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https://www.readbyqxmd.com/read/29029138/the-female-genital-tract-microbiome-is-associated-with-vaginal-antiretroviral-drug-concentrations-in-human-immunodeficiency-virus-infected-women-on-antiretroviral-therapy
#1
Renee Donahue Carlson, Anandi N Sheth, Timothy D Read, Michael B Frisch, C Christina Mehta, Amy Martin, Richard E Haaland, Anar S Patel, Chou-Pong Pau, Colleen S Kraft, Igho Ofotokun
Background: The female genital tract (FGT) microbiome may affect vaginal pH and other factors that influence drug movement into the vagina. We examined the relationship between the microbiome and antiretroviral concentrations in the FGT. Methods: Over one menstrual cycle, 20 human immunodeficiency virus (HIV)-infected women virologically suppressed on tenofovir (TFV) disoproxil fumarate/emtricitabine and ritonavir-boosted atazanavir (ATV) underwent serial paired cervicovaginal and plasma sampling for antiretroviral concentrations using high-performance liquid chromatography-tandem mass spectrometry...
October 5, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29028892/nephele-a-cloud-platform-for-simplified-standardized-and-reproducible-microbiome-data-analysis
#2
Nick Weber, David Liou, Jennifer Dommer, Philip MacMenamin, Mariam Quiñones, Ian Misner, Andrew Oler, Joe Wan, Lewis Kim, Meghan Coakley McCarthy, Samuel Ezeji, Karlynn Noble, Darrell E Hurt
Motivation: Widespread interest in the study of the microbiome has resulted in data proliferation and the development of powerful computational tools. However, many scientific researchers lack the time, training, or infrastructure to work with large datasets or to install and use command line tools. Results: The National Institute of Allergy and Infectious Diseases (NIAID) has created Nephele, a cloud-based microbiome data analysis platform with standardized pipelines and a simple web interface for transforming raw data into biological insights...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028668/the-mycobiome-in-hiv
#3
Christopher L Hager, Mahmoud A Ghannoum
PURPOSE OF REVIEW: There are a limited number of studies investigating the association between the microbiome and HIV. Although the majority of these published investigations have focused on the role of the bacterial community (bacteriome) in this setting, a handful of studies have also characterized the role of the mycobiome in HIV-infected individuals. This review will summarize the most recent reports pertaining to the role of the fungal community in HIV. RECENT FINDINGS: Differences in the composition of the oral and respiratory mycobiome in HIV-infected individuals compared with uninfected individuals have been reported...
October 11, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/29028006/polymorphism-of-antibiotic-inactivating-enzyme-driven-by-ecology-expands-the-environmental-resistome
#4
Dae-Wi Kim, Cung Nawl Thawng, Jung-Hye Choi, Kihyun Lee, Chang-Jun Cha
The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29024170/steroids-stress-and-the-gut-microbiome-brain-axis
#5
REVIEW
Marc J Tetel, Geert J de Vries, Roberto C Melcangi, GianCarlo Panzica, Siobhain M O'Mahony
It is becoming well established that the gut microbiome has a profound impact on human health and disease. In this review, we explore how steroids can influence the gut microbiota, and in turn how the gut microbiota can influence hormone levels. Within the context of the gut microbiome-brain axis, we discuss how perturbations in the gut microbiota can alter the stress axis and behavior. In addition, human studies on the possible role of gut microbiota in depression and anxiety are examined. Finally, we present some of the challenges and important questions that need to be addressed by future research in this exciting new area at the intersection of steroids, stress, gut-brain axis and human health...
October 12, 2017: Journal of Neuroendocrinology
https://www.readbyqxmd.com/read/29023853/antibiotics-gut-microbiome-and-obesity
#6
Karen S W Leong, José G B Derraik, Paul L Hofman, Wayne S Cutfield
Antibiotics have been hailed by many as 'miracle drugs' that have been effectively treating infectious diseases for over a century, leading to a marked reduction in morbidity and mortality. However, with the increasing use of antibiotics, we are now faced not only with the increasing threat of antibiotic resistance, but also with a rising concern about potential long-term effects of antibiotics on human health, including the development of obesity. The obesity pandemic continues to increase, a problem that affects both adults and children alike...
October 12, 2017: Clinical Endocrinology
https://www.readbyqxmd.com/read/29023380/the-gut-microbiome-feelings-of-the-brain-a-perspective-for-non-microbiologists
#7
REVIEW
Aaron Lerner, Sandra Neidhöfer, Torsten Matthias
Objectives: To comprehensively review the scientific knowledge on the gut-brain axis. Methods: Various publications on the gut-brain axis, until 31 July 2017, were screened using the Medline, Google, and Cochrane Library databases. The search was performed using the following keywords: "gut-brain axis", "gut-microbiota-brain axis", "nutrition microbiome/microbiota", "enteric nervous system", "enteric glial cells/network", "gut-brain pathways", "microbiome immune system", "microbiome neuroendocrine system" and "intestinal/gut/enteric neuropeptides"...
October 12, 2017: Microorganisms
https://www.readbyqxmd.com/read/29023288/gut-microbiome-and-its-role-in-cardiovascular-diseases
#8
Shadi Ahmadmehrabi, W H Wilson Tang
PURPOSE OF REVIEW: In recent years, an interest in intestinal microbiota-host interactions has increased due to many findings about the impact of gut bacteria on human health and disease. Dysbiosis, a change in the composition of the gut microbiota, has been associated with much pathology, including cardiovascular diseases (CVD). This article will review normal functions of the gut microbiome, its link to CVD, and potential therapeutic interventions. RECENT FINDINGS: The recently discovered contribution of gut microbiota-derived molecules in the development of heart disease and its risk factors has significantly increased attention towards the connection between our gut and heart...
November 2017: Current Opinion in Cardiology
https://www.readbyqxmd.com/read/29022944/erratum-strains-functions-and-dynamics-in-the-expanded-human-microbiome-project
#9
Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A Brantley Hall, Arthur Brady, Heather H Creasy, Carrie McCracken, Michelle G Giglio, Daniel McDonald, Eric A Franzosa, Rob Knight, Owen White, Curtis Huttenhower
This corrects the article DOI: 10.1038/nature23889.
October 12, 2017: Nature
https://www.readbyqxmd.com/read/29022388/our-gut-microbiota-a-long-walk-to-homeostasis
#10
L M T Dicks, J Geldenhuys, L S Mikkelsen, E Brandsborg, H Marcotte
The microbiome of the human gastrointestinal tract (GIT) consists of billions of bacteria, fungi and viruses, of which bacteria play the most important role in nutrition, immune development, production of vitamins and maintaining a well-balanced (homeostatic) microbial population. Many papers have been published on the microbiota in the human GIT, but little is known about the first group of bacteria that colonises an infant. The intestinal tract of an unborn is, despite general belief, not sterile, but contains bacteria that have been transferred from the mother...
October 12, 2017: Beneficial Microbes
https://www.readbyqxmd.com/read/29019934/a-massively-parallel-sequence-similarity-search-for-metagenomic-sequencing-data
#11
Masanori Kakuta, Shuji Suzuki, Kazuki Izawa, Takashi Ishida, Yutaka Akiyama
Sequence similarity searches have been widely used in the analyses of metagenomic sequencing data. Finding homologous sequences in a reference database enables the estimation of taxonomic and functional characteristics of each query sequence. Because current metagenomic sequencing data consist of a large number of nucleotide sequences, the time required for sequence similarity searches account for a large proportion of the total time. This time-consuming step makes it difficult to perform large-scale analyses...
October 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29018933/from-osteoimmunology-to-osteomicrobiology-how-the-microbiota-and-the-immune-system-regulate-bone
#12
REVIEW
Emory Hsu, Roberto Pacifici
Osteomicrobiology refers to the role of microbiota in bone health and the mechanisms by which the microbiota regulates post-natal skeletal development, bone aging, and pathologic bone loss. Here, we review recent reports linking gut microbiota to changes in bone phenotype. A pro-inflammatory cytokine milieu drives bone resorption in conditions such as sex steroid hormone deficiency. The response of the immune system to activation by the microbiome results in increased circulating osteoclastogenic cytokines in a T cell-dependent mechanism...
October 10, 2017: Calcified Tissue International
https://www.readbyqxmd.com/read/29018902/the-p-n-positive-to-negative-links-ratio-in-complex-networks-a-promising-in-silico-biomarker-for-detecting-changes-occurring-in-the-human-microbiome
#13
Zhanshan Sam Ma
Relatively little progress in the methodology for differentiating between the healthy and diseased microbiomes, beyond comparing microbial community diversities with traditional species richness or Shannon index, has been made. Network analysis has increasingly been called for the task, but most currently available microbiome datasets only allows for the construction of simple species correlation networks (SCNs). The main results from SCN analysis are a series of network properties such as network degree and modularity, but the metrics for these network properties often produce inconsistent evidence...
October 11, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/29018846/antibiotics-and-specialized-metabolites-from-the-human-microbiota
#14
REVIEW
Walaa K Mousa, Bilal Athar, Nishanth J Merwin, Nathan A Magarvey
Covering: 2000 to 2017Decades of research on human microbiota have revealed much of their taxonomic diversity and established their direct link to health and disease. However, the breadth of bioactive natural products secreted by our microbial partners remains unknown. Of particular interest are antibiotics produced by our microbiota to ward off invasive pathogens. Members of the human microbiota exclusively produce evolved small molecules with selective antimicrobial activity against human pathogens. Herein, we expand upon the current knowledge concerning antibiotics derived from human microbiota and their distribution across body sites...
October 11, 2017: Natural Product Reports
https://www.readbyqxmd.com/read/29018426/transfer-and-persistence-of-a-multi-drug-resistance-plasmid-in-situ-of-the-infant-gut-microbiota-in-the-absence-of-antibiotic-treatment
#15
Heidi Gumpert, Jessica Z Kubicek-Sutherland, Andreas Porse, Nahid Karami, Christian Munck, Marius Linkevicius, Ingegerd Adlerberth, Agnes E Wold, Dan I Andersson, Morten O A Sommer
The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018410/next-generation-beneficial-microbes-the-case-of-akkermansia-muciniphila
#16
REVIEW
Patrice D Cani, Willem M de Vos
Metabolic disorders associated with obesity and cardiometabolic disorders are worldwide epidemic. Among the different environmental factors, the gut microbiota is now considered as a key player interfering with energy metabolism and host susceptibility to several non-communicable diseases. Among the next-generation beneficial microbes that have been identified, Akkermansia muciniphila is a promising candidate. Indeed, A. muciniphila is inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018121/dysbiosis-and-its-discontents
#17
Katarzyna B Hooks, Maureen A O'Malley
Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term's historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements...
October 10, 2017: MBio
https://www.readbyqxmd.com/read/29018117/reciprocal-prioritization-to-dietary-glycans-by-gut-bacteria-in-a-competitive-environment-promotes-stable-coexistence
#18
Yunus E Tuncil, Yao Xiao, Nathan T Porter, Bradley L Reuhs, Eric C Martens, Bruce R Hamaker
When presented with nutrient mixtures, several human gut Bacteroides species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression. However, it is unclear how closely these observed physiological changes, often measured by altered transcription of glycan utilization genes, mirror actual glycan depletion. To understand the glycan prioritization strategies of two closely related human gut symbionts, Bacteroides ovatus and Bacteroides thetaiotaomicron, we performed a series of time course assays in which both species were individually grown in a medium with six different glycans that both species can degrade...
October 10, 2017: MBio
https://www.readbyqxmd.com/read/28993762/commentary-lactobacilli-dominance-and-vaginal-ph-why-is-the-human-vaginal-microbiome-unique
#19
COMMENT
Virginia Fuochi, Giovanni Li Volti, Pio Maria Furneri
No abstract text is available yet for this article.
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28993578/characterizations-of-oral-microbiota-in-elderly-nursing-home-residents-with-diabetes
#20
Taiji Ogawa, Mariko Honda-Ogawa, Kazunori Ikebe, Yumiko Notomi, Yoshiko Iwamoto, Itsuki Shirobayashi, Seiko Hata, Masahito Kibi, Shizuko Masayasu, Satoshi Sasaki, Shigetada Kawabata, Yoshinobu Maeda
Over 700 bacterial species have been detected in the oral cavity. Several studies have suggested that periodontitis is associated with systemic disorders such as diabetes mellitus, indicating a key role for oral microbiota in human health. However, the relationship between oral microbiota and diabetes has not been well clarified. Therefore, we conducted microbiome analysis of saliva samples obtained from 15 elderly residents (3 with type 2 diabetes mellitus [DM] and 12 without diabetes [non-DM]) at three different nursing homes, as well as 9 young healthy controls (HC)...
October 6, 2017: Journal of Oral Science
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