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Microbial genomics

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https://www.readbyqxmd.com/read/29782468/potential-role-of-gut-microbiota-in-als-pathogenesis-and-possible-novel-therapeutic-strategies
#1
Letizia Mazzini, Luca Mogna, Fabiola De Marchi, Angela Amoruso, Marco Pane, Irene Aloisio, Nicole Bozzi Cionci, Francesca Gaggìa, Ausiliatrice Lucenti, Enrica Bersano, Roberto Cantello, Diana Di Gioia, Giovanni Mogna
BACKGROUND: Recent preclinical studies suggest that dysfunction of gastrointestinal tract may play a role in amyotrophic lateral sclerosis (ALS) pathogenesis through a modification of the gut microbiota brain axis. Our study is the first focused on microbiota analysis in ALS patients. AIM: Our aim was to study the main human gut microbial groups and the overall microbial diversity in ALS and healthy subjects. Moreover we have examined the influence of a treatment with a specific bacteriotherapy composed of Lactobacillus strains (Lactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus salivarius) acting on the gastrointestinal barrier...
May 18, 2018: Journal of Clinical Gastroenterology
https://www.readbyqxmd.com/read/29781799/an-outbreak-of-a-rare-shiga-toxin-producing-escherichia-coli-serotype-o117-h7-among-men-who-have-sex-with-men
#2
Kate S Baker, Timothy J Dallman, Nicholas R Thomson, Claire Jenkins
Sexually transmissible enteric infections (STEIs) are commonly associated with transmission among men who have sex with men (MSM). In the past decade, the UK has experienced multiple parallel STEI emergences in MSM caused by a range of bacterial species of the genus Shigella, and an outbreak of an uncommon serotype (O117 : H7) of Shiga-toxin-producing Escherichia coli (STEC). Here, we used microbial genomics on 6 outbreak and 30 sporadic STEC O117 : H7 isolates to explore the origins and pathogenic drivers of the STEC O117 : H7 emergence in MSM...
May 21, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29780391/concepts-collide-genomic-immune-and-microbial-influences-on-the-tumor-microenvironment-and-response-to-cancer-therapy
#3
REVIEW
Miles C Andrews, Alexandre Reuben, Vancheswaran Gopalakrishnan, Jennifer A Wargo
Cancer research has seen unprecedented advances over the past several years, with tremendous insights gained into mechanisms of response and resistance to cancer therapy. Central to this has been our understanding of crosstalk between the tumor and the microenvironment, with the recognition that complex interactions exist between tumor cells, stromal cells, overall host immunity, and the environment surrounding the host. This is perhaps best exemplified in cancer immunotherapy, where numerous studies across cancer types have illuminated our understanding of the genomic and immune factors that shape responses to therapy...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29779657/collection-culturing-and-genome-analyses-of-tropical-marine-filamentous-benthic-cyanobacteria
#4
Nathan A Moss, Tiago Leao, Evgenia Glukhov, Lena Gerwick, William H Gerwick
Decreasing sequencing costs has sparked widespread investigation of the use of microbial genomics to accelerate the discovery and development of natural products for therapeutic uses. Tropical marine filamentous cyanobacteria have historically produced many structurally novel natural products, and therefore present an excellent opportunity for the systematic discovery of new metabolites via the information derived from genomics and molecular genetics. Adequate knowledge transfer and institutional know-how are important to maintain the capability for studying filamentous cyanobacteria due to their unusual microbial morphology and characteristics...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29779655/cobalamin-dependent-c-methyltransferases-from-marine-microbes-accessibility-via-rhizobia-expression
#5
Michael F Freeman
Cobalamin-dependent radical S-adenosylmethionine (rSAM) methyltransferases catalyze chemically challenging methylation reactions on diverse natural products at unactivated carbon centers. In vivo reconstitution and biosynthetic studies of natural product gene clusters encoding these enzymes are often severely limited by ineffective heterologous expression hosts, including the otherwise versatile Escherichia coli. In this chapter, we describe the use of rhizobia bacteria as effective expression hosts for cobalamin-dependent rSAM C-methyltransferases...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/29777223/card9-s12n-facilitates-the-production-of-il-5-by-alveolar-macrophages-for-the-induction-of-type-2-immune-responses
#6
Xia Xu, Jin-Fu Xu, Guoxing Zheng, Hai-Wen Lu, Jie-Lin Duan, Wei Rui, Jian-Hong Guan, Li-Qing Cheng, Dan-Dan Yang, Ming-Chao Wang, Quan-Zhen Lv, Jian-Xiong Li, Xueqiang Zhao, Chun-Xia Chen, Peng Shi, Xin-Ming Jia, Xin Lin
The adaptor CARD9 functions downstream of C-type lectin receptors (CLRs) for the sensing of microbial infection, which leads to responses by the TH 1 and TH 17 subsets of helper T cells. The single-nucleotide polymorphism rs4077515 at CARD9 in the human genome, which results in the substitution S12N (CARD9S12N ), is associated with several autoimmune diseases. However, the function of CARD9S12N has remained unknown. Here we generated CARD9S12N knock-in mice and found that CARD9S12N facilitated the induction of type 2 immune responses after engagement of CLRs...
May 18, 2018: Nature Immunology
https://www.readbyqxmd.com/read/29775902/type-1-diabetes-through-the-lens-of-human-genome-and-metagenome-interplay
#7
REVIEW
Sepideh Zununi Vahed, Hakimeh Moghaddas Sani, Yalda Rahbar Saadat, Abolfazl Barzegari, Yadollah Omidi
Diabetes is a genetic- and epigenetic-related disease from which a large population worldwide suffers. Some genetic factors along with various mutations related to the immune system for disease mechanism(s) have contrastively been determined. However, sometimes mechanisms have not been fully managed for the clarification of the initiation and/or progression of diseases to help patients. In the recent years, due to familiarity with the role of gut microbiota in the health, it has been found that the changes of the microbial balance in the industrialized societies can cause a battery of modern diseases, for which we have no specific definition of how they emerge...
May 15, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29775592/dietary-and-microbial-oxazoles-induce-intestinal-inflammation-by-modulating-aryl-hydrocarbon-receptor-responses
#8
Shankar S Iyer, Thomas Gensollen, Amit Gandhi, Sungwhan F Oh, Joana F Neves, Frederic Collin, Richard Lavin, Carme Serra, Jonathan Glickman, Punyanganie S A de Silva, R Balfour Sartor, Gurdyal Besra, Russell Hauser, Anthony Maxwell, Amadeu Llebaria, Richard S Blumberg
Genome-wide association studies have identified risk loci associated with the development of inflammatory bowel disease, while epidemiological studies have emphasized that pathogenesis likely involves host interactions with environmental elements whose source and structure need to be defined. Here, we identify a class of compounds derived from dietary, microbial, and industrial sources that are characterized by the presence of a five-membered oxazole ring and induce CD1d-dependent intestinal inflammation. We observe that minimal oxazole structures modulate natural killer T cell-dependent inflammation by regulating lipid antigen presentation by CD1d on intestinal epithelial cells (IECs)...
May 17, 2018: Cell
https://www.readbyqxmd.com/read/29774086/complete-genome-sequence-of-thiodictyon-syntrophicum-sp-nov-strain-cad16-t-a-photolithoautotrophic-purple-sulfur-bacterium-isolated-from-the-alpine-meromictic-lake-cadagno
#9
Samuel M Luedin, Joël F Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla
" Thiodictyon syntrophicum" sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria . The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29774049/bioreactor-microbial-ecosystems-with-differentiated-methanogenic-phenol-biodegradation-and-competitive-metabolic-pathways-unraveled-with-genome-resolved-metagenomics
#10
Feng Ju, Yubo Wang, Tong Zhang
Background: Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. Results: Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29774017/identifying-group-specific-sequences-for-microbial-communities-using-long-k-mer-sequence-signatures
#11
Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun
Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered " group-specific " in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773613/draft-genome-sequences-of-two-chemosynthetic-arcobacter-strains-isolated-from-hydraulically-fractured-wells-in-marcellus-and-utica-shales
#12
Jenny Panescu, Rebecca A Daly, Kelly C Wrighton, Paula J Mouser
Genome sequences were obtained for two isolates of the genus Arcobacter from saline fluids produced from hydraulically fractured shale gas wells in the Marcellus and Utica formations. These genomes provide insight into microbial sulfur cycles occurring in a high-salt deep terrestrial shale environment.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29772713/genetic-optimization-algorithm-for-metabolic-engineering-revisited
#13
Tobias B Alter, Lars M Blank, Birgitta E Ebert
To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research...
May 16, 2018: Metabolites
https://www.readbyqxmd.com/read/29772089/microevolutionary-selection-dynamics-acting-on-immune-genes-of-the-green-veined-white-butterfly-pieris-napi
#14
Naomi L P Keehnen, Jason Hill, Sören Nylin, Christopher W Wheat
Insects rely on their innate immune system to successfully mediate complex interactions with their microbiota, as well as the microbes present in the environment. Previous work has shown that components of the canonical immune gene repertoire evolve rapidly and have evolutionary characteristics originating from interactions with fast-evolving microorganisms. Although these interactions are likely to vary among populations, there is a poor understanding of the microevolutionary dynamics of immune genes, especially in non-Dipteran insects...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29771380/dbcan2-a-meta-server-for-automated-carbohydrate-active-enzyme-annotation
#15
Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin
Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29771304/laboratory-evolution-for-forced-glucose-xylose-co-consumption-enables-identification-of-mutations-that-improve-mixed-sugar-fermentation-by-xylose-fermenting-saccharomyces-cerevisiae
#16
Ioannis Papapetridis, Maarten D Verhoeven, Sanne J Wiersma, Maaike Goudriaan, Antonius J A van Maris, Jack T Pronk
Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilization of these sugars in batch cultures of Saccharomyces cerevisiae. To force simultaneous utilization of xylose and glucose, the genes encoding glucose-6-phosphate isomerase (PGI1) and ribulose-5-phosphate epimerase (RPE1) were deleted in a xylose-isomerase-based xylose-fermenting strain with a modified oxidative pentose-phosphate pathway...
May 15, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29769716/mutant-phenotypes-for-thousands-of-bacterial-genes-of-unknown-function
#17
Morgan N Price, Kelly M Wetmore, R Jordan Waters, Mark Callaghan, Jayashree Ray, Hualan Liu, Jennifer V Kuehl, Ryan A Melnyk, Jacob S Lamson, Yumi Suh, Hans K Carlson, Zuelma Esquivel, Harini Sadeeshkumar, Romy Chakraborty, Grant M Zane, Benjamin E Rubin, Judy D Wall, Axel Visel, James Bristow, Matthew J Blow, Adam P Arkin, Adam M Deutschbauer
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse bacteria across dozens of growth conditions. We identified mutant phenotypes for 11,779 protein-coding genes that had not been annotated with a specific function. Many genes could be associated with a specific condition because the gene affected fitness only in that condition, or with another gene in the same bacterium because they had similar mutant phenotypes...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29768437/oral-health-status-in-historic-population-macroscopic-and-metagenomic-evidence
#18
Claire Willmann, Xavier Mata, Kristian Hanghoej, Laure Tonasso, Lenka Tisseyre, Céline Jeziorski, Elodie Cabot, Pierre Chevet, Eric Crubézy, Ludovic Orlando, Rémi Esclassan, Catherine Thèves
Recent developments in High-Throughput DNA sequencing (HTS) technologies and ancient DNA (aDNA) research have opened access to the characterization of the microbial communities within past populations. Most studies have, however, relied on the analysis of dental calculus as one particular material type particularly prone to the molecular preservation of ancient microbial biofilms and potential of entire teeth for microbial characterization, both of healthy communities and pathogens in ancient individuals, remains overlooked...
2018: PloS One
https://www.readbyqxmd.com/read/29767666/the-genome-sequence-of-dyella-jiangningensis-fcav-scs01-from-a-lignocellulose-decomposing-microbial-consortium-metagenome-reveals-potential-for-biotechnological-applications
#19
Joana G Desiderato, Danillo O Alvarenga, Milena T L Constancio, Lucia M C Alves, Alessandro M Varani
Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw...
May 14, 2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29767361/making-and-sequencing-heavily-multiplexed-high-throughput-16s-ribosomal-rna-gene-amplicon-libraries-using-a-flexible-two-stage-pcr-protocol
#20
Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J Green
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers...
2018: Methods in Molecular Biology
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