www.readbyqxmd.com/read/28435675/microbiome-effects-on-immunity-health-and-disease-in-the-lung
#15
REVIEW
Shakti D Shukla, Kurtis F Budden, Rachael Neal, Philip M Hansbro
Chronic respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF), are among the leading causes of mortality and morbidity worldwide. In the past decade, the interest in the role of microbiome in maintaining lung health and in respiratory diseases has grown exponentially. The advent of sophisticated multiomics techniques has enabled the identification and characterisation of microbiota and their roles in respiratory health and disease. Furthermore, associations between the microbiome of the lung and gut, as well as the immune cells and mediators that may link these two mucosal sites, appear to be important in the pathogenesis of lung conditions...
March 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/28434033/the-gut-microbiome-as-a-target-for-prevention-and-treatment-of-hyperglycaemia-in-type-2-diabetes-from-current-human-evidence-to-future-possibilities
#16
REVIEW
Louise Brunkwall, Marju Orho-Melander
The totality of microbial genomes in the gut exceeds the size of the human genome, having around 500-fold more genes that importantly complement our coding potential. Microbial genes are essential for key metabolic processes, such as the breakdown of indigestible dietary fibres to short-chain fatty acids, biosynthesis of amino acids and vitamins, and production of neurotransmitters and hormones. During the last decade, evidence has accumulated to support a role for gut microbiota (analysed from faecal samples) in glycaemic control and type 2 diabetes...
April 22, 2017: Diabetologia
https://www.readbyqxmd.com/read/28432400/-the-intestinal-microbiome-and-metabolic-diseases-from-obesity-to-diabetes-and-nonalcoholic-steatohepatitis
#17
S C Bischoff
BACKGROUND: The intestinal microbiome consists of about 10 million genes, many of which encode digestive enzymes. This explains why animal and human experiments revealed that the intestinal microbiome adapts to food intake and optimizes energy harvest from food. This function is considered beneficial in states of lack of food, but following overnutrition, it might support the development of obesity. OBJECTIVES: The relevance of the intestinal microbiome for the pathogenesis of obesity and associated metabolic diseases such as fatty liver disease and type 2 diabetes mellitus and for the clinical management of such diseases shall be discussed...
April 21, 2017: Der Internist
https://www.readbyqxmd.com/read/28431252/engineered-regulatory-systems-modulate-gene-expression-of-human-commensals-in-the-gut
#18
Bentley Lim, Michael Zimmermann, Natasha A Barry, Andrew L Goodman
The gut microbiota is implicated in numerous aspects of health and disease, but dissecting these connections is challenging because genetic tools for gut anaerobes are limited. Inducible promoters are particularly valuable tools because these platforms allow real-time analysis of the contribution of microbiome gene products to community assembly, host physiology, and disease. We developed a panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431238/reducing-recurrence-of-c-difficile-infection
#19
Michael G Dieterle, Vincent B Young
Clostridium difficile infection (CDI) is facilitated by alteration of the microbiome following antibiotic administration. Antimicrobial therapy directed against the pathogen can treat CDI. Unfortunately, ∼20% of successfully treated patients will suffer recurrence. Bezlotoxumab, a human monoclonal antibody, binds to C. difficile toxin B (TcdB), reducing recurrence presumably by limiting epithelial damage and facilitating microbiome recovery.
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431222/principles-of-chemical-biology-from-magic-to-gut-fungi-via-plug-and-play-biosensors
#20
(no author information available yet)
This month: New MAGIC linking mitochondrial biology and proteostasis, split RNA polymerase based biosensors, and a role that fungi play in human gut microbiome.
April 20, 2017: Cell Chemical Biology
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