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https://www.readbyqxmd.com/read/28735325/characterization-of-endolithic-culturable-microbial-communities-in-carbonate-rocks-from-a-typical-karst-canyon-in-guizhou-china
#1
Yuan Tang, Jian-Zhong Cheng, Bin Lian
The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that all bacteria isolated from dolomite and limestone rocks were divided into 4 bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes...
January 2, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28735305/molecular-study-of-indigenous-bacterial-community-composition-on-exposure-to-soil-arsenic-concentration-gradient
#2
Semanti Basu, Tanima Paul, Priya Yadav, Abhijit Debnath, Keka Sarkar
Community structure of bacteria present in arsenic contaminated agricultural soil was studied with qPCR (quantitative PCR) and DGGE (Denaturing Gradient Gel Electrophoresis) as an indicator of extreme stresses. Copy number of six common bacterial taxa (Acidobacteria, Actinobacteria, α-, β- and γ-Proteobacteria, Firmicutes) was calculated using group specific primers of 16S rDNA. It revealed that soil contaminated with low concentration of arsenic was dominated by both Actinobacteria and Proteobacteria but a shift towards Proteobacteria was observed with increasing arsenic concentration, and number of Actinobacteria eventually decreases...
July 6, 2017: Polish Journal of Microbiology
https://www.readbyqxmd.com/read/28735230/granulometry-microbial-composition-and-biological-activity-of-dusts-collected-in-french-dairy-farms
#3
Hugo Pfister, Claudie Morzadec, Pierre Le Cann, Laurent Madec, Valérie Lecureur, Martine Chouvet, Stéphane Jouneau, Laurent Vernhet
BACKGROUND: Dairy working increases the prevalence of lower airway respiratory diseases, especially COPD and asthma. Epidemiological studies have reported that chronic inhalation of organic dusts released during specific daily tasks could represent a major risk factor for development of these pathologies in dairy workers. Knowledge on size, nature and biological activity of such organic dusts remain however limited. OBJECTIVE: To compare size distribution, microbial composition and cellular effects of dusts liberated by the spreading of straw bedding in five French dairy farms located in Brittany...
July 20, 2017: Environmental Research
https://www.readbyqxmd.com/read/28734695/response-of-the-bacterial-community-in-an-on-farm-biopurification-system-to-which-diverse-pesticides-are-introduced-over-an-agricultural-season
#4
Peter N Holmsgaard, Simone Dealtry, Vincent Dunon, Holger Heuer, Lars H Hansen, Dirk Springael, Kornelia Smalla, Leise Riber, Søren J Sørensen
A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA...
July 19, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28733903/the-effect-of-aspartate-supplementation-on-the-microbial-composition-and-innate-immunity-on-mice
#5
Peng Bin, Shaojuan Liu, Shuai Chen, Zhaoying Zeng, Ruilin Huang, Yulong Yin, Gang Liu
The study was conducted to investigate the changes of intestinal microbiota composition and innate immunity with different dietary dosages of aspartate (Asp) supplementation. Thirty-six female ICR mice were divided randomly to four groups and thereafter fed the basal diets (controls) or those supplemented with additional 0.5, 1.0 and 2.0% aspartate. After 2 week feeding, microbial composition in ileum and feces, gene expression of pro-inflammatory cytokine, and innate immune factors in ileum were determined...
July 21, 2017: Amino Acids
https://www.readbyqxmd.com/read/28733895/clinical-impact-of-pre-transplant-gut-microbial-diversity-on-outcomes-of-allogeneic-hematopoietic-stem-cell-transplantation
#6
Noriko Doki, Masahiro Suyama, Satoshi Sasajima, Junko Ota, Aiko Igarashi, Iyo Mimura, Hidetoshi Morita, Yuki Fujioka, Daisuke Sugiyama, Hiroyoshi Nishikawa, Yutaka Shimazu, Wataru Suda, Kozue Takeshita, Koji Atarashi, Masahira Hattori, Eiichi Sato, Kyoko Watakabe-Inamoto, Kosuke Yoshioka, Yuho Najima, Takeshi Kobayashi, Kazuhiko Kakihana, Naoto Takahashi, Hisashi Sakamaki, Kenya Honda, Kazuteru Ohashi
Post-transplant microbial diversity in the gastrointestinal tract is closely associated with clinical outcomes following allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about the impact of the fecal microbiota before allo-HSCT. We analyzed fecal samples approximately 2 weeks before conditioning among 107 allo-HSCT recipients between 2013 and 2015. Microbial analysis was performed using 16S rRNA gene sequencing. Operational taxonomic unit-based microbial diversity was estimated by calculating the Shannon index...
July 21, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28733288/bacillomycin-d-produced-by-bacillus-amyloliquefaciens-is-involved-in-the-antagonistic-interaction-with-the-plant-pathogenic-fungus-fusarium-graminearum
#7
Qin Gu, Yang Yang, Qiming Yuan, Guangming Shi, Liming Wu, Zhiying Lou, Rong Huo, Huijun Wu, Rainer Borriss, Xuewen Gao
Fusarium graminearum (teleomorph: Ascomycota, Hypocreales, Gibberella, Gibberella zeae) is a destructive fungal pathogen that threatens the production and quality of wheat and barley worldwide. Controlling this toxin-producing pathogen is a significant challenge. In the present study, the commercially available strain Bacillus amyloliquefaciens (Bacteria, Firmicutes, Bacillales, Bacillus) FZB42 showed strong activity against F. graminearum The lipopeptide, bacillomycin D, produced by FZB42, was proven to contribute to the antifungal activity...
July 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#8
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28729863/effects-of-physiochemical-factors-on-prokaryotic-biodiversity-in-malaysian-circumneutral-hot-springs
#9
Chia S Chan, Kok-Gan Chan, Robson Ee, Kar-Wai Hong, María S Urbieta, Edgardo R Donati, Mohd S Shamsir, Kian M Goh
Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28729860/burn-injury-leads-to-increase-in-relative-abundance-of-opportunistic-pathogens-in-the-rat-gastrointestinal-microbiome
#10
Guangtao Huang, Kedai Sun, Supeng Yin, Bei Jiang, Yu Chen, Yali Gong, Yajie Chen, Zichen Yang, Jing Chen, Zhiqiang Yuan, Yizhi Peng
The gastrointestinal microbiome is crucial in human health. With greater than 10 times the cell count of an individual, the gastrointestinal microbiome provides many benefits to the host. It plays an important role in chronic illnesses and immune diseases and also following burns and trauma. This study aimed to determine whether severe burns affect the gastrointestinal microbiome during the early stages of after burn injury and the extent to which the microbiome is disturbed by such burns. We used a rat burn model to investigate any changes occurring in the microbiome after the burn trauma using 16S rRNA sequencing and downstream α-diversity, β-diversity, and taxonomy analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28725891/fecal-excretion-of-maillard-reaction-products-and-the-gut-microbiota-composition-of-rats-fed-with-bread-crust-or-bread-crumb
#11
C Helou, P M Anton, C Niquet-Léridon, M Spatz, F J Tessier, P Gadonna-Widehem
A comparison between the impacts of advanced (N(ε)-carboxymethyllysine - CML) and terminal (melanoidins) Maillard reaction products from bread on gut microbiota was carried out in this study. Gut microbiota composition as well as fecal excretion of CML from both bread crust and bread crumb, and of melanoidins from bread crust were assessed on a rodent model. Rats were fed with pellets supplemented or not with 13% of bread crust, bread crumb, a fiber-free bread crust model (glucose, starch and gluten heated together) or a fiber-free-melanoidin-free bread model (glucose-starch and gluten heated separately) for four weeks...
July 20, 2017: Food & Function
https://www.readbyqxmd.com/read/28725266/highly-efficient-methane-generation-from-untreated-microalgae-biomass
#12
Viktor Klassen, Olga Blifernez-Klassen, Daniel Wibberg, Anika Winkler, Jörn Kalinowski, Clemens Posten, Olaf Kruse
BACKGROUND: The fact that microalgae perform very efficiently photosynthetic conversion of sunlight into chemical energy has moved them into the focus of regenerative fuel research. Especially, biogas generation via anaerobic digestion is economically attractive due to the comparably simple apparative process technology and the theoretical possibility of converting the entire algal biomass to biogas/methane. In the last 60 years, intensive research on biogas production from microalgae biomass has revealed the microalgae as a rather challenging substrate for anaerobic digestion due to its high cell wall recalcitrance and unfavorable protein content, which requires additional pretreatment and co-fermentation strategies for sufficient fermentation...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28724921/saliva-and-tooth-biofilm-bacterial-microbiota-in-adolescents-in-a-low-caries-community
#13
Linda Eriksson, Pernilla Lif Holgerson, Ingegerd Johansson
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724659/human-milk-microbial-community-structure-is-relatively-stable-and-related-to-variations-in-macronutrient-and-micronutrient-intakes-in-healthy-lactating-women
#14
Janet E Williams, Janae M Carrothers, Kimberly A Lackey, Nicola F Beatty, Mara A York, Sarah L Brooker, Bahman Shafii, William J Price, Matthew L Settles, Mark A McGuire, Michelle K McGuire
Background: The human milk microbiome has been somewhat characterized, but little is known about changes over time and relations with maternal factors such as nutrient intake.Objective: We sought to characterize the human milk microbiome and described associations with maternal nutrient intake, time postpartum, delivery mode, and body mass index (BMI; in kg/m(2)).Methods: Milk samples (n = 104) and 24-h diet recalls were collected 9 times from 21 healthy lactating women from day 2 to 6 mo postpartum. Women were classified by BMI as healthy weight (<25) or overweight or obese (≥25)...
July 19, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28720084/sequence-based-identification-of-inositol-monophosphatase-like-histidinol-phosphate-phosphatases-hisn-in-corynebacterium-glutamicum-actinobacteria-and-beyond
#15
Robert Kasimir Kulis-Horn, Christian Rückert, Jörn Kalinowski, Marcus Persicke
BACKGROUND: The eighth step of L-histidine biosynthesis is carried out by an enzyme called histidinol-phosphate phosphatase (HolPase). Three unrelated HolPase families are known so far. Two of them are well studied: HAD-type HolPases known from Gammaproteobacteria like Escherichia coli or Salmonella enterica and PHP-type HolPases known from yeast and Firmicutes like Bacillus subtilis. However, the third family of HolPases, the inositol monophosphatase (IMPase)-like HolPases, present in Actinobacteria like Corynebacterium glutamicum (HisN) and plants, are poorly characterized...
July 18, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28717594/effect-of-freshwater-mussels-on-the-vertical-distribution-of-anaerobic-ammonia-oxidizers-and-other-nitrogen-transforming-microorganisms-in-upper-mississippi-river-sediment
#16
Ellen M Black, Michael S Chimenti, Craig L Just
Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0...
2017: PeerJ
https://www.readbyqxmd.com/read/28716923/molecular-mechanism-of-environmental-d-xylose-perception-by-a-xylfii-lyts-complex-in-bacteria
#17
Jianxu Li, Chengyuan Wang, Gaohua Yang, Zhe Sun, Hui Guo, Kai Shao, Yang Gu, Weihong Jiang, Peng Zhang
d-xylose, the main building block of plant biomass, is a pentose sugar that can be used by bacteria as a carbon source for bio-based fuel and chemical production through fermentation. In bacteria, the first step for d-xylose metabolism is signal perception at the membrane. We previously identified a three-component system in Firmicutes bacteria comprising a membrane-associated sensor protein (XylFII), a transmembrane histidine kinase (LytS) for periplasmic d-xylose sensing, and a cytoplasmic response regulator (YesN) that activates the transcription of the target ABC transporter xylFGH genes to promote the uptake of d-xylose...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28713353/functional-characterization-of-novel-faecalibacterium-prausnitzii-strains-isolated-from-healthy-volunteers-a-step-forward-in-the-use-of-f-prausnitzii-as-a-next-generation-probiotic
#18
Rebeca Martín, Sylvie Miquel, Leandro Benevides, Chantal Bridonneau, Véronique Robert, Sylvie Hudault, Florian Chain, Olivier Berteau, Vasco Azevedo, Jean M Chatel, Harry Sokol, Luis G Bermúdez-Humarán, Muriel Thomas, Philippe Langella
Faecalibacterium prausnitzii is a major member of the Firmicutes phylum and one of the most abundant bacteria in the healthy human microbiota. F. prausnitzii depletion has been reported in several intestinal disorders, and more consistently in Crohn's disease (CD) patients. Despite its importance in human health, only few microbiological studies have been performed to isolate novel F. prausnitzii strains in order to better understand the biodiversity and physiological diversity of this beneficial commensal species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713349/the-gut-microbiota-of-healthy-chilean-subjects-reveals-a-high-abundance-of-the-phylum-verrucomicrobia
#19
Sayaka Fujio-Vejar, Yessenia Vasquez, Pamela Morales, Fabien Magne, Patricia Vera-Wolf, Juan A Ugalde, Paola Navarrete, Martin Gotteland
The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28713344/outer-membrane-proteome-of-veillonella-parvula-a-diderm-firmicute-of-the-human-microbiome
#20
Daniel I Poppleton, Magalie Duchateau, Véronique Hourdel, Mariette Matondo, Jennifer Flechsler, Andreas Klingl, Christophe Beloin, Simonetta Gribaldo
Veillonella parvula is a biofilm-forming commensal found in the lungs, vagina, mouth, and gastro-intestinal tract of humans, yet it may develop into an opportunistic pathogen. Furthermore, the presence of Veillonella has been associated with the development of a healthy immune system in infants. Veillonella belongs to the Negativicutes, a diverse clade of bacteria that represent an evolutionary enigma: they phylogenetically belong to Gram-positive (monoderm) Firmicutes yet maintain an outer membrane (OM) with lipopolysaccharide similar to classic Gram-negative (diderm) bacteria...
2017: Frontiers in Microbiology
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