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https://www.readbyqxmd.com/read/29244002/higher-recall-in-metagenomic-sequence-classification-exploiting-overlapping-reads
#1
Samuele Girotto, Matteo Comin, Cinzia Pizzi
BACKGROUND: In recent years several different fields, such as ecology, medicine and microbiology, have experienced an unprecedented development due to the possibility of direct sequencing of microbioimic samples. Among problems that researchers in the field have to deal with, taxonomic classification of metagenomic reads is one of the most challenging. State of the art methods classify single reads with almost 100% precision. However, very often, the performance in terms of recall falls at about 50%...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29243150/characterization-of-multiple-antibiotic-resistance-of-culturable-microorganisms-and-metagenomic-analysis-of-total-microbial-diversity-of-marine-fish-sold-in-retail-shops-in-mumbai-india
#2
Onkar A Naik, Ravindranath Shashidhar, Devashish Rath, Jayant R Bandekar, Archana Rath
Marine fish species were analyzed for culturable and total metagenomic microbial diversity, antibiotic resistance (AR) pattern, and horizontal gene transfer in culturable microorganisms. We observed a high AR microbial load of 3 to 4 log CFU g-1. Many fish pathogens like Providencia, Staphylococcus, Klebsiella pneumoniae, Enterobacter, Vagococcus, and Aeromonas veronii were isolated. Photobacterium and Vibrio were two major fish and human pathogens which were identified in the fish metagenome. Other pathogens that were identified were Shewanella, Acinetobacter, Psychrobacter, and Flavobacterium...
December 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29242543/the-twilight-of-immunity-emerging-concepts-in-aging-of-the-immune-system
#3
REVIEW
Janko Nikolich-Žugich
Immunosenescence is a series of age-related changes that affect the immune system and, with time, lead to increased vulnerability to infectious diseases. This Review addresses recent developments in the understanding of age-related changes that affect key components of immunity, including the effect of aging on cells of the (mostly adaptive) immune system, on soluble molecules that guide the maintenance and function of the immune system and on lymphoid organs that coordinate both the maintenance of lymphocytes and the initiation of immune responses...
January 2018: Nature Immunology
https://www.readbyqxmd.com/read/29242367/subspecies-in-the-global-human-gut-microbiome
#4
Paul I Costea, Luis Pedro Coelho, Shinichi Sunagawa, Robin Munch, Jaime Huerta-Cepas, Kristoffer Forslund, Falk Hildebrand, Almagul Kushugulova, Georg Zeller, Peer Bork
Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies)...
December 14, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29241587/associations-between-infant-fungal-and-bacterial-dysbiosis-and-childhood-atopic-wheeze-in-a-nonindustrialized-setting
#5
Marie-Claire Arrieta, Andrea Arévalo, Leah Stiemsma, Pedro Dimitriu, Martha E Chico, Sofia Loor, Maritza Vaca, Rozlyn C T Boutin, Evan Morien, Mingliang Jin, Stuart E Turvey, Jens Walter, Laura Wegener Parfrey, Philip J Cooper, Brett Finlay
BACKGROUND: Asthma is the most prevalent chronic disease of childhood. Recently, we identified a critical window early in the life of both mice and Canadian infants during which gut microbial changes (dysbiosis) affect asthma development. Given geographic differences in human gut microbiota worldwide, we studied the effects of gut microbial dysbiosis on atopic wheeze in a population living in a distinct developing world environment. OBJECTIVE: We sought to determine whether microbial alterations in early infancy are associated with the development of atopic wheeze in a nonindustrialized setting...
November 30, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29240834/discovery-of-carbamate-degrading-enzymes-by-functional-metagenomics
#6
Lisa Ufarté, Elisabeth Laville, Sophie Duquesne, Diego Morgavi, Patrick Robe, Christophe Klopp, Angeline Rizzo, Sandra Pizzut-Serin, Gabrielle Potocki-Veronese
Bioremediation of pollutants is a major concern worldwide, leading to the research of new processes to break down and recycle xenobiotics and environment contaminating polymers. Among them, carbamates have a very broad spectrum of uses, such as toxinogenic pesticides or elastomers. In this study, we mined the bovine rumen microbiome for carbamate degrading enzymes. We isolated 26 hit clones exhibiting esterase activity, and were able to degrade at least one of the targeted polyurethane and pesticide carbamate compounds...
2017: PloS One
https://www.readbyqxmd.com/read/29238752/colonic-butyrate-producing-communities-in-humans-an-overview-using-omics-data
#7
Marius Vital, André Karch, Dietmar H Pieper
Given the key role of butyrate for host health, understanding the ecology of intestinal butyrate-producing communities is a top priority for gut microbiota research. To this end, we performed a pooled analysis on 2,387 metagenomic/transcriptomic samples from 15 publicly available data sets that originated from three continents and encompassed eight diseases as well as specific interventions. For analyses, a gene catalogue was constructed from gene-targeted assemblies of all genes from butyrate synthesis pathways of all samples and from an updated reference database derived from genome screenings...
November 2017: MSystems
https://www.readbyqxmd.com/read/29235710/localized-high-abundance-of-marine-group-ii-archaea-in-the-subtropical-pearl-river-estuary-implications-for-their-niche-adaptation
#8
Wei Xie, Haiwei Luo, Senthil K Murugapiran, Jeremy A Dodsworth, Songze Chen, Ying Sun, Brian P Hedlund, Peng Wang, Huaying Fang, Minghua Deng, Chuanlun Zhang
Marine group II archaea are widely distributed in global oceans and dominate the total archaeal community within the upper euphotic zone of temperate waters. However, factors controlling the distribution of MGII are poorly delineated and the physiology and ecological functions of these still-uncultured organisms remain elusive. In this study, we investigated the planktonic MGII associated with particles and in free-living forms in the Pearl River Estuary (PRE) over a 10-month period. We detected high abundance of particle-associated MGII in PRE (up to ∼108 16S rRNA gene copies/L), which was around 10-fold higher than the free-living MGII in the same region, and an order of magnitude higher than previously reported in other marine environments...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29235707/tales-from-the-tomb-the-microbial-ecology-of-exposed-rock-surfaces
#9
Tess E Brewer, Noah Fierer
Although a broad diversity of eukaryotic and bacterial taxa reside on rock surfaces where they can influence the weathering of rocks and minerals, these communities and their contributions to mineral weathering remain poorly resolved. To build a more comprehensive understanding of the diversity, ecology, and potential functional attributes of microbial communities living on rock, we sampled 149 tombstones across three continents and analyzed their bacterial and eukaryotic communities via marker gene and shotgun metagenomic sequencing...
December 13, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29235578/are-we-any-closer-to-screening-for-colorectal-cancer-using-microbial-markers-a-critical-review
#10
Lubomir Stary, Kristyna Mezerova, Pavel Skalicky, Pavel Zboril, Vladislav Raclavsky
The role of gut microbiota in the development of sporadic colorectal cancer (CRC) is supported by a number of studies, however, the conclusiveness of published metagenomic studies is questioned by technical pitfalls and limited by small cohort sizes. In this review, we evaluate the current knowledge critically and outline practical solutions. We also list candidate CRC risk markers that are - in our opinion - well supported by available data and thus deserve clinical validation. Last but not least, we summarise available knowledge useful for improving care for patients immediately...
December 13, 2017: Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia
https://www.readbyqxmd.com/read/29235508/genetic-adaptation-of-microbial-populations-present-in-high-intensity-catfish-production-systems-with-therapeutic-oxytetracycline-treatment
#11
Qifan Zeng, Xiangli Tian, Luxin Wang
Microbial communities that are present in aquaculture production systems play significant roles in degrading organic matter, controlling diseases, and formation of antibiotic resistance. It is important to understand the diversity and abundance of microbial communities and their genetic adaptations associated with environmental physical and chemical changes. Here we collected water and sediment samples from a high-intensity catfish production system and its original water reservoir. The metagenomic analysis showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were the top five phyla identified from all samples...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29234309/rokubacteria-genomic-giants-among-the-uncultured-bacterial-phyla
#12
Eric D Becraft, Tanja Woyke, Jessica Jarett, Natalia Ivanova, Filipa Godoy-Vitorino, Nicole Poulton, Julia M Brown, Joseph Brown, M C Y Lau, Tullis Onstott, Jonathan A Eisen, Duane Moser, Ramunas Stepanauskas
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29234139/author-correction-recovery-of-nearly-8-000-metagenome-assembled-genomes-substantially-expands-the-tree-of-life
#13
Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson
In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc...
December 12, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/29233840/microbiome-in-pten-hamartoma-tumor-syndrome
#14
Victoria Byrd, Ted M Getz, Roshan Padmanabhan, Hans Arora, Charis Eng
Germline PTEN mutations defining PTEN hamartoma tumor syndrome [PHTS] confer heritable predisposition to breast, endometrial, thyroid, and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA-gene sequencing...
December 12, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29232848/a-metagenomic-and-in-silico-functional-prediction-of-gut-microbiota-profiles-may-concur-in-discovering-new-cystic-fibrosis-patient-targeted-probiotics
#15
Pamela Vernocchi, Federica Del Chierico, Andrea Quagliariello, Danilo Ercolini, Vincenzina Lucidi, Lorenza Putignani
Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction...
December 9, 2017: Nutrients
https://www.readbyqxmd.com/read/29230681/the-metagenomic-approach-to-characterization-of-the-microbial-community-shift-during-the-long-term-cultivation-of-anammox-enriched-granular-sludge
#16
Slawomir Ciesielski, Krzysztof Czerwionka, Dominika Sobotka, Tomasz Dulski, Jacek Makinia
A metagenomic approach was used to investigate how the microbial community composition changes when an anammox-based granular sludge reactor is seeded with nitritation-anammox biomass from a wastewater treatment plant. In the seed sample, the abundance of Candidatus Kuenenia stuttgartiensis was similar to Candidatus Jettenia caeni (12.63 vs. 11.68%). This biomass was typical in terms of microbial nitrogen conversion; both ammonia (Nitrosomonas sp.) and nitrite (Nitrospira sp.) oxidizing bacteria were detected...
December 11, 2017: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29229913/a-metagenome-derived-thermostable-%C3%AE-glucanase-with-an-unusual-module-architecture-which-defines-the-new-glycoside-hydrolase-family-gh148
#17
Angel Angelov, Vu Thuy Trang Pham, Maria Übelacker, Silja Brady, Benedikt Leis, Nicole Pill, Judith Brolle, Matthias Mechelke, Matthias Moerch, Bernard Henrissat, Wolfgang Liebl
The discovery of novel and robust enzymes for the breakdown of plant biomass bears tremendous potential for the development of sustainable production processes in the rapidly evolving new bioeconomy. By functional screening of a metagenomic library from a volcano soil sample a novel thermostable endo-β-glucanase (EngU) which is unusual with regard to its module architecture and cleavage specificity was identified. Various recombinant EngU variants were characterized. Assignment of EngU to an existing glycoside hydrolase (GH) family was not possible...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229530/trichoderma-harzianum-mtcc-5179-impacts-the-population-and-functional-dynamics-of-microbial-community-in-the-rhizosphere-of-black-pepper-piper-nigrum-l
#18
Palaniyandi Umadevi, Muthuswamy Anandaraj, Vivek Srivastav, Sailas Benjamin
Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1...
November 29, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29228991/the-rumen-microbiome-as-a-reservoir-of-antimicrobial-resistance-and-pathogenicity-genes-is-directly-affected-by-diet-in-beef-cattle
#19
Marc D Auffret, Richard J Dewhurst, Carol-Anne Duthie, John A Rooke, R John Wallace, Tom C Freeman, Robert Stewart, Mick Watson, Rainer Roehe
BACKGROUND: The emergence and spread of antimicrobial resistance is the most urgent current threat to human and animal health. An improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal gut will have a major role in reducing the contribution of animal production to this problem. Here, the influence of diet on the ruminal resistome and abundance of pathogenicity genes was assessed in ruminal digesta samples taken from 50 antibiotic-free beef cattle, comprising four cattle breeds receiving two diets containing different proportions of concentrate...
December 11, 2017: Microbiome
https://www.readbyqxmd.com/read/29228901/the-relation-between-blastocystis-and-the-intestinal-microbiota-in-swedish-travellers
#20
Joakim Forsell, Johan Bengtsson-Palme, Martin Angelin, Anders Johansson, Birgitta Evengård, Margareta Granlund
BACKGROUND: Blastocystis sp. is a unicellular eukaryote that is commonly found in the human intestine. Its ability to cause disease is debated and a subject for ongoing research. In this study, faecal samples from 35 Swedish university students were examined through shotgun metagenomics before and after travel to the Indian peninsula or Central Africa. We aimed at assessing the impact of travel on Blastocystis carriage and seek associations between Blastocystis and the bacterial microbiota...
December 11, 2017: BMC Microbiology
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