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Metatranscriptome

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https://www.readbyqxmd.com/read/28912815/feasibility-of-metatranscriptome-analysis-from-infant-gut-microbiota-adaptation-to-solid-foods-results-in-increased-activity-of-firmicutes-at-six-months
#1
Floor Hugenholtz, Jarmo Ritari, Lotta Nylund, Mark Davids, Reetta Satokari, Willem M de Vos
Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth...
2017: International Journal of Microbiology
https://www.readbyqxmd.com/read/28912444/pan-genomic-and-transcriptomic-analyses-of-leuconostoc-mesenteroides-provide-insights-into-its-genomic-and-metabolic-features-and-roles-in-kimchi-fermentation
#2
Byung Hee Chun, Kyung Hyun Kim, Hye Hee Jeon, Se Hee Lee, Che Ok Jeon
The genomic and metabolic features of Leuconostoc (Leu) mesenteroides were investigated through pan-genomic and transcriptomic analyses. Relatedness analysis of 17 Leu. mesenteroides strains available in GenBank based on 16S rRNA gene sequence, average nucleotide identity, in silico DNA-DNA hybridization, molecular phenotype, and core-genome indicated that Leu. mesenteroides has been separated into different phylogenetic lineages. Pan-genome of Leu. mesenteroides strains, consisting of 999 genes in core-genome, 1,432 genes in accessory-genome, and 754 genes in unique genome, and their COG and KEGG analyses showed that Leu...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28900024/metabolic-roles-of-uncultivated-bacterioplankton-lineages-in-the-northern-gulf-of-mexico-dead-zone
#3
J Cameron Thrash, Kiley W Seitz, Brett J Baker, Ben Temperton, Lauren E Gillies, Nancy N Rabalais, Bernard Henrissat, Olivia U Mason
Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown...
September 12, 2017: MBio
https://www.readbyqxmd.com/read/28895945/excess-labile-carbon-promotes-the-expression-of-virulence-factors-in-coral-reef-bacterioplankton
#4
Anny Cárdenas, Matthew J Neave, Mohamed Fauzi Haroon, Claudia Pogoreutz, Nils Rädecker, Christian Wild, Astrid Gärdes, Christian R Voolstra
Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows...
September 12, 2017: ISME Journal
https://www.readbyqxmd.com/read/28893194/de-novo-metatranscriptome-assembly-and-coral-gene-expression-profile-of-montipora-capitata-with-growth-anomaly
#5
Monika Frazier, Martin Helmkampf, M Renee Bellinger, Scott M Geib, Misaki Takabayashi
BACKGROUND: Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals ("healthy"), GA lesion tissue from diseased corals ("GA-affected") and apparently healthy tissue from diseased corals ("GA-unaffected")...
September 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28892300/thermodynamically-diverse-syntrophic-aromatic-compound-catabolism
#6
Masaru Konishi Nobu, Takashi Narihiro, Miaomiao Liu, Kyohei Kuroda, Ran Mei, Wen-Tso Liu
Specialized organotrophic Bacteria "syntrophs" and methanogenic Archaea "methanogens" form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2 . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum, and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility...
September 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28877764/perilipin-2-modulates-dietary-fat-induced-microbial-global-gene-expression-profiles-in-the-mouse-intestine
#7
Xuejian Xiong, Elise S Bales, Diana Ir, Charles E Robertson, James L McManaman, Daniel N Frank, John Parkinson
BACKGROUND: Intestinal microbiota are critical determinants of obesity and metabolic disease risk. In previous work, we showed that deletion of the cytoplasmic lipid droplet (CLD) protein perilipin-2 (Plin2) modulates gut microbial community structure and abrogates long-term deleterious effects of a high-fat (HF) diet in mice. However, the impact of Plin2 on microbiome function is unknown. RESULTS: Here, we used metatranscriptomics to identify differences in microbiome transcript expression in WT and Plin2-null mice following acute exposure to high-fat/low-carbohydrate (HF) or low-fat/high-carbohydrate (LF) diets...
September 6, 2017: Microbiome
https://www.readbyqxmd.com/read/28874813/functionannotator-a-versatile-and-efficient-web-tool-for-non-model-organism-annotation
#8
Ting-Wen Chen, Ruei-Chi Gan, Yi-Kai Fang, Kun-Yi Chien, Wei-Chao Liao, Chia-Chun Chen, Timothy H Wu, Ian Yi-Feng Chang, Chi Yang, Po-Jung Huang, Yuan-Ming Yeh, Cheng-Hsun Chiu, Tzu-Wen Huang, Petrus Tang
Along with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization...
September 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28873456/molecular-prediction-of-lytic-vs-lysogenic-states-for-microcystis-phage-metatranscriptomic-evidence-of-lysogeny-during-large-bloom-events
#9
Joshua M A Stough, Xiangming Tang, Lauren E Krausfeldt, Morgan M Steffen, Guang Gao, Gregory L Boyer, Steven W Wilhelm
Microcystis aeruginosa is a freshwater bloom-forming cyanobacterium capable of producing the potent hepatotoxin, microcystin. Despite increased interest in this organism, little is known about the viruses that infect it and drive nutrient mobilization and transfer of genetic material between organisms. The genomic complement of sequenced phage suggests these viruses are capable of integrating into the host genome, though this activity has not been observed in the laboratory. While analyzing RNA-sequence data obtained from Microcystis blooms in Lake Tai (Taihu, China), we observed that a series of lysogeny-associated genes were highly expressed when genes involved in lytic infection were down-regulated...
2017: PloS One
https://www.readbyqxmd.com/read/28863779/optimization-of-a-metatranscriptomic-approach-to-study-the-lignocellulolytic-potential-of-the-higher-termite-gut-microbiome
#10
Martyna Marynowska, Xavier Goux, David Sillam-Dussès, Corinne Rouland-Lefèvre, Yves Roisin, Philippe Delfosse, Magdalena Calusinska
BACKGROUND: Thanks to specific adaptations developed over millions of years, the efficiency of lignin, cellulose and hemicellulose decomposition of higher termite symbiotic system exceeds that of many other lignocellulose utilizing environments. Especially, the examination of its symbiotic microbes should reveal interesting carbohydrate-active enzymes, which are of primary interest for the industry. Previous metatranscriptomic reports (high-throughput mRNA sequencing) highlight the high representation and overexpression of cellulose and hemicelluloses degrading genes in the termite hindgut digestomes, indicating the potential of this technology in search for new enzymes...
September 1, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28861526/metabolic-network-analysis-and-metatranscriptomics-reveal-auxotrophies-and-nutrient-sources-of-the-cosmopolitan-freshwater-microbial-lineage-aci
#11
Joshua J Hamilton, Sarahi L Garcia, Brittany S Brown, Ben O Oyserman, Francisco Moya-Flores, Stefan Bertilsson, Rex R Malmstrom, Katrina T Forest, Katherine D McMahon
An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E...
July 2017: MSystems
https://www.readbyqxmd.com/read/28861070/environmental-pollutant-benzo-a-pyrene-impacts-the-volatile-metabolome-and-transcriptome-of-the-human-gut-microbiota
#12
Clémence Defois, Jérémy Ratel, Sylvain Denis, Bérénice Batut, Réjane Beugnot, Eric Peyretaillade, Erwan Engel, Pierre Peyret
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding, metatranscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28836742/thriving-or-surviving-evaluating-active-microbial-guilds-in-baltic-sea-sediment
#13
Laura A Zinke, Megan M Mullis, Jordan T Bird, Ian P G Marshall, Bo Barker Jørgensen, Karen G Lloyd, Jan P Amend, Brandi Kiel Reese
Microbial life in the deep subsurface biosphere is taxonomically and metabolically diverse, but it is vigorously debated whether the resident organisms are thriving (metabolizing, maintaining cellular integrity, and expressing division genes) or just surviving. As part of Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea Paleoenvironment, we extracted and sequenced RNA from organic carbon-rich, nutrient-replete, and permanently anoxic sediment. In stark contrast to the oligotrophic subsurface biosphere, Baltic Sea Basin samples provided a unique opportunity to understand the balance between metabolism and other cellular processes...
August 24, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28835538/genomic-diversification-of-giant-enteric-symbionts-reflects-host-dietary-lifestyles
#14
David Kamanda Ngugi, Sou Miyake, Matt Cahill, Manikandan Vinu, Timothy J Hackmann, Jochen Blom, Matthew D Tietbohl, Michael L Berumen, Ulrich Stingl
Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes...
August 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#15
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#16
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28797298/community-characteristics-of-the-gut-microbiomes-of-competitive-cyclists
#17
Lauren M Petersen, Eddy J Bautista, Hoan Nguyen, Blake M Hanson, Lei Chen, Sai H Lek, Erica Sodergren, George M Weinstock
BACKGROUND: Changes in diet and exercise can alter the gut microbiome of humans and mice; however, few studies to date have assessed the microbiomes of highly fit athletes. In this pilot study, we used metagenomic whole genome shotgun (mWGS) and metatranscriptomic (RNA-Seq) sequencing to show what organisms are both present and active in the gut microbiomes of both professional and amateur level competitive cyclists and to determine if any significant differences exist between these two groups...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28797279/huanglongbing-impairs-the-rhizosphere-to-rhizoplane-enrichment-process-of-the-citrus-root-associated-microbiome
#18
Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
BACKGROUND: Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease...
August 10, 2017: Microbiome
https://www.readbyqxmd.com/read/28793929/shifts-in-coastal-sediment-oxygenation-cause-pronounced-changes-in-microbial-community-composition-and-associated-metabolism
#19
Elias Broman, Johanna Sjöstedt, Jarone Pinhassi, Mark Dopson
BACKGROUND: A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability...
August 9, 2017: Microbiome
https://www.readbyqxmd.com/read/28793203/rna-extraction-from-decaying-wood-for-meta-transcriptomic-analyses
#20
Martino Adamo, Samuele Voyron, Mariangela Girlanda, Roland Marmeisse
Wood decomposition is a key step of the terrestrial carbon cycle and of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating to wood decay we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms...
August 9, 2017: Canadian Journal of Microbiology
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