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John Slattery, Derrick F MacFabe, Stephen G Kahler, Richard E Frye
BACKGROUND: Many lines of scientific research suggest that Autism Spectrum Disorders (ASDs) may be associated with alterations in the enteric ecosystem, including alterations of the enteric macrobiome (i.e. helminthes and fungi) and changes in predominant microbiome species, particularly a reduction in microbiome diversity. METHODS: We performed and comprehensive review of the literature and summarized the major findings. RESULTS: These alterations are believed to be due to a variety of factors including changes in the post-industrial society related to decreased exposure to symbiotic organisms, increased human migration, overuse of antibiotics and changes in dietary habits...
September 5, 2016: Current Pharmaceutical Design
Bjorn Tytgat, Elie Verleyen, Maxime Sweetlove, Sofie D'hondt, Pia Clercx, Eric Van Ranst, Karolien Peeters, Stephen Roberts, Zorigto Namsaraev, Annick Wilmotte, Wim Vyverman, Anne Willems
Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high-altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analyzed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica), using the Illumina MiSeq platform in combination with ARISA fingerprinting...
September 2016: FEMS Microbiology Ecology
William C Gause, Rick M Maizels
Important insights have recently been gained in our understanding of the intricate relationship in the intestinal milieu between the vertebrate host mucosal immune response, commensal bacteria, and helminths. Helminths are metazoan worms (macrobiota) and trigger immune responses that include potent regulatory components capable of controlling harmful inflammation, protecting barrier function and mitigating tissue damage. They can secrete a variety of products that directly affect immune regulatory function but they also have the capacity to influence the composition of microbiota, which can also then impact immune function...
August 2016: Current Opinion in Microbiology
Benny Kwok Kan Chan, Teng-Wei Wang, Pin-Chen Chen, Chia-Wei Lin, Tin-Yam Chan, Ling Ming Tsang
Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution...
2016: PloS One
Concetta De Santi, Bjørn Altermark, Donatella de Pascale, Nils-Peder Willassen
We have investigated the biotechnological potential of Arctic marine bacteria for their ability to produce a broad spectrum of cold-active enzymes. Marine bacteria exhibiting these features are of great interest for both fundamental research and industrial applications. Macrobiota, water and sediment samples have been collected during 2010 and 2011 expeditions around the Lofoten and Svalbard islands. Bacteria were isolated from this material and identified through 16S rRNA gene sequence analysis for the purpose of establishing a culture collection of marine Arctic bacteria...
March 2016: Journal of Basic Microbiology
Shawn A Steffan, Yoshito Chikaraishi, Cameron R Currie, Heidi Horn, Hannah R Gaines-Day, Jonathan N Pauli, Juan E Zalapa, Naohiko Ohkouchi
In most ecosystems, microbes are the dominant consumers, commandeering much of the heterotrophic biomass circulating through food webs. Characterizing functional diversity within the microbiome, therefore, is critical to understanding ecosystem functioning, particularly in an era of global biodiversity loss. Using isotopic fingerprinting, we investigated the trophic positions of a broad diversity of heterotrophic organisms. Specifically, we examined the naturally occurring stable isotopes of nitrogen ((15)N:(14)N) within amino acids extracted from proteobacteria, actinomycetes, ascomycetes, and basidiomycetes, as well as from vertebrate and invertebrate macrofauna (crustaceans, fish, insects, and mammals)...
December 8, 2015: Proceedings of the National Academy of Sciences of the United States of America
José Félix Aguirre-Garrido, Hugo César Ramírez-Saad, Nicolás Toro, Francisco Martínez-Abarca
Isabel Lake is a moderate saline soda crater lake located in Isabel Island in the eastern tropical Pacific coast of Mexico. Lake is mainly formed by rainfall and is strongly affected by evaporation and high input of nutrients derived from excretions of a large bird community inhabiting the island. So far, only the island macrobiota has been studied. The knowledge of the prokaryotic biota inhabiting the upper layers of this meromictic lake can give clues for the maintenance of this ecosystem. We assessed the diversity and composition of prokaryotic community in sediments and water of the lake by DGGE profiling, 16S rRNA gene amplicon pyrosequencing, and cultivation techniques...
January 2016: Microbial Ecology
Richard W Smith, Penny Vlahos, J K Böhlke, Thivanka Ariyarathna, Mark Ballentine, Christopher Cooper, Stephen Fallis, Thomas J Groshens, Craig Tobias
2,4,6-Trinitrotoluene (TNT) has been used as a military explosive for over a hundred years. Contamination concerns have arisen as a result of manufacturing and use on a large scale; however, despite decades of work addressing TNT contamination in the environment, its fate in marine ecosystems is not fully resolved. Here we examine the cycling and fate of TNT in the coastal marine systems by spiking a marine mesocosm containing seawater, sediments, and macrobiota with isotopically labeled TNT ((15)N-[TNT]), simultaneously monitoring removal, transformation, mineralization, sorption, and biological uptake over a period of 16 days...
October 20, 2015: Environmental Science & Technology
Elizabeth A Nesbitt, Ruth A Martin, David E Martin, Jude Apple
Foraminiferal assemblages in sediment grab samples were utilized to evaluate the impacts of anthropogenic activities on benthic habitats in Bellingham Bay, Washington State, U.S.A. Seventy-three samples taken in 1987, 1997, 2006 and 2010 yielded 35 species of foraminifera from 28 genera. Assemblage composition and diversity data indicate a marked deterioration between 1987 and 2010, contrary to the published Chemical Index, but analogous to the situation with macrobiota. Correlation of diversity with chemical pollutants and metals did not identify any significant correlations, however, an unrelated but highly relevant study of bottom water dissolved oxygen concentrations and pH in Bellingham Bay suggests eutrophication with accompanying hypoxia and acidification may be part of the cause...
August 15, 2015: Marine Pollution Bulletin
Leena von Hertzen, Bruce Beutler, John Bienenstock, Martin Blaser, Patrice D Cani, Johan Eriksson, Martti Färkkilä, Tari Haahtela, Ilkka Hanski, Maria C Jenmalm, Juha Kere, Mikael Knip, Kimmo Kontula, Markku Koskenvuo, Charlotte Ling, Thomas Mandrup-Poulsen, Erika von Mutius, Mika J Mäkelä, Tiina Paunio, Göran Pershagen, Harald Renz, Graham Rook, Maria Saarela, Outi Vaarala, Marc Veldhoen, Willem M de Vos
Urban living in built environments, combined with the use of processed water and food, may not provide the microbial stimulation necessary for a balanced development of immune function. Many chronic inflammatory disorders, including allergic, autoimmune, metabolic, and even some behavioural disorders, are linked to alteration in the human commensal microbiota. Sedentary lifestyle is associated with reduced exposure to a broad spectrum of environmental micro-organisms and surplus energy balance, both risk factors of chronic inflammatory disorders...
May 2015: Annals of Medicine
Raven L Bier, Kristofor A Voss, Emily S Bernhardt
Microbial community composition and diversity change along chemical gradients, leading to the expectation that microbial community information might provide new gradient characterizations. Here we examine stream bacteria composition and diversity along a strong chemical gradient in Central Appalachian streams. Coal mining in the region generates alkaline mine drainage (AlkMD), causing dramatic increases in conductivity, alkalinity, sulfate and metals sufficient to degrade stream macrobiota communities throughout the ecoregion...
June 2015: ISME Journal
Catherine A Pfister, Jack A Gilbert, Sean M Gibbons
Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates...
2014: PeerJ
Daniel S Read, Hyun S Gweon, Michael J Bowes, Lindsay K Newbold, Dawn Field, Mark J Bailey, Robert I Griffiths
Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing...
February 2015: ISME Journal
Orna Nitzan, Mazen Elias, Bibiana Chazan, Raul Raz, Walid Saliba
Clostridium difficile (C. difficile) is the leading cause of antibiotic associated colitis and nosocomial diarrhea. Patients with inflammatory bowel disease (IBD) are at increased risk of developing C. difficile infection (CDI), have worse outcomes of CDI-including higher rates of colectomy and death, and experience higher rates of recurrence. However, it is still not clear whether C. difficile is a cause of IBD or a consequence of the inflammatory state in the intestinal environment. The burden of CDI has increased dramatically over the past decade, with severe outbreaks described in many countries, which have been attributed to a new and more virulent strain...
November 21, 2013: World Journal of Gastroenterology: WJG
David A Stahl, José R de la Torre
The discovery of ammonia-oxidizing archaea (AOA), now generally recognized to exert primary control over ammonia oxidation in terrestrial, marine, and geothermal habitats, necessitates a reassessment of the nitrogen cycle. In particular, the unusually high affinity of marine and terrestrial AOA for ammonia indicates that this group may determine the oxidation state of nitrogen available to associated micro- and macrobiota, altering our current understanding of trophic interactions. Initial comparative genomics and physiological studies have revealed a novel, and as yet unresolved, primarily copper-based pathway for ammonia oxidation and respiration distinct from that of known ammonia-oxidizing bacteria and possibly relevant to the production of atmospherically active nitrogen oxides...
2012: Annual Review of Microbiology
Dorota L Porazinska, Robin M Giblin-Davis, Thomas O Powers, W Kelley Thomas
Large scale diversity patterns are well established for terrestrial macrobiota (e.g. plants and vertebrates), but not for microscopic organisms (e.g. nematodes). Due to small size, high abundance, and extensive dispersal, microbiota are assumed to exhibit cosmopolitan distributions with no biogeographical patterns. This assumption has been extrapolated from local spatial scale studies of a few taxonomic groups utilizing morphological approaches. Recent molecularly-based studies, however, suggest something quite opposite...
2012: PloS One
D Acosta-Mercado, N Cancel-Morales, J D Chinea, C J Santos-Flores, I Sastre De Jesús
The mechanisms that ultimately regulate the diversity of microbial eukaryotic communities in bryophyte ecosystems remain a contentious topic in microbial ecology. Although there is robust consensus that abiotic factors, such as water chemistry of the bryophyte and pH, explain a significant proportion of protist and microcrustacean diversity, there is no systematic assessment of the role of bryophyte habitat complexity on such prominent microbial groups. Water-holding capacity is correlated with bryophyte morphology and canopy structure...
July 2012: Microbial Ecology
A Lerner
Alum (AlK(SO(4))(2)) is an adjuvant commonly utilized in vaccines, and is a ubiquitous element used extensively in contemporary life. Food, air, water, waste, the earth's surface, and pharmaceuticals all represent pathways of aluminum (Al) exposure. Crohn's disease (CD) is a chronic relapsing intestinal inflammation in genetically susceptible individuals and is caused by yet unidentified environmental factors. Al is a potential factor for the induction of inflammation in CD, and its immune activities share many characteristics with the immune pathology of CD: many luminal bacterial or dietary compounds can be adsorbed to the metal surface and induce Th1 profile cytokines, shared cytokines/chemokines, co-stimulatory molecules, and intracellular pathways and stress-related molecular expression enhancement, affecting intestinal macrobiota, trans-mural granuloma formation, and colitis induction in an animal CD model...
February 2012: Lupus
C B Santos, G R Leite, A Falqueto
This study evaluates the importance of native bromeliads growing on rocky outcrops interspersed with urbanized areas as breeding sites for the Aedes aegypti (L.) in Vitória, state of Espírito Santo, Brazil. Oviposition traps were installed in backyards of houses in two separate zones. In the first zone houses were up to 50 m away from the rocky outcrops, while in the second zone they were at least at 200 m from the rocky outcrops. Aedes aegypti was significantly more abundant in the latter zone. The finding was that rocky outcrops with native bromeliads, even with the greater availability of potential breeding sites, do not play an important role as breeding sites for A...
March 2011: Neotropical Entomology
Dorota L Porazinska, Robin M Giblin-Davis, Alejandro Esquivel, Thomas O Powers, Way Sung, W Kelley Thomas
The general patterns of increasing biodiversity from the poles to the equator have been well documented for large terrestrial organisms such as plants and vertebrates but are largely unknown for microbiota. In contrast to macrobiota, microbiota have long been assumed to exhibit cosmopolitan, random distributions and a lack of spatial patterns. To evaluate the assumption, we conducted a survey of nematode diversity within the soil, litter and canopy habitats of the humid lowland tropical rainforest of Costa Rica using an ultrasequencing ecometagenetic approach at a species-equivalent taxonomic level...
December 2010: Molecular Ecology
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