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https://www.readbyqxmd.com/read/28655159/two-distinct-metacommunities-characterize-the-gut-microbiota-in-crohn-s-disease-patients
#1
Qing He, Yuan Gao, Zhuye Jie, Xinlei Yu, Janne Marie Laursen, Liang Xiao, Ying Li, Lingling Li, Faming Zhang, Qiang Feng, Xiaoping Li, Jinghong Yu, Chuan Liu, Ping Lan, Ting Yan, Xin Liu, Xun Xu, Huanming Yang, Jian Wang, Lise Madsen, Susanne Brix, Jianping Wang, Karsten Kristiansen, Huijue Jia
Background: The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition (EEN)...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28654183/impact-of-drinking-water-treatment-and-distribution-on-the-microbiome-continuum-an-ecological-disturbance-s-perspective
#2
Ya Zhang, Seungdae Oh, Wen-Tso Liu
While microbes are known to be present at different stages of a drinking water system, their potential functions and ability to grow in such systems are poorly understood. In this study, we demonstrated that treatment and distribution processes could be viewed as ecological disturbances exhibited over space on the microbiome continuum in a groundwater-derived system. Results from 16S rRNA gene amplicon analysis and metagenomics suggested that disturbances in the system were intense as the community diversity was substantially reduced during the treatment steps...
May 18, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28654083/targeted-metagenomic-sequencing-data-of-human-gut-microbiota-associated-with-blastocystis-colonization
#3
Léa Siegwald, Christophe Audebert, Gaël Even, Eric Viscogliosi, Ségolène Caboche, Magali Chabé
In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity...
June 27, 2017: Scientific Data
https://www.readbyqxmd.com/read/28651652/the-association-between-measurements-of-antimicrobial-use-and-resistance-in-the-faeces-microbiota-of-finisher-batches
#4
V D Andersen, L V DE Knegt, P Munk, M S Jensen, Y Agersø, F M Aarestrup, H Vigre
The objectives were to present three approaches for calculating antimicrobial (AM) use in pigs that take into account the rearing period and rearing site, and to study the association between these measurements and phenotypical resistance and abundance of resistance genes in faeces samples from 10 finisher batches. The AM use was calculated relative to the rearing period of the batches as (i) 'Finisher Unit Exposure' at unit level, (ii) 'Lifetime Exposure' at batch level and (iii) 'Herd Exposure' at herd level...
June 27, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28651381/meta-barcoding-in-combination-with-palynological-inference-is-a-potent-diagnostic-marker-for-honey-floral-composition
#5
Rama Chandra Laha, Surajit De Mandal, Lalhmanghai Ralte, Laldinfeli Ralte, Nachimuthu Senthil Kumar, Guruswami Gurusubramanian, Ramalingam Satishkumar, Raja Mugasimangalam, Nagesh Aswathnarayana Kuravadi
Identification of floral samples present in honey is important in order to determine the medicinal value, enhance the production of honey as well as to conserve the honey bees. Traditional approaches for studying pollen samples are based on microscopic observation which is laborious, time intensive and requires specialized palynological knowledge. Present study compares two composite honey metagenome collected from 20 samples in Mizoram, Northeast India using three gene loci- rbcL, matK and ITS2 that was sequenced using a next-generation sequencing (NGS) platform (Illumina Miseq)...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28649415/unexplored-diversity-and-strain-level-structure-of-the-skin-microbiome-associated-with-psoriasis
#6
Adrian Tett, Edoardo Pasolli, Stefania Farina, Duy Tin Truong, Francesco Asnicar, Moreno Zolfo, Francesco Beghini, Federica Armanini, Olivier Jousson, Veronica De Sanctis, Roberto Bertorelli, Giampiero Girolomoni, Mario Cristofolini, Nicola Segata
Psoriasis is an immune-mediated inflammatory skin disease that has been associated with cutaneous microbial dysbiosis by culture-dependent investigations and rRNA community profiling. We applied, for the first time, high-resolution shotgun metagenomics to characterise the microbiome of psoriatic and unaffected skin from 28 individuals. We demonstrate psoriatic ear sites have a decreased diversity and psoriasis is associated with an increase in Staphylococcus, but overall the microbiomes of psoriatic and unaffected sites display few discriminative features at the species level...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28649327/are-we-ready-to-detect-nematode-diversity-by-next-generation-sequencing
#7
Thomas Peham, Florian M Steiner, Birgit C Schlick-Steiner, Wolfgang Arthofer
In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439-1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649326/viral-gut-metagenomics-of-sympatric-wild-and-domestic-canids-and-monitoring-of-viruses-insights-from-an-endangered-wolf-population
#8
Nádia Conceição-Neto, Raquel Godinho, Francisco Álvares, Claude K Yinda, Ward Deboutte, Mark Zeller, Lies Laenen, Elisabeth Heylen, Sara Roque, Francisco Petrucci-Fonseca, Nuno Santos, Marc Van Ranst, João R Mesquita, Jelle Matthijnssens
Animal host-microbe interactions are a relevant concern for wildlife conservation, particularly regarding generalist pathogens, where domestic host species can play a role in the transmission of infectious agents, such as viruses, to wild animals. Knowledge on viral circulation in wild host species is still scarce and can be improved by the recent advent of modern molecular approaches. We aimed to characterize the fecal virome and identify viruses of potential conservation relevance of diarrheic free-ranging wolves and sympatric domestic dogs from Central Portugal, where a small and threatened wolf population persists in a highly anthropogenically modified landscape...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649277/diversity-of-microbial-carbohydrate-active-enzymes-in-danish-anaerobic-digesters-fed-with-wastewater-treatment-sludge
#9
Casper Wilkens, Peter Kamp Busk, Bo Pilgaard, Wen-Jing Zhang, Kåre L Nielsen, Per Halkjær Nielsen, Lene Lange
BACKGROUND: Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry. RESULTS: Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28648853/next-generation-sequencing-of-oral-microbiota-in-type-2-diabetes-mellitus-prior-to-and-after-neem-stick-usage-and-correlation-with-serum-monocyte-chemoattractant-1
#10
Rubini Anbalagan, Padma Srikanth, Monika Mani, Ramya Barani, Krishna G Seshadri, R Janarthanan
INTRODUCTION: Oral microbiome impacts health and disease. T2DM and periodontitis are associated. Neem (Azadiracta indica) has antibacterial activity against oral microbiota. OBJECTIVES: To characterize oral microbiota (OMB) in saliva samples of T2DM patients by Next generation sequencing. To analyze MCP-1 levels among the T2DM patients before and after a month of neem stick usage as a toothbrush. MATERIALS AND METHODS: Blood and saliva samples were collected from adult T2DM patients before and after the neem stick usage...
June 13, 2017: Diabetes Research and Clinical Practice
https://www.readbyqxmd.com/read/28646670/a-metagenomic-assessment-of-viral-contamination-on-fresh-parsley-plants-irrigated-with-fecally-tainted-river-water
#11
X Fernandez-Cassi, N Timoneda, E Gonzales-Gustavson, J F Abril, S Bofill-Mas, R Girones
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food...
June 21, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28646651/use-of-sequence-independent-single-primer-amplification-sispa-for-rapid-detection-identification-and-characterization-of-avian-rna-viruses
#12
Klaudia Chrzastek, Dong-Hun Lee, Diane Smith, Poonam Sharma, David L Suarez, Mary Pantin-Jackwood, Darrell R Kapczynski
Current technologies with next generation sequencing have revolutionized metagenomics analysis of clinical samples. To achieve the non-selective amplification and recovery of low abundance genetic sequences, a simplified Sequence-Independent, Single-Primer Amplification (SISPA) technique in combination with MiSeq platform was applied to target negative- and positive-sense single-stranded RNA viral sequences. This method allowed successful sequence assembly of full or near full length avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) viral genome...
June 21, 2017: Virology
https://www.readbyqxmd.com/read/28646502/the-liver-gut-microbiota-axis-modulates-hepatotoxicity-of-tacrine-in-the-rat
#13
Lian Yee Yip, Chiu Cheong Aw, Sze Han Lee, Yi Shuen Hong, Han Chen Ku, Winston Hecheng Xu, Jessalyn Mei Xuan Chan, Eleanor Jing Yi Cheong, Kern Rei Chng, Amanda Hui Qi Ng, Niranjan Nagarajan, Ratha Mahendran, Yuan Kun Lee, Edward R Browne, Eric Chun Yong Chan
The gut microbiota possesses diverse metabolic activities but its contribution towards heterogeneous toxicological responses is poorly understood. Here, we elucidate the role of the liver-gut microbiota axis in underpinning the hepatotoxicity of tacrine. We employed an integrated strategy combining pharmacokinetics, toxicology, metabonomics, genomics and metagenomics to elucidate and validate the mechanism of tacrine-induced hepatotoxicity in Lister hooded rats. Pharmacokinetic studies in rats demonstrated 3...
June 23, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28646219/efficient-and-unbiased-metagenomic-recovery-of-rna-virus-genomes-from-human-plasma-samples
#14
Carmen F Manso, David F Bibby, Jean L Mbisa
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses - HIV, HCV and HEV...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28644444/energy-and-carbon-metabolisms-in-a-deep-terrestrial-subsurface-fluid-microbial-community
#15
Lily Momper, Sean P Jungbluth, Michael D Lee, Jan P Amend
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28643787/single-virus-genomics-reveals-hidden-cosmopolitan-and-abundant-viruses
#16
Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B Sullivan, Silvia G Acinas, Manuel Martinez-Garcia
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28642744/unexpected-dominance-of-elusive-acidobacteria-in-early-industrial-soft-coal-slags
#17
Carl-Eric Wegner, Werner Liesack
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642737/pheno-and-genotyping-of-hopanoid-production-in-acidobacteria
#18
Jaap S Sinninghe Damsté, W Irene C Rijpstra, Svetlana N Dedysh, Bärbel U Foesel, Laura Villanueva
Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28641882/ferredoxin-dependent-bilin-reductases-in-eukaryotic-algae-ubiquity-and-diversity
#19
Nathan C Rockwell, J Clark Lagarias
Linear tetrapyrroles (bilins) are produced from heme by heme oxygenase, usually forming biliverdin IXα (BV). Fungi and bacteria use BV as chromophore for phytochrome photoreceptors. Oxygenic photosynthetic organisms use BV as a substrate for ferredoxin-dependent bilin reductases (FDBRs), enzymes that produce diverse reduced bilins used as light-harvesting pigments in phycobiliproteins and as photoactive photoreceptor chromophores. Bilin biosynthesis is essential for phototrophic growth in Chlamydomonas reinhardtii despite the absence of phytochromes or phycobiliproteins in this organism, raising the possibility that bilins are more generally required for phototrophic growth by algae...
May 31, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28640714/an-unexplored-brain-gut-microbiota-axis-in-stroke
#20
Shu Wen Wen, Connie H Y Wong
Microbiota research, in particular that of the gut, has recently gained much attention in medical research owing to technological advances in metagenomics and metabolomics. Despite this, much of the research direction has focused on long-term or chronic effects of microbiota manipulation on health and disease. In this addendum, we reflect on our recent publication that reported findings addressing a rather unconventional hypothesis. Bacterial pneumonia is highly prevalent and is one of the leading contributors to stroke morbidity and mortality worldwide...
June 22, 2017: Gut Microbes
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