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Microbial diversity

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https://www.readbyqxmd.com/read/29166320/exercise-alters-gut-microbiota-composition-and-function-in-lean-and-obese-humans
#1
Jacob M Allen, Lucy J Mailing, Grace M Niemiro, Rachel Moore, Mark D Cook, Bryan A White, Hannah D Holscher, Jeffrey A Woods
PURPOSE: Exercise is associated with altered gut microbial composition, but studies have not investigated whether the gut microbiota and associated metabolites are modulated by exercise training in humans. We explored the impact of six weeks of endurance exercise on the composition, functional capacity, and metabolic output of the gut microbiota in lean and obese adults with multiple-day dietary controls prior to outcome variable collection. METHODS: Thirty-two lean (n=18 [9 female]) and obese (n=14 [11 female]), previously sedentary subjects participated in six weeks of supervised, endurance-based exercise training (3 days/wk) that progressed from 30 to 60 minutes/day and from moderate (60% of heart rate reserve [HRR]) to vigorous intensity (75% HRR)...
November 20, 2017: Medicine and Science in Sports and Exercise
https://www.readbyqxmd.com/read/29166166/coevolution-between-mutualists-and-parasites-in-symbiotic-communities-may-lead-to-the-evolution-of-lower-virulence
#2
Paul G Nelson, Georgiana May
Most eukaryotes harbor a diverse community of parasitic, mutualistic, and commensal microbial symbionts. Although the diversity of these microbial symbiotic communities has recently drawn considerable attention, theory regarding the evolution of interactions among symbionts and with the host is still in its nascent stages. Here we evaluate the role of interactions among coinfecting symbionts in the evolution of symbiont virulence toward the host. To do so, we place the virulence-transmission trade-off into a community context and model the evolution of symbiont trophic modes along the continuum from parasitism (virulence) to mutualism (negative virulence)...
December 2017: American Naturalist
https://www.readbyqxmd.com/read/29164717/antibiotics-reduce-genetic-diversity-of-core-species-in-the-honeybee-gut-microbiome
#3
Kasie Raymann, Louis-Marie Bobay, Nancy A Moran
The gut microbiome plays a key role in animal health, and perturbing it can have detrimental effects. One major source of perturbation to microbiomes, in humans and human-associated animals, is exposure to antibiotics. Most studies of how antibiotics affect the microbiome have used amplicon sequencing of highly conserved 16S rRNA sequences, as in a recent study showing that antibiotic treatment severely alters the species-level composition of the honeybee gut microbiome. But because the standard 16S rRNA-based methods cannot resolve closely related strains, strain-level changes could not be evaluated...
November 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29163572/root-and-rhizosphere-bacterial-phosphatase-activity-varies-with-tree-species-and-soil-phosphorus-availability-in-puerto-rico-tropical-forest
#4
Kristine G Cabugao, Collin M Timm, Alyssa A Carrell, Joanne Childs, Tse-Yuan S Lu, Dale A Pelletier, David J Weston, Richard J Norby
Tropical forests generally occur on highly weathered soils that, in combination with the immobility of phosphorus (P), often result in soils lacking orthophosphate, the form of P most easily metabolized by plants and microbes. In these soils, mineralization of organic P can be the major source for orthophosphate. Both plants and microbes encode for phosphatases capable of mineralizing a range of organic P compounds. However, the activity of these enzymes depends on several edaphic factors including P availability, tree species, and microbial communities...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163454/low-molecular-weight-chitosan-supplementation-increases-the-population-of-prevotella-in-the-cecal-contents-of-weanling-pigs
#5
Ting Yu, Yu Wang, Shicheng Chen, Min Hu, Zhiling Wang, Guozhong Wu, Xianyong Ma, Zhuang Chen, Chuntian Zheng
Low-molecular-weight chitosan (LC) promoted growth in weaned piglets as an alternative to feed-grade antibiotics. To investigate the influence of LC supplementation on piglets' gut microbiome and compare the differences in community composition between LC and antibiotics with ZnO addition, we assessed the cecal microbial community by 16S rRNA gene sequencing with three treatments consisting of basal diet (CTR group), basal diet with low-molecular-weight chitosan (LC group), and basal diet with antibiotic and ZnO (AZ group)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163453/an-integrated-insight-into-the-relationship-between-soil-microbial-community-and-tobacco-bacterial-wilt-disease
#6
Hongwu Yang, Juan Li, Yunhua Xiao, Yabing Gu, Hongwei Liu, Yili Liang, Xueduan Liu, Jin Hu, Delong Meng, Huaqun Yin
The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163432/stratified-bacterial-and-archaeal-community-in-mangrove-and-intertidal-wetland-mudflats-revealed-by-high-throughput-16s-rrna-gene-sequencing
#7
Zhichao Zhou, Han Meng, Yang Liu, Ji-Dong Gu, Meng Li
The stratified distribution of bacterial and archaeal communities has been detected in many sediment profiles from various natural environments. A better understanding of microbial composition and diversity pattern in coastal mangrove wetlands in relation to physicochemical and spatial-temporal influences could provide more insights into the ecological functions of microbes in coastal wetlands. In this study, seasonal variations of microbial communities within sediment profiles from two sediment types (mangrove forest and intertidal mudflats) at three sampling locations in coastal Mai Po wetland were characterized using MiSeq high throughput sequencing and 16S rRNA quantitative PCR methods...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163420/microbial-diversity-and-community-structure-of-sulfate-reducing-and-sulfur-oxidizing-bacteria-in-sediment-cores-from-the-east-china-sea
#8
Yu Zhang, Xungong Wang, Yu Zhen, Tiezhu Mi, Hui He, Zhigang Yu
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163411/diversity-within-italian-cheesemaking-brine-associated-bacterial-communities-evidenced-by-massive-parallel-16s-rrna-gene-tag-sequencing
#9
Marilena Marino, Nadia Innocente, Michela Maifreni, Jérôme Mounier, José F Cobo-Díaz, Emmanuel Coton, Lisa Carraro, Barbara Cardazzo
This study explored the bacterial diversity of brines used for cheesemaking in Italy, as well as their physicochemical characteristics. In this context, 19 brines used to salt soft, semi-hard, and hard Italian cheeses were collected in 14 commercial cheese plants and analyzed using a culture-independent amplicon sequencing approach in order to describe their bacterial microbiota. Large NaCl concentration variations were observed among the selected brines, with hard cheese brines exhibiting the highest values...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163394/cadaver-thanatomicrobiome-signatures-the-ubiquitous-nature-of-clostridium-species-in-human-decomposition
#10
Gulnaz T Javan, Sheree J Finley, Tasia Smith, Joselyn Miller, Jeremy E Wilkinson
Human thanatomicrobiome studies have established that an abundant number of putrefactive bacteria within internal organs of decaying bodies are obligate anaerobes, Clostridium spp. These microorganisms have been implicated as etiological agents in potentially life-threatening infections; notwithstanding, the scale and trajectory of these microbes after death have not been elucidated. We performed phylogenetic surveys of thanatomicrobiome signatures of cadavers' internal organs to compare the microbial diversity between the 16S rRNA gene V4 hypervariable region and V3-4 conjoined regions from livers and spleens of 45 cadavers undergoing forensic microbiological studies...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163383/microbial-taxa-distribution-is-associated-with-ecological-trophic-cascades-along-an-elevation-gradient
#11
Fei Yao, Shan Yang, Zhirui Wang, Xue Wang, Ji Ye, Xugao Wang, Jennifer M DeBruyn, Xue Feng, Yong Jiang, Hui Li
The elevational pattern of soil microbial diversity along mountain slopes has received considerable interest over the last decade. An increasing amount of taxonomic data on soil microbial community composition along elevation gradients have been collected, however the trophic patterns and environmental drivers of elevational changes remain largely unclear. Here, we examined the distribution patterns of major soil bacterial and fungal taxa along the northern slope of Changbai Mountain, Northeast China, at five typical vegetation types located between 740 and 2,691 m above sea level...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29162884/copolymers-enhance-selective-bacterial-community-colonization-for-potential-root-zone-applications
#12
Vy T H Pham, Pandiyan Murugaraj, Falko Mathes, Boon K Tan, Vi Khanh Truong, Daniel V Murphy, David E Mainwaring
Managing the impact of anthropogenic and climate induced stress on plant growth remains a challenge. Here we show that polymeric hydrogels, which maintain their hydrous state, can be designed to exploit functional interactions with soil microorganisms. This microbial enhancement may mitigate biotic and abiotic stresses limiting productivity. The presence of mannan chains within synthetic polyacrylic acid (PAA) enhanced the dynamics and selectivity of bacterial ingress in model microbial systems and soil microcosms...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29161642/microbial-diversity-of-consumption-milk-during-processing-and-storage
#13
Davide Porcellato, Marina Aspholm, Siv Borghild Skeie, Marte Monshaugen, Johanne Brendehaug, Hilde Mellegård
Bovine milk contains a complex microbial community that affects the quality and safety of the product. Detailed knowledge of this microbiota is, therefore, of importance for the dairy industry. In this study, the bacterial composition of consumption milk was assessed during different stages in the production line and throughout the storage in cartons by using culturing techniques and 16S rRNA marker gene sequencing. Monthly samples from two dairies were analyzed to capture the seasonal variations in the milk microbiota...
November 8, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29161571/effects-of-inorganic-carbon-on-the-nitrous-oxide-emissions-and-microbial-diversity-of-an-anaerobic-ammonia-oxidation-reactor
#14
Wenjie Zhang, Dunqiu Wang, Yue Jin
Inorganic carbon (IC) is important for anaerobic ammonium oxidation (anammox). In this study, the effects of the IC concentration on N2O emissions and microbial diversity in an anammox reactor were investigated. N2O emissions were positively correlated with IC concentrations, and IC concentrations in the range of 55-130 mg/L were optimal, considering the nitrogen removal rate and N2O emissions. High IC concentrations resulted in the formation of CaCO3 on the surface of anammox granules, which impacted the diffusion conditions of the substrate...
November 11, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/29161087/the-hygiene-hypothesis-in-the-age-of-the-microbiome
#15
Markus J Ege
The original version of the hygiene hypothesis suggested that infections transmitted early in life by "unhygienic contact" prevented allergies. Examples were endemic fecal-oral infections by viral, bacterial, or protozoic pathogens, such as hepatitis A virus, Helicobacter pylori, or Toxoplasma gondii. Later, this concept also included microorganisms beyond pathogens, such as commensals and symbionts, and the hygiene hypothesis was extended to inflammatory diseases in general. An impressive illustration of the hygiene hypothesis was found in the consistent farm effect on asthma and allergies, which has partly been attributed to immunomodulatory properties of endotoxin as emitted by livestock...
November 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29161086/potential-role-of-the-lung-microbiome-in-shaping-asthma-phenotypes
#16
Kian Fan Chung
The introduction of 16s ribosomal RNA sequencing as a nonculture technique has led to the discovery of the presence of microbiota in the lower airways of healthy individuals. These bacterial communities may originate from the mouth and nasopharynx or from the environment by inhalation. The microbial composition of the lower airways may be modulated by dietary factors, antibiotic therapy, and microbial infections, particularly in early life. In addition, circulatory products from gut microbiota may influence the lung microbiota to maintain mucosal immunity...
November 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29160815/assessment-of-bifidobacterium-species-using-groel-gene-on-the-basis-of-illumina-miseq-high-throughput-sequencing
#17
Lujun Hu, Wenwei Lu, Linlin Wang, Mingluo Pan, Hao Zhang, Jianxin Zhao, Wei Chen
The next-generation high-throughput sequencing techniques have introduced a new way to assess the gut's microbial diversity on the basis of 16S rRNA gene-based microbiota analysis. However, the precise appraisal of the biodiversity of Bifidobacterium species within the gut remains a challenging task because of the limited resolving power of the 16S rRNA gene in different species. The groEL gene, a protein-coding gene, evolves quickly and thus is useful for differentiating bifidobacteria. Here, we designed a Bifidobacterium-specific primer pair which targets a hypervariable sequence region within the groEL gene that is suitable for precise taxonomic identification and detection of all recognized species of the genus Bifidobacterium so far...
November 21, 2017: Genes
https://www.readbyqxmd.com/read/29160034/free-living-chemoautotrophic-and-particle-attached-heterotrophic-prokaryotes-dominate-microbial-assemblages-along-a-pelagic-redox-gradient
#18
Elizabeth A Suter, Maria Pachiadaki, Gordon T Taylor, Yrene Astor, Virginia P Edgcomb
Using the anoxic Cariaco Basin as a natural laboratory, particle association of bacterial and archaeal taxa was assessed by iTag sequencing and qPCR gene assays of samples spanning an oxic-anoxic-euxinic gradient. Ten to twelve percent of all bacterial and archaeal cells were found in the particle-associated (PA) fraction, operationally defined as prokaryotes captured on 2.7µm membranes. Both redox condition and size fraction segregated bacterial taxa. Archaeal taxa varied according to redox conditions, but were similar between size fractions...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29159926/deep-ocean-prokaryotic-communities-are-remarkably-malleable-when-facing-long-term-starvation
#19
Marta Sebastián, Jean-Christophe Auguet, Claudia Ximena Restrepo Ortiz, Maria Montserrat Sala, Celia Marrasé, Josep M Gasol
The bathypelagic ocean is one of the largest ecosystems on Earth, and sustains half of the ocean's microbial activity. This microbial activity strongly relies on surface-derived particles, but there is growing evidence that the carbon released through solubilisation of these particles may not be sufficient to meet the energy demands of deep ocean prokaryotes. To explore how bathypelagic prokaryotes respond to the absence of external inputs of carbon, we followed the long-term (1 yr) dynamics of an enclosed community...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29159222/data-on-metagenomic-profiles-of-activated-sludge-from-a-full-scale-wastewater-treatment-plant
#20
Jianhua Guo, Bing-Jie Ni, Xiaoyu Han, Xueming Chen, Philip Bond, Yongzhen Peng, Zhiguo Yuan
The data in this article mainly present the sequences of activated sludge from a full-scale municipal wastewater treatment plant (WWTP) carrying out simultaneous nitrogen and phosphorous removal in Beijing, China. Data include the operational conditions and performance, dominant microbes and taxonomic analysis in this WWTP, and function annotation results based on SEED, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Sequencing data were generated by using Illumina HiSeq...
December 2017: Data in Brief
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