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Vedrana Vidulin, Tomislav Šmuc, Sašo Džeroski, Fran Supek
BACKGROUND: The function of many genes is still not known even in model organisms. An increasing availability of microbiome DNA sequencing data provides an opportunity to infer gene function in a systematic manner. RESULTS: We evaluated if the evolutionary signal contained in metagenome phyletic profiles (MPP) is predictive of a broad array of gene functions. The MPPs are an encoding of environmental DNA sequencing data that consists of relative abundances of gene families across metagenomes...
July 10, 2018: Microbiome
Jose M Haro-Moreno, Mario López-Pérez, José R de la Torre, Antonio Picazo, Antonio Camacho, Francisco Rodriguez-Valera
BACKGROUND: The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment...
July 10, 2018: Microbiome
Xue-Ying Zhang, Gansukh Sukhchuluun, Ting-Bei Bo, Qing-Sheng Chi, Jun-Jie Yang, Bin Chen, Lei Zhang, De-Hua Wang
Following publication of the original article [1], the authors reported an error in the caption of Fig. 4.
July 9, 2018: Microbiome
Jian-Qiang Su, Xin-Li An, Bing Li, Qing-Lin Chen, Michael R Gillings, Hong Chen, Tong Zhang, Yong-Guan Zhu
Unfortunately, after publication of this article [1], it was noticed that the accession numbers for the study were missing. The correct numbers are PRJNA438554, SRP148953.
July 9, 2018: Microbiome
Donald D Nyangahu, Katie S Lennard, Bryan P Brown, Matthew G Darby, Jerome M Wendoh, Enock Havyarimana, Peter Smith, James Butcher, Alain Stintzi, Nicola Mulder, William Horsnell, Heather B Jaspan
BACKGROUND: Early life microbiota is an important determinant of immune and metabolic development and may have lasting consequences. The maternal gut microbiota during pregnancy or breastfeeding is important for defining infant gut microbiota. We hypothesized that maternal gut microbiota during pregnancy and breastfeeding is a critical determinant of infant immunity. To test this, pregnant BALB/c dams were fed vancomycin for 5 days prior to delivery (gestation; Mg), 14 days postpartum during nursing (Mn), or during gestation and nursing (Mgn), or no vancomycin (Mc)...
July 7, 2018: Microbiome
Johan Bengtsson-Palme
BACKGROUND: Antibiotic resistance is considered one of the most urgent threats to modern healthcare, and the role of the environment in resistance development is increasingly recognized. It is often assumed that the abundance and diversity of known resistance genes are representative also for the non-characterized fraction of the resistome in a given environment, but this assumption has not been verified. In this study, this hypothesis is tested, using the resistance gene profiles of 1109 metagenomes from various environments...
July 7, 2018: Microbiome
Masood Ur Rehman Kayani, Shawn M Doyle, Naseer Sangwan, Guanqun Wang, Jack A Gilbert, Brent C Christner, Ting F Zhu
BACKGROUND: Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska. RESULTS: DNA and RNA were extracted from samples of the Matanuska Glacier basal ice...
July 5, 2018: Microbiome
Sara N Lundgren, Juliette C Madan, Jennifer A Emond, Hilary G Morrison, Brock C Christensen, Margaret R Karagas, Anne G Hoen
BACKGROUND: The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of maternal microbes to infants during vaginal delivery and breastfeeding. We aimed to examine the association of maternal diet during pregnancy with the infant gut microbiome 6 weeks post-delivery in mother-infant dyads enrolled in the New Hampshire Birth Cohort Study...
July 5, 2018: Microbiome
Evan P Starr, Shengjing Shi, Steven J Blazewicz, Alexander J Probst, Donald J Herman, Mary K Firestone, Jillian F Banfield
BACKGROUND: The transformation of plant photosynthate into soil organic carbon and its recycling to CO2 by soil microorganisms is one of the central components of the terrestrial carbon cycle. There are currently large knowledge gaps related to which soil-associated microorganisms take up plant carbon in the rhizosphere and the fate of that carbon. RESULTS: We conducted an experiment in which common wild oats (Avena fatua) were grown in a 13 CO2 atmosphere and the rhizosphere and non-rhizosphere soil was sampled for genomic analyses...
July 3, 2018: Microbiome
Muhammad Farhan Ul Haque, Andrew T Crombie, Scott A Ensminger, Calin Baciu, J Colin Murrell
BACKGROUND: Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the subsurface before it reaches the atmosphere. Methanotrophs are usually obligate, i.e. grow only on methane and not on longer chain alkanes. Bacteria that grow on the other gaseous alkanes in natural gas such as propane have also been characterised, but they do not grow on methane...
June 28, 2018: Microbiome
Janina A Krumbeck, Heather E Rasmussen, Robert W Hutkins, Jennifer Clarke, Krista Shawron, Ali Keshavarzian, Jens Walter
BACKGROUND: One way to improve both the ecological performance and functionality of probiotic bacteria is by combining them with a prebiotic in the form of a synbiotic. However, the degree to which such synbiotic formulations improve probiotic strain functionality in humans has not been tested systematically. Our goal was to use a randomized, double-blind, placebo-controlled, parallel-arm clinical trial in obese humans to compare the ecological and physiological impact of the prebiotic galactooligosaccharides (GOS) and the probiotic strains Bifidobacterium adolescentis IVS-1 (autochthonous and selected via in vivo selection) and Bifidobacterium lactis BB-12 (commercial probiotic allochthonous to the human gut) when used on their own or as synbiotic combinations...
June 28, 2018: Microbiome
Marcos Parras-Moltó, Ana Rodríguez-Galet, Patricia Suárez-Rodríguez, Alberto López-Bueno
BACKGROUND: Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias...
June 28, 2018: Microbiome
Aline C Freitas, Alan Bocking, Janet E Hill, Deborah M Money
BACKGROUND: The bacterial community present in the female lower genital tract plays an important role in maternal and neonatal health. Imbalances in this microbiota have been associated with negative reproductive outcomes, such as spontaneous preterm birth (sPTB), but the mechanisms underlying the association between a disturbed microbiota and sPTB remain poorly understood. An intrauterine infection ascending from the vagina is thought to be an important contributor to the onset of preterm labour...
June 28, 2018: Microbiome
Karoline Faust, Franziska Bauchinger, Béatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D Washburne, Didier Gonze, Stefanie Widder
BACKGROUND: Growth rates, interactions between community members, stochasticity, and immigration are important drivers of microbial community dynamics. In sequencing data analysis, such as network construction and community model parameterization, we make implicit assumptions about the nature of these drivers and thereby restrict model outcome. Despite apparent risk of methodological bias, the validity of the assumptions is rarely tested, as comprehensive procedures are lacking. Here, we propose a classification scheme to determine the processes that gave rise to the observed time series and to enable better model selection...
June 28, 2018: Microbiome
Ramesh J Pandit, Ankit T Hinsu, Namrata V Patel, Prakash G Koringa, Subhash J Jakhesara, Jalpa R Thakkar, Tejas M Shah, Georgina Limon, Androniki Psifidi, Javier Guitian, David A Hume, Fiona M Tomley, Dharamshibhai N Rank, M Raman, K G Tirumurugaan, Damer P Blake, Chaitanya G Joshi
BACKGROUND: The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence. METHODS: Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing...
June 23, 2018: Microbiome
Hirokazu Toju, Akifumi S Tanabe, Hirotoshi Sato
BACKGROUND: Although a number of recent studies have uncovered remarkable diversity of microbes associated with plants, understanding and managing dynamics of plant microbiomes remain major scientific challenges. In this respect, network analytical methods have provided a basis for exploring "hub" microbial species, which potentially organize community-scale processes of plant-microbe interactions. METHODS: By compiling Illumina sequencing data of root-associated fungi in eight forest ecosystems across the Japanese Archipelago, we explored hubs within "metacommunity-scale" networks of plant-fungus associations...
June 23, 2018: Microbiome
Bernhard Tschitschko, Susanne Erdmann, Matthew Z DeMaere, Simon Roux, Pratibha Panwar, Michelle A Allen, Timothy J Williams, Sarah Brazendale, Alyce M Hancock, Emiley A Eloe-Fadrosh, Ricardo Cavicchioli
BACKGROUND: The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, in the case of Antarctic communities, can be caused by intergenera gene exchange. To expand understanding of genome variation and biogeography of Antarctic haloarchaea, here we assessed genomic variation between two strains of Halorubrum lacusprofundi that were isolated from Antarctic hypersaline lakes from different regions (Vestfold Hills and Rauer Islands)...
June 20, 2018: Microbiome
Brandon Brooks, Matthew R Olm, Brian A Firek, Robyn Baker, David Geller-McGrath, Sophia R Reimer, Karina R Soenjoyo, Jennifer S Yip, Dylan Dahan, Brian C Thomas, Michael J Morowitz, Jillian F Banfield
BACKGROUND: The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it has been previously shown that the gut microbiomes of these infants often resemble the microbes found in the NICU. Little is known, however, about the identity, persistence, and absolute abundance of NICU room-associated bacteria over long stretches of time. Here, we couple droplet digital PCR (ddPCR), 16S rRNA gene surveys, and recently published metagenomics data from infant gut samples to infer the extent to which the NICU microbiome is shaped by its room occupants...
June 20, 2018: Microbiome
Marie-Lara Bouffaud, Sébastien Renoud, Audrey Dubost, Yvan Moënne-Loccoz, Daniel Muller
BACKGROUND: Complex plant-microbe interactions have been established throughout evolutionary time, many of them with beneficial effects on the host in terms of plant growth, nutrition, or health. Some of the corresponding modes of action involve a modulation of plant hormonal balance, such as the deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). Despite its ecological importance, our understanding of ACC deamination is impaired by a lack of direct molecular tools...
June 20, 2018: Microbiome
Lee Call, Barbara Stoll, Berthe Oosterloo, Nadim Ajami, Fariha Sheikh, Anja Wittke, Rosaline Waworuntu, Brian Berg, Joseph Petrosino, Oluyinka Olutoye, Douglas Burrin
BACKGROUND: Major risk factors for necrotizing enterocolitis (NEC) include premature birth and formula feeding in the context of microbial colonization of the gastrointestinal tract. We previously showed that feeding formula composed of lactose vs. corn syrup solids protects against NEC in preterm pigs; however, the microbial and metabolic effects of these different carbohydrates used in infant formula has not been explored. OBJECTIVE: Our objective was to characterize the effects of lactose- and corn syrup solid-based formulas on the metabolic and microbial profiles of preterm piglets and to determine whether unique metabolomic or microbiome signatures correlate with severity or incidence of NEC...
June 19, 2018: Microbiome
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