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https://www.readbyqxmd.com/read/29145612/developmental-and-gut-related-changes-to-microbiomes-of-the-cultured-juvenile-spiny-lobster-panulirus-ornatus
#1
Mei C Ooi, Evan F Goulden, Gregory G Smith, Barbara F Nowak, Andrew R Bridle
With recent technologies making it possible for commercial scale closed life-cycle aquaculture production of spiny lobster (Panulirus ornatus) comes a strong impetus to further understand aspects of lobster health. The gut microbiome plays a crucial role in host health, affecting growth, digestion, immune responses and pathogen resistance. Herein we characterise and compare gut microbiomes across different developmental stages (6-7 d post-emergence [dpe], 52 dpe and 13 months post-emergence [mpe]) and gut regions (foregut, midgut and hindgut) of cultured P...
November 14, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29145425/statistical-analysis-of-co-occurrence-patterns-in-microbial-presence-absence-datasets
#2
Kumar P Mainali, Sharon Bewick, Peter Thielen, Thomas Mehoke, Florian P Breitwieser, Shishir Paudel, Arjun Adhikari, Joshua Wolfe, Eric V Slud, David Karig, William F Fagan
Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/29142271/structural-and-functional-differences-in-gut-microbiome-composition-in-patients-undergoing-haemodialysis-or-peritoneal-dialysis
#3
Vanessa Stadlbauer, Angela Horvath, Werner Ribitsch, Bianca Schmerböck, Gernot Schilcher, Sandra Lemesch, Philipp Stiegler, Alexander R Rosenkranz, Peter Fickert, Bettina Leber
Complications of end-stage renal disease (ESRD) are critically related to inflammation. The gut microbiome is a key driver of inflammation. Since dialysis modalities may differently influence the gut microbiome, we aimed to compare the effects of haemodialysis (HD) and peritoneal dialysis (PD) on patients' gut microbiome composition and function. We therefore studied faecal microbiome composition and function as well as inflammation and gut permeability in 30 patients with ESRD (15 HD, 15 PD) and compared to 21 healthy controls...
November 15, 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
#4
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/29130306/evaluating-in-vitro-culture-medium-of-gut-microbiome-with-orthogonal-experimental-design-and-metaproteomics-approach
#5
Leyuan Li, Xu Zhang, Zhibin Ning, Janice Mayne, Jasmine I Moore, James Butcher, Cheng-Kang Chiang, David R Mack, Alain Stintzi, Daniel Figeys
In vitro culture-based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtain functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin and short chain fatty acids...
November 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29127885/summary-of-the-2016-alcohol-and-immunology-research-interest-group-airig-meeting
#6
REVIEW
Lisbeth A Boule, Cynthia Ju, Marisela Agudelo, Tiyash Parira, Abigail Cannon, Booker Davis, Jonathan Eby, Gail Cresci, Derrick R Samuelson, Pradeep Shukla, Waddah A Alrefai, Suhas Sureshchandra, Subhash C Pandey, Bernd Schnabl, Brenda J Curtis, Todd A Wyatt, Mashkoor A Choudhry, Elizabeth J Kovacs
On November 18, 2016 the 21st annual Alcohol and Immunology Research Interest Group (AIRIG) meeting was held at the Center for Translational Research and Education at Loyola University Chicago's Health Sciences Campus in Maywood, IL. The 2016 meeting focused broadly on alcohol and inflammation, epigenetics, and the microbiome. The four plenary sessions of the meeting were Alcohol, Inflammation, and Immunity; Alcohol and Epigenetics; Alcohol, Transcriptional Regulation, and Epigenetics; and Alcohol, Intestinal Mucosa, and the Gut Microbiome...
September 23, 2017: Alcohol
https://www.readbyqxmd.com/read/29127829/bioaugmentation-of-rapid-sand-filters-by-microbiome-priming-with-a-nitrifying-consortium-will-optimize-production-of-drinking-water-from-groundwater
#7
Christian Nyrop Albers, Lea Ellegaard-Jensen, Lars Hestbjerg Hansen, Sebastian R Sørensen
Ammonium oxidation to nitrite and then to nitrate (nitrification) is a key process in many waterworks treating groundwater to make it potable. In rapid sand filters, nitrifying microbial communities may evolve naturally from groundwater bacteria entering the filters. However, in new filters this may take several months, and in some cases the nitrification process is never sufficiently rapid to be efficient or is only performed partially, with nitrite as an undesired end product. The present study reports the first successful priming of nitrification in a rapid sand filter treating groundwater...
November 6, 2017: Water Research
https://www.readbyqxmd.com/read/29124895/defining-the-core-microbiome-of-the-symbiotic-dinoflagellate-symbiodinium
#8
Caitlin A Lawson, Jean-Baptiste Raina, Tim Kahlke, Justin R Seymour, David J Suggett
Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterised the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome...
November 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29124056/microbial-therapeutics-designed-for-infant-health
#9
REVIEW
Claire Watkins, Catherine Stanton, C Anthony Ryan, R Paul Ross
Acknowledgment of the gut microbiome as a vital asset to health has led to multiple studies attempting to elucidate its mechanisms of action. During the first year of life, many factors can cause fluctuation in the developing gut microbiome. Host genetics, maternal health status, mode of delivery, gestational age, feeding regime, and perinatal antibiotic usage, are known factors which can influence the development of the infant gut microbiome. Thus, the microbiome of vaginally born, exclusively breastfed infants at term, with no previous exposure to antibiotics, either directly or indirectly from the mother, is to be considered the "gold standard...
2017: Frontiers in Nutrition
https://www.readbyqxmd.com/read/29122007/pancreatic-cyst-fluid-harbors-a-unique-microbiome
#10
Shan Li, Gwenny M Fuhler, Nahush Bn, Tony Jose, Marco J Bruno, Maikel P Peppelenbosch, Sergey R Konstantinov
BACKGROUND: It is clear that specific intestinal bacteria are involved in the development of different premalignant conditions along the gastrointestinal tract. An analysis of the microbial constituents in the context of pancreatic cystic lesions has, however, as yet not been performed. This consideration prompted us to explore whether endoscopically obtained pancreatic cyst fluids (PCF) contain bacterial DNA and to determine the genera of bacteria present in such material. METHODS: Total DNA was isolated from 69 PCF samples...
November 9, 2017: Microbiome
https://www.readbyqxmd.com/read/29118851/targeted-metatranscriptomics-of-compost-derived-consortia-reveals-a-gh11-exerting-an-unusual-exo-1-4-%C3%AE-xylanase-activity
#11
Bruno L Mello, Anna M Alessi, Diego M Riaño-Pachón, Eduardo R deAzevedo, Francisco E G Guimarães, Melissa C Espirito Santo, Simon McQueen-Mason, Neil C Bruce, Igor Polikarpov
Background: Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29117584/environmental-and-health-effects-of-the-herbicide-glyphosate
#12
REVIEW
A H C Van Bruggen, M M He, K Shin, V Mai, K C Jeong, M R Finckh, J G Morris
The herbicide glyphosate, N-(phosphonomethyl) glycine, has been used extensively in the past 40years, under the assumption that side effects were minimal. However, in recent years, concerns have increased worldwide about the potential wide ranging direct and indirect health effects of the large scale use of glyphosate. In 2015, the World Health Organization reclassified glyphosate as probably carcinogenic to humans. A detailed overview is given of the scientific literature on the movement and residues of glyphosate and its breakdown product aminomethyl phosphonic acid (AMPA) in soil and water, their toxicity to macro- and microorganisms, their effects on microbial compositions and potential indirect effects on plant, animal and human health...
November 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29116183/time-resolved-analysis-of-a-denitrifying-bacterial-community-revealed-a-core-microbiome-responsible-for-the-anaerobic-degradation-of-quinoline
#13
Yun Wang, Hao Tian, Fei Huang, Wenmin Long, Qianpeng Zhang, Jing Wang, Ying Zhu, Xiaogang Wu, Guanzhou Chen, Liping Zhao, Lars R Bakken, Åsa Frostegård, Xiaojun Zhang
Quinoline is biodegradable under anaerobic conditions, but information about the degradation kinetics and the involved microorganisms is scarce. Here, the dynamics of a quinoline-degrading bacterial consortium were studied in anoxic batch cultures containing nitrate. The cultures removed 83.5% of the quinoline during the first 80 hours, which were dominated by denitrification, and then switched to methanogenesis when the nitrogen oxyanions were depleted. Time-resolved community analysis using pyrosequencing revealed that denitrifiying bacteria belonging to the genus Thauera were enriched during the denitrification stage from 12...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29108068/rapid-communication-16s-ribosomal-ribonucleic-acid-characterization-of-liver-abscesses-in-feedlot-cattle-from-three-states-in-the-united-states
#14
M D Weinroth, C R Carlson, J N Martin, J L Metcalf, P S Morley, K E Belk
Liver abscesses are a major economic burden to beef producers. Although a few causative organisms have been cultured from purulent material, the full polymicrobial diversity of liver abscesses has not been reported. The objective of this study was to characterize purulent material collected from liver abscess in beef cattle produced in different production systems in 3 cattle producing states in the United States using 16S rRNA gene sequencing. Differences between purulent material microbial communities among geographic region of feeding and application of a common antimicrobial were also investigated...
October 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/29107285/host-microbiota-interaction-induces-bi-phasic-inflammation-and-glucose-intolerance-in-mice
#15
Antonio Molinaro, Robert Caesar, Louise Mannerås Holm, Valentina Tremaroli, Patrice D Cani, Fredrik Bäckhed
OBJECTIVE: Gut microbiota modulates adiposity and glucose metabolism in humans and mice. Here we investigated how colonization of germ-free (GF) mice affects kinetics of adiposity and glucose metabolism. METHODS: Adiposity and glucose metabolism were evaluated at different time points in ex-GF and antibiotic treated mice after colonization with gut microbiota from a conventionally raised (CONV-R) mouse. Mouse physiology, microbiome configuration, serum cytokine levels, and gene expression for inflammatory markers were performed in different tissues...
November 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/29106690/metabolic-syndrome-and-associated-diseases-from-the-bench-to-the-clinic
#16
Donna L Mendrick, Anna Mae Diehl, Lisa S Topor, Rodney R Dietert, Yvonne Will, Michele A La Merrill, Sebastien Bouret, Vijayalaskshmi Varma, Kenneth L Hastings, Thaddeus T Schug, Susan G Emeigh Hart, Florence G Burleson
Metabolic Syndrome and Associated Diseases: From the Bench to the Clinic, a Society of Toxicology Contemporary Concepts in Toxicology (CCT) workshop was held on March 11, 2017. The meeting was convened to raise awareness of metabolic syndrome and its associated diseases and serve as a melting pot with scientists of multiple disciplines (e.g., toxicologists, clinicians, regulators) so as to spur research and understanding of this condition. The criteria for metabolic syndrome include obesity, dyslipidemia (low HDL and/or elevated triglycerides), elevated blood pressure, and alterations in glucose metabolism...
November 2, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29106667/microbiomedb-a-systems-biology-platform-for-integrating-mining-and-analyzing-microbiome-experiments
#17
Francislon S Oliveira, John Brestelli, Shon Cade, Jie Zheng, John Iodice, Steve Fischer, Cristina Aurrecoechea, Jessica C Kissinger, Brian P Brunk, Christian J Stoeckert, Gabriel R Fernandes, David S Roos, Daniel P Beiting
MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29106396/purinyl-cobamide-is-a-native-prosthetic-group-of-reductive-dehalogenases
#18
Jun Yan, Meng Bi, Allen K Bourdon, Abigail T Farmer, Po-Hsiang Wang, Olivia Molenda, Andrew T Quaile, Nannan Jiang, Yi Yang, Yongchao Yin, Burcu Şimşir, Shawn R Campagna, Elizabeth A Edwards, Frank E Löffler
Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon-halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense...
November 6, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29101193/methicillin-resistant-staphylococcus-aureus-sequence-type-st-5-isolates-from-health-care-and-agricultural-sources-adhere-equivalently-to-human-keratinocytes
#19
Samantha J Hau, Steven Kellner, Kirsten C Eberle, Ursula Waack, Susan L Brockmeier, Jisun S Haan, Peter R Davies, Timothy Frana, Tracy L Nicholson
Staphylococcus aureus is part of the nasal microbiome of many humans and has become a significant public health burden due to infections with antibiotic resistant strains, including methicillin resistant S. aureus (MRSA). Several lineages of S. aureus including MRSA are found in livestock species and can be acquired by humans through contact with animals. These livestock associated MRSA (LA-MRSA) isolates raise public health concerns because of the potential for livestock to act as reservoirs for MRSA outside of the hospital setting...
November 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29098118/gut-microbiota-and-salivary-diagnostics-the-mouth-is-salivating-to-tell-us-something
#20
REVIEW
Krishna Kodukula, Douglas V Faller, David N Harpp, Iphigenia Kanara, Julie Pernokas, Mark Pernokas, Whitney R Powers, Nikolaos S Soukos, Kosta Steliou, Walter H Moos
The microbiome of the human body represents a symbiosis of microbial networks spanning multiple organ systems. Bacteria predominantly represent the diversity of human microbiota, but not to be forgotten are fungi, viruses, and protists. Mounting evidence points to the fact that the "microbial signature" is host-specific and relatively stable over time. As our understanding of the human microbiome and its relationship to the health of the host increases, it is becoming clear that many and perhaps most chronic conditions have a microbial involvement...
2017: BioResearch Open Access
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