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Microbial diversity

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https://www.readbyqxmd.com/read/28346928/diet-and-gut-microbiota-in-health-and-disease
#1
Ting-Chin David Shen
Gut microbiota plays an important role in host health maintenance and disease pathogenesis. The development of a stable and diverse gut microbiota is essential to various host physiologic functions such as immunoregulation, pathogen prevention, energy harvest, and metabolism. At the same time, a dysbiotic gut microbiota associated with disease is altered in structure and function, and often characterized by a decrease in species richness and proliferation of pathogenic bacterial taxa. As a shared substrate between the host and the gut microbiota, diet significantly impacts the health and disease states of the host both directly and through gut microbial metabolite production...
2017: Nestlé Nutrition Institute Workshop Series
https://www.readbyqxmd.com/read/28346927/microbiota-in-functional-gastrointestinal-disorders-in-infancy-implications-for-management
#2
Thomas R Abrahamsson, Richard Y Wu, Philip M Sherman
The complex and diverse intestinal microbiome is recognized as important in promoting human health. An altered gut microflora, referred to as dysbiosis, is increasingly recognized as having an etiologic role in a variety of conditions, including functional gastrointestinal disorders: colic in infants and irritable bowel syndrome in older children. Probiotics are defined as live microorganisms that, if ingested in sufficient amounts, restore microbial homeostasis and have a benefit on health. Randomized controlled trials indicate that probiotics can be effective in a variety of intestinal conditions, including colic and irritable bowel syndrome...
2017: Nestlé Nutrition Institute Workshop Series
https://www.readbyqxmd.com/read/28346511/is-manure-an-alternative-to-topsoil-in-road-embankment-restoration
#3
Begoña Peco, Desirée Rivera, Pablo García-Palacios, Berta M Jauregui
One of the main steps in road and railway embankment restoration is the spreading of previously removed topsoil, which provides an input of seeds, organic matter and microorganisms and encourages the establishment of a vegetation cover, essential to stabilise the embankment and blend it with the landscape. However, topsoil is a scarce resource, prompting the search for economic alternatives with similar results. The present study compares the results of spreading topsoil with an organic amendment (manure) for the soil's physico-chemical properties, erosion resistance and microbial activity, floristic richness and composition, and bare soil cover...
2017: PloS One
https://www.readbyqxmd.com/read/28346358/genomic-evidence-for-bacterial-determinants-influencing-obesity-development
#4
Raphael D Isokpehi, Shaneka S Simmons, Matilda O Johnson, Marinelle Payton
Obesity is a major global public health problem requiring multifaceted interventional approaches including dietary interventions with probiotic bacteria. High-throughput genome sequencing of microbial communities in the mammalian gastrointestinal system continues to present diverse protein function information to understand the bacterial determinants that influence obesity development. The goal of the research reported in this article was to identify biological processes in probiotic bacteria that could influence the mechanisms for the extraction of energy from diet in the human gastrointestinal system...
March 26, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28345666/members-of-gammaproteobacteria-as-indicator-species-of-healthy-banana-plants-on-fusarium-wilt-infested-fields-in-central-america
#5
Martina Köberl, Miguel Dita, Alfonso Martinuz, Charles Staver, Gabriele Berg
Culminating in the 1950's, bananas, the world's most extensive perennial monoculture, suffered one of the most devastating disease epidemics in history. In Latin America and the Caribbean, Fusarium wilt (FW) caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (FOC), forced the abandonment of the Gros Michel-based export banana industry. Comparative microbiome analyses performed between healthy and diseased Gros Michel plants on FW-infested farms in Nicaragua and Costa Rica revealed significant shifts in the gammaproteobacterial microbiome...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28344573/submarine-basaltic-glass-colonization-by-the-heterotrophic-fe-ii-oxidizing-and-siderophore-producing-deep-sea-bacterium-pseudomonas-stutzeri-vs-10-the-potential-role-of-basalt-in-enhancing-growth
#6
Lisa A Sudek, Greg Wanger, Alexis S Templeton, Hubert Staudigel, Bradley M Tebo
Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu'u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28344572/gut-colonization-by-methanogenic-archaea-is-associated-with-organic-dairy-consumption-in-children
#7
Jeroen A A van de Pol, Niels van Best, Catherine A Mbakwa, Carel Thijs, Paul H Savelkoul, Ilja C W Arts, Mathias W Hornef, Monique Mommers, John Penders
The gut microbiota represents a complex and diverse ecosystem with a profound impact on human health, promoting immune maturation, and host metabolism as well as colonization resistance. Important members that have often been disregarded are the methanogenic archaea. Methanogenic archaea reduce hydrogen levels via the production of methane, thereby stimulating food fermentation by saccharolytic bacteria. On the other hand, colonization by archaea has been suggested to promote a number of gastrointestinal and metabolic diseases such as colorectal cancer, inflammatory bowel disease, and obesity...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28342597/bacteria-bacteriophage-coevolution-in-the-human-gut-implications-for-microbial-diversity-and-functionality
#8
REVIEW
Pauline D Scanlan
Antagonistic coevolution (AC) between bacteria and bacteriophages plays a key role in driving and maintaining microbial diversity. Consequently, AC is predicted to affect all levels of biological organisation, from the individual to ecosystem scales. Nonetheless, we know nothing about bacteria-bacteriophage AC in perhaps the most important and clinically relevant microbial ecosystem known to humankind - the human gut microbiome. In this opinion piece I review current research on bacteria-phage AC in in vitro and natural populations of microbes...
March 22, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28341678/defining-the-core-citrus-leaf-and-root-associated-microbiota-factors-associated-with-community-structure-and-implications-for-managing-huanglongbing-citrus-greening-disease
#9
Ryan A Blaustein, Graciela L Lorca, Julie L Meyer, Claudio F Gonzalez, Max Teplitski
Stable associations between plants and microbes are critical to promoting host health and productivity. The objective of this work was to test the hypothesis that re-structuring of core microbiota may be associated with the progression of Huanlongbing (HLB), the devastating citrus disease caused by Liberibacter asiaticus, L. americanus, and L. africanus The microbial communities of leaves (n=94) and roots (n=79) from citrus trees that varied by HLB symptom severity, cultivar, location, and season/time were characterized with Illumina sequencing of 16S rDNA...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28341673/a-next-generation-sequencing-approach-to-characterize-the-impacts-of-land-based-sources-of-pollution-on-the-microbiota-of-southeast-florida-coral-reefs
#10
Christopher Staley, Thomas Kaiser, Maribeth L Gidley, Ian C Enochs, Paul R Jones, Kelly D Goodwin, Christopher D Sinigalliano, Michael J Sadowsky, Chan Lan Chun
Coral reefs are dynamic ecosystems known for decades to be endangered due, in large part, to anthropogenic impacts from land-based sources of pollution (LBSP). In this study, we utilized an Illumina-based next-generation sequencing approach to characterize prokaryotic and fungal communities from samples collected off the southeast coast of Florida. Water samples from coastal inlet discharges, oceanic outfalls of municipal wastewater treatment plants, treated wastewater effluent before discharge, open ocean samples, and coral tissue samples (mucus and polyps) were characterized to determine relationships between microbial communities in these matrices and those in reef water and coral tissues...
March 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28340372/shotgun-metagenomic-sequencing-reveals-freshwater-beach-sands-as-reservoir-of-bacterial-pathogens
#11
Mahi M Mohiuddin, Yasser Salama, Herb E Schellhorn, G Brian Golding
Recreational waters and adjacent beach sands harbor complex microbial communities which may contain human pathogens that cannot be detected by conventional methods. Here, we investigate the diversity of bacterial populations inhabiting four freshwater beaches of the Great Lakes region using shotgun metagenomic sequencing approach. Our analysis suggests that average taxonomic richness and alpha diversity are significantly higher (P < 0.001) in beach sands compared to the corresponding water environments...
March 1, 2017: Water Research
https://www.readbyqxmd.com/read/28339946/pasture-flock-chicken-cecal-microbiome-responses-to-prebiotics-and-plum-fiber-feed-amendments
#12
S H Park, A Perrotta, I Hanning, S Diaz-Sanchez, S Pendleton, E Alm, S C Ricke
When prebiotics and other fermentation substrates are delivered to animals as feed supplements, the typical goal is to improve weight gain and feed conversion. In this work, we examined pasture flock chicken cecal contents using next generation sequencing (NGS) to identify and understand the composition of the microbiome when prebiotics and fermentation substrates were supplemented. We generated 16S rRNA sequencing data for 120 separate cecal samples from groups of chickens receiving one of 3 prebiotics or fiber feed additives...
March 3, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339832/effects-of-feeding-original-xpc%C3%A2-to-broilers-with-a-live-coccidiosis-vaccine-under-industrial-conditions-part-2-cecal-microbiota-analysis
#13
S H Park, S Roto, H Pavlidis, D McIntyre, K Striplin, L Brammer, S C Ricke
Biological supplements in poultry feed are of continued interest due to the improvements in growth performance, protection from pathogen invasion, and benefits in overall host health. The fermentation metabolites of Diamond V Original XPC™ (XPC) have previously been shown to improve commercial performance and reduce Salmonella in poultry. The current study sought to characterize the cecal microbiota using culture-independent analysis based on 16S rRNA gene in Coccivac-D sprayed broilers supplemented with XPC and/or Salinomycin (SAL)...
March 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/28338095/the-effect-of-microbial-mats-in-the-decay-of-anurans-with-implications-for-understanding-taphonomic-processes-in-the-fossil-record
#14
M Iniesto, I Villalba, A D Buscalioni, M C Guerrero, A I López-Archilla
The pattern and sequence of the decomposition of the Pipidae African dwarf frog (Hymenochirus boettgeri) is tracked in an experiment with microbial mats in order to explore soft tissue preservation over three years. Frog decay in microbial mats is preceded by rapid entombment (25-30 days) and mediated by the formation of a sarcophagus, which is built by a complex microbial community. The frog carcasses maintained a variety of soft tissues for years. Labile organic structures show greater durability within the mat, cells maintain their general shape (bone marrow cells and adipocytes), and muscles and connective tissues (adipose and fibrous tendons) exhibit their original organic structures...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337900/the-fingerprint-of-the-human-gastrointestinal-tract-microbiota-a-hypothesis-of-molecular-mapping
#15
G Tomasello, M Mazzola, A Jurjus, F Cappello, F Carini, P Damiani, A Gerges Geagea, M N Zeenny, A Leone
The precise etiology of Inflammatory Bowel Disease (IDB) remains unclear and several factors are believed to play a role in its development and progression, including the composition of microbial communities resident in the gastrointestinal tract. Human intestinal microbiota are extensive with at least 15,000-36,000 bacterial species. However, thanks to the new development in sequencing and molecular taxonomic methodologies, our understanding of the microbiota population composition, dynamics, and ecology has greatly increased...
January 2017: Journal of Biological Regulators and Homeostatic Agents
https://www.readbyqxmd.com/read/28337568/hospital-microbial-surface-colonization-revealed-during-monitoring-of-klebsiella-spp-pseudomonas-aeruginosa-and-non-tuberculous-mycobacteria
#16
Pedro Geadas Farias, Fernando Gama, Diogo Reis, Susana Alarico, Nuno Empadinhas, José Carlos Martins, Ana Figueiredo de Almeida, Paula Vasconcelos Morais
Hospital environmental conditions, human occupancy, and the characteristics of the equipment influence the survival of microbial communities and raise a concern with regard to nosocomial infections. The objective of the present work was to use the monitoring of Pseudomonas aeruginosa, Klebsiella spp. and non-tuberculous mycobacteria as a strategy to improve knowledge on microbial colonization of non-critical equipment and surfaces, in a tertiary hospital from Central Portugal. A 3-month microbiological survey was performed in a district teaching hospital...
March 23, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28337073/real-time-dna-sequencing-in-the-antarctic-dry-valleys-using-the-oxford-nanopore-sequencer
#17
Sarah S Johnson, Elena Zaikova, David S Goerlitz, Yu Bai, Scott W Tighe
The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epidemics. Here, we demonstrate the application of offline DNA sequencing of environmental samples using a hand-held nanopore sequencer in a remote field location: the McMurdo Dry Valleys, Antarctica. Sequencing was performed using a MK1B MinION sequencer from Oxford Nanopore Technologies (ONT; Oxford, United Kingdom) that was equipped with software to operate without internet connectivity...
March 22, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28336973/microbial-community-composition-is-related-to-soil-biological-and-chemical-properties-and-bacterial-wilt-outbreak
#18
Rui Wang, Hongchun Zhang, Liguang Sun, Gaofu Qi, Shu Chen, Xiuyun Zhao
Soil microbes play important roles in plant growth and health. Little is known about the differences of soil microbes between healthy and bacterial wilt infected soils with Ralstonia solanacearum. By Illumina-MiSeq sequencing of 16S rRNA and 18S rRNA gene amplicons, we found the soil microbial composition and diversity were distinct between healthy and bacterial wilt infected soils. Soil microbial community varied at different plant growth stages due to changes of root exudates composition and soil pH. Healthy soils exhibited higher microbial diversity than the bacterial wilt infected soils...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336094/distinct-succession-patterns-of-abundant-and-rare-bacteria-in-temporal-microcosms-with-pollutants
#19
Shuo Jiao, Yantao Luo, Mingmei Lu, Xiao Xiao, Yanbing Lin, Weimin Chen, Gehong Wei
Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl2) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples...
March 21, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28335605/opportunistic-sampling-of-roadkill-as-an-entry-point-to-accessing-natural-products-assembled-by-bacteria-associated-with-non-anthropoidal-mammalian-microbiomes
#20
Jeremy L Motley, Blake W Stamps, Carter A Mitchell, Alec T Thompson, Jayson Cross, Jianlan You, Douglas R Powell, Bradley S Stevenson, Robert H Cichewicz
Few secondary metabolites have been reported from mammalian microbiome bacteria despite the large numbers of diverse taxa that inhabit warm-blooded higher vertebrates. As a means to investigate natural products from these microorganisms, an opportunistic sampling protocol was developed, which focused on exploring bacteria isolated from roadkill mammals. This initiative was made possible through the establishment of a newly created discovery pipeline, which couples laser ablation electrospray ionization mass spectrometry (LAESIMS) with bioassay testing, to target biologically active metabolites from microbiome-associated bacteria...
March 24, 2017: Journal of Natural Products
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