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https://www.readbyqxmd.com/read/29141044/high-dimensional-linear-state-space-models-for-dynamic-microbial-interaction-networks
#1
Iris Chen, Yogeshwar D Kelkar, Yu Gu, Jie Zhou, Xing Qiu, Hulin Wu
Medical researchers are increasingly interested in knowing how the complex community of micro-organisms living on human body impacts human health. Key to this is to understand how the microbes interact with each other. Time-course studies on human microbiome indicate that the composition of microbiome changes over short time periods, primarily as a consequence of synergistic and antagonistic interactions of the members of the microbiome with each other and with the environment. Knowledge of the abundance of bacteria-which are the predominant members of the human microbiome-in such time-course studies along with appropriate mathematical models will allow us to identify key dynamic interaction networks within the microbiome...
2017: PloS One
https://www.readbyqxmd.com/read/29141029/correction-the-microbiome-in-urogenital-schistosomiasis-and-induced-bladder-pathologies
#2
Adewale S Adebayo, Mangesh Survayanshi, Shrikanth Bhute, Atinuke M Agunloye, Raphael D Isokpehi, Chiaka I Anumudu, Yogesh S Shouche
[This corrects the article DOI: 10.1371/journal.pntd.0005826.].
November 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29140991/a-bayesian-method-for-detecting-pairwise-associations-in-compositional-data
#3
Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower
Compositional data consist of vectors of proportions normalized to a constant sum from a basis of unobserved counts. The sum constraint makes inference on correlations between unconstrained features challenging due to the information loss from normalization. However, such correlations are of long-standing interest in fields including ecology. We propose a novel Bayesian framework (BAnOCC: Bayesian Analysis of Compositional Covariance) to estimate a sparse precision matrix through a LASSO prior. The resulting posterior, generated by MCMC sampling, allows uncertainty quantification of any function of the precision matrix, including the correlation matrix...
November 15, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29140397/progress-in-the-understanding-of-the-pathology-of-allergic-asthma-and-the-potential-of-fruit-proanthocyanidins-as-modulators-of-airway-inflammation
#4
REVIEW
Sara L Coleman, Odette M Shaw
Allergic asthma is a chronic inflammatory lung disease characterized by sensitization of the airways, and the development of immunoglobulin E antibodies, to benign antigens. The established pathophysiology of asthma includes recurrent lung epithelial inflammation, excessive mucus production, bronchial smooth muscle hyperreactivity, and chronic lung tissue remodeling, resulting in reversible airflow restriction. Immune cells, including eosinophils and the recently characterized type 2 innate lymphoid cells, infiltrate into the lung tissue as part of the inflammatory response in allergic asthma...
November 15, 2017: Food & Function
https://www.readbyqxmd.com/read/29140081/the-human-milk-glycome-as-a-defense-against-infectious-diseases-rationale-challenges-and-opportunities
#5
Kelly M Craft, Steven D Townsend
Each year over 3 million people die from infectious diseases with most of these deaths being poor and young children who live in low- and middle-income countries. Infectious diseases emerge for a multitude of reasons. On the social front, reasons include a breakdown of public health standards, international travel, and immigration (for financial, civil, and social reasons). At the molecular level, the modern rise of infectious diseases is tied to the juxtaposition of drug-resistant pathogens and a lack of new antimicrobials...
November 15, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29138961/blastocystis-subtypes-isolated-from-irritable-bowel-syndrome-patients-and-co-infection-with-helicobacter-pylori
#6
Ayman A El-Badry, Wegdan M Abd El Wahab, Doaa A Hamdy, Alaa Aboud
Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disease presenting clinically by abdominal pain with alteration of bowel habits. Although IBS has uncertain etiology, chronic gut inflammation due to persistent exposure to an infectious agent including Blastocystis sp. was proposed. The aim of this study was to detect the prevalence of Blastocystis sp. subtype (ST) isolated from stool of IBS patients and to assess Blastocystis sp. and H. pylori co-infection in IBS patients from Beni-Suef Governorate, Egypt...
November 14, 2017: Parasitology Research
https://www.readbyqxmd.com/read/29138692/transcriptomics-driven-lipidomics-tdl-identifies-the-microbiome-regulated-targets-of-ileal-lipid-metabolism
#7
Anirikh Chakrabarti, Mathieu Membrez, Delphine Morin-Rivron, Jay Siddharth, Chieh Jason Chou, Hugues Henry, Stephen Bruce, Sylviane Metairon, Frederic Raymond, Bertrand Betrisey, Carole Loyer, Scott J Parkinson, Mojgan Masoodi
The gut microbiome and lipid metabolism are both recognized as essential components in the maintenance of metabolic health. The mechanisms involved are multifactorial and (especially for microbiome) poorly defined. A strategic approach to investigate the complexity of the microbial influence on lipid metabolism would facilitate determination of relevant molecular mechanisms for microbiome-targeted therapeutics. E. coli is associated with obesity and metabolic syndrome and we used this association in conjunction with gnotobiotic models to investigate the impact of E...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29138485/evaluating-the-impact-of-domestication-and-captivity-on-the-horse-gut-microbiome
#8
Jessica L Metcalf, Se Jin Song, James T Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie, Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly modified...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138298/first-insights-into-the-diverse-human-archaeome-specific-detection-of-archaea-in-the-gastrointestinal-tract-lung-and-nose-and-on-skin
#9
Kaisa Koskinen, Manuela R Pausan, Alexandra K Perras, Michael Beck, Corinna Bang, Maximilian Mora, Anke Schilhabel, Ruth Schmitz, Christine Moissl-Eichinger
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29137160/the-influence-of-toothpaste-containing-australian-melaleuca-alternifolia-oil-and-ethanolic-extract-of-polish-propolis-on-oral-hygiene-and-microbiome-in-patients-requiring-conservative-procedures
#10
Tomasz Piekarz, Anna Mertas, Karolina Wiatrak, Rafał Rój, Patryk Kownacki, Joanna Śmieszek-Wilczewska, Ewelina Kopczyńska, Maciej Wrzoł, Maria Cisowska, Ewelina Szliszka, Zenon P Czuba, Iwona Niedzielska, Tadeusz Morawiec
The study was based on the use of a toothpaste with antiphlogistic activity, containing Australian Melaleuca alternifolia oil (tea tree oil-TTO) and ethanolic extract of Polish propolis (EEP). Fifty-one patients with varying conditions of the gingiva were divided into two groups. The study group received the toothpaste with TTO and EEP, while the control group received the same toothpaste but without TTO and EEP. Approximal plaque index (API), simplified oral hygiene index (OHI-s) and modified sulcus bleeding index (mSBI) were assessed in three subsequent stages...
November 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29136663/phylogenic-inference-using-alignment-free-methods-for-applications-in-microbial-community-surveys-using-16s-rrna-gene
#11
Yifei Zhang, Alexander V Alekseyenko
The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data...
2017: PloS One
https://www.readbyqxmd.com/read/29136126/risk-of-subsequent-sepsis-within-90-days-of-a-previous-hospital-stay-by-type-of-antibiotic-exposure
#12
James Baggs, Johm A Jernigan, Alison Laufer Halpin, Lauren H Epstein, Kelly M Hatfield, L Clifford McDonald
Background: We examined the risk of sepsis within 90 days after discharge from a previous hospital stay by type of antibiotic received during the previous stay. Methods: We retrospectively identified a cohort of hospitalized patients from the Truven Health MarketScan Hospital Drug Database. We examined the association between the use of certain antibiotics, determined a priori, during the initial hospital stay and risk of post-discharge sepsis controlling for potential confounding factors in a multivariable logistic regression model...
November 9, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29135490/the-microbiome-and-hiv-persistence-implications-for-viral-remission-and-cure
#13
Wei Li A Koay, Lilly V Siems, Deborah Persaud
PURPOSE OF REVIEW: This article discusses the interaction between HIV infection, the gut microbiome, inflammation and immune activation, and HIV reservoirs, along with interventions to target the microbiome and their implications for HIV remission and cure. RECENT FINDINGS: Most studies show that HIV-infected adults have a gut microbiome associated with decreased bacterial richness and diversity, and associated systemic inflammation and immune activation. A unique set of individuals, elite controllers, who spontaneously control HIV replication, have a similar microbiome to HIV-uninfected individuals...
November 10, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/29135334/maternal-high-fat-diet-and-its-consequence-on-the-gut-microbiome-a-rat-model
#14
Phyllis E Mann, Kevin Huynh, Giovanni Widmer
The biological changes that occur during pregnancy in the female mammal include shifts in hormonal regulation in preparation for parturition and lactation, and changes in energy metabolism. In women, studies have also shown that during pregnancy there is a reduction in bacterial species richness in the gut. In the current experiment rats were used to model the interaction of diet, reproductive status, and intestinal bacterial microbiota during pregnancy and lactation. In Experiment 1 rats were exposed to either standard chow or high-fat chow (60%) and were divided into two groups: unmated (NULL) or mated (RE)...
November 14, 2017: Gut Microbes
https://www.readbyqxmd.com/read/29134939/the-nursing-home-elder-microbiome-stability-and-associations-with-age-frailty-nutrition-and-physical-location
#15
John P Haran, Vanni Bucci, Protiva Dutta, Doyle Ward, Beth McCormick
PURPOSE: The microbiome from nursing home (NH) residents is marked by a loss in diversity that is associated with increased frailty. Our objective was to explore the associations of NH environment, frailty, nutritional status and residents' age to microbiome composition and potential metabolic function. METHODOLOGY: We conducted a prospective longitudinal cohort study of 23 residents, 65 years or older, from one NH that had four floors: two separate medical intensive floors and two floors with active elders...
November 14, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29134436/common-cutaneous-bacteria-isolated-from-snakes-inhibit-growth-of-ophidiomyces-ophiodiicola
#16
Aubree J Hill, Jacob E Leys, Danny Bryan, Fantasia M Erdman, Katherine S Malone, Gabrielle N Russell, Roger D Applegate, Heather Fenton, Kevin Niedringhaus, Andrew N Miller, Matthew C Allender, Donald M Walker
There is increasing concern regarding potential impacts of snake fungal disease (SFD), caused by Ophidiomyces ophiodiicola (Oo), on free-ranging snake populations in the eastern USA. The snake cutaneous microbiome likely serves as the first line of defense against Oo and other pathogens; however, little is known about microbial associations in snakes. The objective of this study was to better define the composition and immune function of the snake cutaneous microbiome. Eight timber rattlesnakes (Crotalus horridus) and four black racers (Coluber constrictor) were captured in Arkansas and Tennessee, with some snakes exhibiting signs of SFD...
November 13, 2017: EcoHealth
https://www.readbyqxmd.com/read/29134359/anxiety-depression-and-the-microbiome-a-role-for-gut-peptides
#17
REVIEW
Gilliard Lach, Harriet Schellekens, Timothy G Dinan, John F Cryan
The complex bidirectional communication between the gut and the brain is finely orchestrated by different systems, including the endocrine, immune, autonomic, and enteric nervous systems. Moreover, increasing evidence supports the role of the microbiome and microbiota-derived molecules in regulating such interactions; however, the mechanisms underpinning such effects are only beginning to be resolved. Microbiota-gut peptide interactions are poised to be of great significance in the regulation of gut-brain signaling...
November 13, 2017: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/29134235/correction-to-the-p-n-positive-to-negative-links-ratio-in-complex-networks-a-promising-in-silico-biomarker-for-detecting-changes-occurring-in-the-human-microbiome
#18
Zhanshan Sam Ma
The original version of this article unfortunately contained a missing image. The flowchart was not captured in PDF version. The original article was corrected.
November 13, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/29134155/foliar-microbiome-transplants-confer-disease-resistance-in-a-critically-endangered-plant
#19
Geoffrey Zahn, Anthony S Amend
There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped...
2017: PeerJ
https://www.readbyqxmd.com/read/29133882/discovery-of-an-expansive-bacteriophage-family-that-includes-the-most-abundant-viruses-from-the-human-gut
#20
Natalya Yutin, Kira S Makarova, Ayal B Gussow, Mart Krupovic, Anca Segall, Robert A Edwards, Eugene V Koonin
Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery (1-3) . A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome (4) . Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study...
November 13, 2017: Nature Microbiology
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