Category Archives: Metabolomics

August 7, 2017

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General microbiome

Viruses in the 21st Century: From the Curiosity-Driven Discovery of Giant Viruses to New Concepts and Definition of Life – Patrick Forterre, Clinical Infectious Diseases

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities – Arnaud Bridier, Frontiers in Microbiology

Functions and emerging applications of bacteriocins – Michael L Chikindas, Current Opinion in Biotechnology

Pregnancy and early life

Ontogenesis of the Gut Microbiota Composition in Healthy, Full-Term, Vaginally Born and Breast-Fed Infants over the First 3 Years of Life: A Quantitative Bird’s-Eye View – Ravinder Nagpal, Frontiers in Microbiology

Multi-site human microbiome

Profiling of faecal water and urine metabolites among Papua New Guinea highlanders believed to be adapted to low protein intake – Eriko Tomitsuka, Metabolomics

Evidence based selection of probiotic strains to promote astronaut health or alleviate symptoms of illness on long duration spaceflight missions – G.L. Douglas, Beneficial Microbes

Human oral microbiome

Salivary microbiome in non-oral disease: A summary of evidence and commentary – Aneesha Acharya, Archives of Oral Biology

Human gut microbiome

Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction – Yael Litvak, Current Opinion in Microbiology

Role of gut microbiota in idiopathic nephrotic syndrome in children – Kazunari Kaneko, Medical Hypotheses

A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults – Jason R. Anderson, Sleep Medicine

Diarrhea after bariatric procedures: Diagnosis and therapy – Yves M Borbély, World Journal of Gastroenterology

The Intestinal Microbiome and Childhood Obesity – Jessica McCann, Current Pediatrics Reports

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens

Animal experiments

Streptococcus pneumoniae colonization is required to alter the nasal microbiota in cigarette smoke-exposed mice – Pamela Shen, Infection and Immunity

Fenugreek galactomannan and citrus pectin improve several parameters associated with glucose metabolism, and modulate gut microbiota in mice  – Miriam G. Shtriker, Nutrition

Animal microbiome

The B Vitamin Nutrition of Insects: The contributions of diet, microbiome and horizontally-acquired genes – Angela E. Douglas, Current Opinion in Insect Science

Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community – Wei Jin, Current Microbiology

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) – Obed Hernández-Gómez, Frontiers in Microbiology

Microorganisms associated with microscopic insects Megaphragma amalphitanum and Scydosella musawasensis – A. V. Nedoluzhko, Microbiology

Plant, root, and soil microbiome

Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil – Lívia Fabiana Braga, Brazilian Journal of Microbiology

Taxonomic and functional patterns across soil microbial communities of global biomes – Melline Fontes Noronha, Science of The Total Environment

Phylloplane bacteria of Jatropha curcas : diversity, metabolic characteristics and growth promoting attributes towards vigor of maize seedling – Garima Dubey, Canadian Journal of Microbiology

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Root exudates of potato onion are involved in the suppression of clubroot in a Chinese cabbage-potato onion-Chinese cabbage crop rotation – Shaocan Chen, European Journal of Plant Pathology

Isolation, characterization and inter-relationship of Phosphate Solubilizing Bacteria from the Rhizosphere of Sugarcane and Rice – Muhammad Awais, Biocatalysis and Agricultural Biotechnology

Distribution of Rhizosphere and Endosphere Fungi on the First-Class Endangered Plant Cypripedium japonicum – Geun-Hye Gang, Mycobiology

Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest – Guoyong Yan, Ecosphere

Temporal assessment of microbial communities in soils of two contrasting mangroves – Janaina Rigonato, Brazilian Journal of Microbiology

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome – Wu Xiong, Soil Biology and Biochemistry

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce – Apostolos Kalivas, Genomics Data

Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting PseudomonasSpecies Isolated from Sugarcane Rhizosphere – Hai-Bi Li, Frontiers in Microbiology

A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat – Adam Kuzdraliński, Journal of Molecular Microbiology and Biotechnology

Effect of mixed edible bacterial inoculants on the early development of improved cultivars of cocoa (Theobroma cacao L.) in a traditional agroforestry system in northern Oaxaca, Mexico – E. Hipólito-Romero, Argentina Journal of Microbiology

Draft Genome Sequence of Cronobacter sakazakiiGP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato’s Rhizoplane/Rhizosphere Continuum – Hannah R. Chase, Genome Anouncements

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria – Chiun-Kang Hsu, International Journal of Food Microbiology

Water and extremophile microbiome

Assessment upon heterotrophic microalgae screened from wastewater microbiota for concurrent pollutants removal and biofuel production – Liang Shen, Bioresource Technology

Compositions of the Microbial Consortia Present in Biological Sulphate Reduction Processes During Mine Effluent Treatment – Marja Salo, Mine Water and Circular Economy

An underappreciated hotspot of antibiotic resistance: The groundwater near the municipal solid waste landfill – Qing-Lin Chen, Science of The Total Environment

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea – Connor T. Skennerton, mBio

A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia’s Central Queensland, and Heron Island, a nearby fringing platform reef – D.J. Beale, Science of The Total Environment

Glaciers and Ice Sheets As Analog Environments of Potentially Habitable Icy Worlds –  Eva Garcia-Lopez, Frontiers in Microbiology

Changes in microbial community structure in response to changing oxygen stress in column tests of denitrification and selenium reduction – Chiachi Hwang, Mine Water and Circular Economy

Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source – Yingliang Ge, Tropical Journal of Pharmaceutical Research

Microbial community dynamics in aerated biological fluidized bed (ABFB) with continuously increased p-nitrophenol loads – Fangzhou Ji, Process Biochemistry

Food microbiology

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d’Arnad – Ilario Ferrocino, Applied and Environmental Microbiology

The individual contribution of starter and non-starter lactic acid bacteria to the volatile organic compound composition of Caciocavallo Palermitano cheese – Valeria Guarrasi, International Journal of Food Microbiology

Antimicrobial resistance of Lactobacillus spp. from fermented foods and human gut – Qinqin Ma, LWT – Food Science and Technology

Probiotics / prebiotics

Applications of prebiotics in food industry: A review – Vinti Singla,
Food Science and Technology International

Human milk oligosaccharide consumption by probiotic and human-associated bifidobacteria and lactobacilli – Taksawan Thongaram, Journal of Dairy Science

Probiotic properties of Weissella cibaria and Leuconostoc citreum isolated from tejuino – A typical Mexican beverage – Monique Suela Silva, LWT – Food Science and Technology

A Consumer’s Guide for Probiotics: 10 Golden Rules for a Correct Use – Marco Toscano, Digestive and Liver Disease

Bioinformatics

PATRIC as a unique resource for studying antimicrobial resistance – Dionysios A. Antonopoulos, Briefings in Bioinformatics

Techniques

Optimized experimental workflow for tandem mass spectrometry molecular networking in metabolomics – Florent Olivon, Analytical and Bioanalytical Chemistry

Microbes in the news

Taking too many antibiotics to treat eczema may worsen your condition – DR. LESLIE BAUMANN, Miami Herald

August 3, 2017

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The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature

July 31, 2017

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Short digest today, with many articles from Applied and Environmental Microbiology (AEM)!

General microbiome
Review: Bacterial infection increases risk of carcinogenesis by targeting mitochondria – Jesper A.B. Strickertsson – Seminars in Cancer Biology

Pregnancy and early life
Iron in Micronutrient Powder Promotes an Unfavorable Gut Microbiota in Kenyan Infants – Minghua Tang – Nutrients

Multi-site human microbiome
Review: Role of uremic toxin indoxyl sulfate in the progression of cardiovascular disease – Huichang Gao – Life Sciences

Human gut microbiome
The sortase-dependent fimbriome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue – Christian Milani – Applied and Environmental Microbiology

Repression of Salmonella host cell invasion by aromatic small molecules from the human fecal metabolome – Rafael J.M. Peixoto – Applied and Environmental Microbiology

Animal experiments
Antibiotic-Induced Microbiota Dysbiosis Impairs Neuromuscular Function in Juvenile Mice – Valentina Caputi – British Journal of Pharmacology

10-oxo-12(Z)-octadecenoic acid, a linoleic acid metabolite produced by gut lactic acid bacteria, enhances energy metabolism by activation of TRPV1 – Minji Kim – FASEB

Water and extremophile microbiome
Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Community Diversity – Cuina Bu – Scientific Reports

Built environment
Phage-host associations in a full-scale activated sludge plant during sludge bulking – Ruyin Liu – Applied Microbiology and Biotechnology

Phages and viruses
Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures – Veronica Barragan – Applied and Environmental Microbiology

Microbes in the news
Flesh-Eating Vibrio Can Come From Cleaning Fish…As Well As Swimming – Judy Stone – Forbes

Burp! Singapore scientists hope for probiotic beer hit – Reuters – Deccan Chronicle

Bacteria Hysteria
Blowing out birthday candles increases bacteria on cake’s icing – study –
Daily Mail

Deadly mix: Brewing faecal bacteria in your coffee cup? – Jagruti Verma – Deccan Chronicle

July 23, 2017

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General microbiome

Systems biology of lactic acid bacteria: For food and thought – Bas Teusink, Current Opinion in Systems Biology

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) – Susan H. Brawley, PNAS

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions – Nolwenn M. Dheilly, mSystems

Human respiratory microbiome

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung – Stéphane Mouraux, Journal of Allergy and Clinical Immunology

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross, mSystems

Human oral microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund, mSystems

Human gut microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu, Hepatology

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients – Guoqin Yu, Frontiers in Microbiology

Inulin-type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial – Raylene A. Reimer, Molecular Research and Food Research

Incomplete metabolism of phytoestrogens by gut microbiota from children under the age of three – Pilar Gaya, International Journal of Food Sciences and Nutrition

Animal experiments

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli – Roderick M. Card, mBio

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva – Jean-Pierre Farine, Scientific Reports

Burn Injury Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Rat Gastrointestinal Microbiome – Guangtao Huang, Scientific Reports

Linking Sex Differences in Non-Alcoholic Fatty Liver Disease to Bile Acid Signaling, Gut Microbiota, and High Fat Diet  – John Y.L. Chiang, The American Journal of Pathology

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie, Nature Communication

In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments – Kamarul Zaman Zarkasia,  Research in Microbiology

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs – Annie E. Newell-Fugate, PLoS ONE

Effect of acute ozone exposure on the lung metabolomes of obese and lean mice – Joel Andrew Mathews, PLoS ONE

Animal microbiome

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis) – Arnaud Bataille, Microbial Ecology

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste – Grace Tzun-Wen Shaw, PLoS ONE

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation – Olov Svartström, ISME

Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867) – Hyun-Hee Hong, Genome Anouncements

Feather-Degrading Bacteria: Their Biochemical and Genetic Characteristics – Paweł Kowalczyk, Arabian Journal for Science and Engineering

Plant, root, and soil microbiome

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Soil bacterial community response to vegetation succession after fencing in the grassland of China – Quanchao Zeng, Science of The Total Environment

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes – Christian Santos-Medellín, mBio

Improved grain yield of cowpea (Vigna unguiculata) under water deficit after inoculation with Bradyrhizobium elkaniiand Rhizophagus irregularis – Rui S. Oliveira, Crop and Pasture Science

Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares, Current Opinion in Microbiology

Pseudomonas fluorescens R68 assisted enhancement in growth and fertilizer utilization of Amaranthus tricolor (L.) – C. Jimtha John, 3Biotech

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa – Deidré A. B. van Wyk, Journal of Basic Microbiology

A genomic perspective on stoichiometric regulation of soil carbon cycling – Wyatt H Hartman, ISME

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils – Antonio J. Fernández-González, Scientific Reports

Biological control of potential antagonistic bacteria isolates to restrict Magnaporthe grisea infection on rice – David P. Tokpah, African Journal of Microbiology Research

Bacteria associated to plants naturally selected in a historical PCB polluted soil show potential to sustain natural attenuation – Lorenzo Vergani, Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies – Chandni Sidhu, Frontiers in Microbiology

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su, Microbiome

Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams – Erick S. LeBrun, Microbial Ecology

Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica – Hyunmin Koo, Frontiers in Microbiology

Draft genome sequence of Exiguobacterium aurantiacumstrain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile – Erwin Strahsburger, Brazilian Journal of Microbiology

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera, World Journal of Microbiology and Biotechnology

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons – Pedro C. Junger, Microbial Ecology

Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H – Sudipto Munshi, Extremophiles

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor – Alma E Parada, ISME

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars – Shino Suzuki, ISME

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept – Melissa B. Duhaime, Frontier in Microbiology

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs – Chia S. Chan, Frontiers in Microbiology

Climate oscillations reflected within the microbiome of Arabian Sea sediments – William D. Orsi, Scientific Reports

Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre – Mary R. Gradoville, Frontiers in Microbiology

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols – Manuel Dall’Osto, Scientific Reports

Built environment

A role for microbial selection in frescoes’ deterioration in Tomba degli Scudi in Tarquinia, Italy – Maria Cristina Tomassetti, Scientific Reports

Food microbiology

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting–Phase II) for Agaricus bisporus Cultivation – Fabricio Rocha Vieira, Microbial Ecology

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments – Conor J Doyle, Environmental Microbiology

Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese – Ewelina Stefanovic, Genome Anouncements

Bioinformatics

Cohesion: a method for quantifying the connectivity of microbial communities – Cristina M Herren, ISME

Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank – Jun Wen, Journal of Systematics and Evolution

Techniques

Rapid differentiation of bacterial communities using high resolution melting analysis – Steven Everman, Journal of Microbiological Methods

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models – Fadi H. Mourad, Digestive Diseases and Sciences

17, July 2017

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In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

July 6, 2017

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The microbiota of spotted hyenas, a review of potential interactions between olfactory sensation and the microbiome-gut-brain axis, phylogenetic analysis of host-microbe symbioses to examine the evolution of dependence over time.

General microbiome

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia – Sami Ben Said – Frontiers in Microbiology

The evolution of host-symbiont dependence – Roberta M Fisher – Nature Communications

Review: The microbiota revolution: Excitement and caution – Maria Rescigno – European Journal of Immunology

Review: The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure? – Souhaila Al Khodor – Frontiers in Pediatrics

Human oral microbiome

Suppression of αvβ6 Integrin Expression by Polymicrobial Oral Biofilms in Gingival Epithelial Cells – Jiarui Bi – Scientific Reports

Proteomic shifts in multi-species oral biofilms caused by Anaeroglobus geminatus – Kai Bao – Scientific Reports

Human vaginal microbiome

Quantifying the human vaginal community state types (CSTs) with the species specificity index – Zhanshan Ma – PeerJ

Animal experiments

Effects of iron supplementation on growth, gut microbiota, metabolomics and cognitive development of rat pups – Erica E Alexeev – PLOS ONE

Review: Disruptive physiology: olfaction and the microbiome-gut-brain axis – John Bienenstock – Biological Reviews Cambridge Philosophical Society

Effects of melanin from Sepiella Maindroni ink (MSMI) on the intestinal Microbiome of mice – Hui Dong – BMC Microbiology

Animal microbiome

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition – Emanuel Heitlinger – Frontiers in Cellular and Infection Microbiology

Plant, root, and soil microbiome

Perspective: The deep, hot biosphere: Twenty-five years of retrospection – Daniel R Colman – PNAS

Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus “Hitchhiker” from the Soybean Rhizosphere – Gabriel L Lozano – Genome Announcements

Warmer winters increase the rhizosphere carbon flow to mycorrhizal fungi more than to other microorganisms in a temperate grassland – Johanna Birgander – Global Change Biology

Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework – Briana K Whitaker – Ecology Letters

Water and extremophile microbiome

Size and composition of subseafloor microbial community in the Benguela upwelling area examined from intact membrane lipid and DNA analysis – Thomas W Evans – Organic Geochemistry

FurukawaMarine microbes as a valuable resource for brand new industrial biocatalysts – Azadeh Beygmoradi – Biocatalysts and Agricultural Biotechnology

Antagonistic Interactions and Biofilm Forming Capabilities Among Bacterial Strains Isolated from the Egg Surfaces of Lake Sturgeon (Acipenser fulvescens) – M Fujimoto – Microbial Ecology

Probiotics/prebiotics

Effects of the probiotic Bifidobacterium animalis subsp. lactis on the non-surgical treatment of periodontitis. A histomorphometric, microtomographic and immunohistochemical study in rats – Milla S T Ricoldi – PLOS ONE

Phages and viruses

Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics – Mohammad Moniruzzaman – Nature Communications

Occurrence of Bacillus thuringensis Bacteriophages in the Egyptian Arid Soil – Amel S M Abo-Senna – International Journal of Virology and Molecular Biology

Bioinformatics

A conceptual framework for quality assessment and management of biodiversity data – Allan Koch Veiga – PLOS ONE

Techniques

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures – Joost Willemse – bioRxiv

Mapping-based all-RNA-information sequencing analysis (ARIseq) pipeline simultaneously revealed taxonomic composition, gene expression, and their correlation in an acidic stream ecosystem – Arisa Tsuboi – bioRxiv

More microbes

Review: Metabolic engineering pathways for rare sugars biosynthesis, physiological functionalities, and applications – A review – Muhammad Bilal – Critical Reviews in Food Science and Nutrition

Microbes in the news

Microbes aren’t the enemy, they’re a big part of who we are – Amy Loughman – Medical Xpress

What Cheese Can Tell Us About Antibiotic Resistance – Jason Tetro – Huffington Post Canada

Cases of recurrent Clostridium difficile infection are soaring – Medical Xpress

Helium ions reveal how viruses attack bacteria – ScienceDaily

June 22, 2017

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Effects of weight loss treatment on gut microbiota and serum metabolites, mouse gut microbiota can alter visceral sensitivity, a review discussing the microbiota’s ability to shape the maternal immune system.

Pregnancy and early life

Review: The unique immunological and microbial aspects of pregnancy – Gil Mor – Nature Reviews Immunology

Human oral microbiome

Review: Microbiome and Microbial Biofilm Profiles of Peri-Implantitis: A Systematic Review – Gloria Inés Lafaurie – Journal of Periodontology

Human gut microbiome

Bifidobacterium-Rich Fecal Donor May Be a Positive Predictor for Successful Fecal Microbiota Transplantation in Patients with Irritable Bowel Syndrome – S Mizuno – Digestion

Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests – Francesca Borgo – PLOS ONE

Animal experiments

Fructo-oligosaccharides and intestinal barrier function in a methionine–choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS ONE

Microbiota regulates visceral pain in the mouse – Pauline Luczynski – eLife

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle – Milton Thomas – bioRxiv

Animal microbiome

Combining ‘omics and microscopy to visualize interactions between the Asian citrus psyllid vector and the Huanglongbing pathogen Candidatus Liberibacter asiaticus in the insect gut – Angela Kruse – PLOS ONE

Plant, root, and soil microbiome

Application of struvite alters the antibiotic resistome in soil, rhizosphere, and phyllosphere – Qing-Lin Chen – Environmental Science & Technology

Water and extremophile microbiome

Synergistic hydrolysis of xylan using novel xylanases, β-xylosidases, and an α-l-arabinofuranosidase from Geobacillus thermodenitrificans NG80-2 – Di Huang – Applied Microbiology and Biotechnology

Longitudinal variation of microbial communitiesin benthic biofilms and association with hydrological and physicochemical conditions in glacier-fed streams – Ze Ren – Freshwater Science

Control of Sulfide Production in High Salinity Bakken Shale Oil Reservoirs by Halophilic Bacteria Reducing Nitrate to Nitrite – Biwin A An – Frontiers in Microbiology

Phages and viruses

Viral and Bacterial Communities of Colorectal Cancer – Geoffrey D Hannigan – bioRxiv

Plasmids, Viruses, And Other Circular Elements In Rat Gut – Tue Sparholt Jørgensen – bioRxiv

Bioinformatics

The metagenomic data life-cycle: standards and best practices – Petra ten Hoopen – GigaScience

PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies – Ludovic Mallet – Bioinformatics

Metabolomics

Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention – Ruixin Liu – Nature Medicine

Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease – Robert A Quinn – American Journal of Respiratory and Critical Care Medicine

Coupling targeted and untargeted mass spectrometry for metabolome-microbiome-wide association studies of human fecal samples – Alexey V Melnik – Analytical Chemistry

Techniques

Incorporating comparative genomics into the Design-Test-Learn cycle of microbial strain engineering – Maria Sardi – FEMS Yeast Research

Different amplicon targets for sequencing-based studies of fungal diversity – Francesca De Filippis – Applied and Environmental Microbiology

Microbes in the news

Modified viruses deliver death to antibiotic-resistant bacteria – Sara Reardon – Nature

Microbes on the market

EnteroBiotix raises £500k in first round of equity funding – Philip Gates – Insider.co.uk

Microbiotica To Present At Microbiome Drug Development Summit – BioSpace

Bacteria art

MIT Researchers Use Light-Illuminated Bacteria to Make ‘Living’ Pictures – Kristin Fawcett – Mental Floss

The world’s art is under attack—by microbes – Kate Baggaley – Popular Science

Science, publishing, and career

Editorial: Don’t let Europe’s open-science dream drift – Nature

June 13, 2017

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Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research

June 10, 2017

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Jobs and events

Two tenure-track assistant professor or associate professors – Department of Plant and Microbial Biology – College of Biological Sciences, University of Minnesota

Sign up for the webinar by Edward Messick, GENEWIZ – Topic: Metagenomics for Biomarker Discovery: Applications in Precision Medicine – Webinar date and time: June 14, 2017 at 5 PM

 

General microbiome

Ferrous Iron Efflux Systems in Bacteria – H Pi – Metallomics

Metagenomics of microbial and viral life in terrestrial geothermal environments – A Strazzulli – Reviews in Environmental Science and Bio/Technology

Bacterial Infections in Neonates Following Mupirocin-Based MRSA Decolonization: A Multicenter Cohort Study – R Pierce – Infection Control & Hospital Epidemiology

 

Human gut microbiome

Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model –  N Yin – Chemosphere

Report: Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases – SC Kleiman – European Eating Disorders Review

 

Animal experiment

A Targeted Metabolomics Analysis Identifies Intestinal Microbiota-Derived Urinary Biomarkers of Colonization Resistance in Antibiotic-Treated Mice – ME Obrenovich – Antimicrobial Agents and Chemotherapy

 

Animal microbiome

Molecular dialogues with the microbiota: Lessons from the zebrafish intestine – K Guillemin – Mechanisms of Development

 

Plant, root and soil microbiome

The nodule microbiome; N2-fixing rhizobia do not live alone  – P  Martínez-Hidalgo – Phytobiomes Journal

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity – X Zhang – Global Change Biology

Turnover of carbon and phosphorus in the microbial biomass depending on phosphorus availability – M Spohn – Soil Biology and Biochemistry

Effect of soil preparation techniques on the biochemical properties and microbial communities of a citrus orchard after replanting and conversion into organic management – A Pérez-Piqueres – Applied Soil Ecology

 

Water microbiome and extremophile

Review: The Vulnerability and Resilience of Reef-Building Corals – HM Putnam – Current Biology

Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing – X Lin – Acta Oceanologica Sinica

Genetic diversity of nitrate reducing bacteria in marine and brackish water nitrifying bacterial consortia generated for activating nitrifying bioreactors in recirculating aquaculture systems – PG Preena – Aquaculture Research

 

Techniques

Integrated transcriptomic, proteomic and epigenomic analysis of Plasmodium vivax salivary-gland sporozoites – A Jex – bioRxiv

Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis – NE Dina – Journal of Raman Spectroscopy

 

Metabolomics

Comparative metabolomics in vanilla pod and vanilla bean revealing the biosynthesis of vanillin during the curing process of vanilla –  F Gu – AMB Express

 

Phages

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome – BJ O’ Hara – PLoS Genetics

 

Built environment microbiome

Warm and wet: robust lipase-producing bacteria from the indoor environment – K Tanner – bioRxiv

Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater – M Liu – Water Research

 

More microbes

Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances – PGE Kennedy – Viruses

Protozoa and microbiome  – SL Burgess – Infection and Immunity

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens  – JE Heindl – bioRxiv

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans – J Kaspar – bioRxiv

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle – SL Sokol – bioRxiv

 

Microbes in news

Engineering ‘good’ bacteria to kill bad ones – The Straits Times

White or wholemeal? It depends on your gut bacteria – A Middleton – Cosmos

Ixcela Announces Partnership with ORACLE TEAM USA to Improve Athletes’ Internal Health and Performance – Business Wire

New Study Finds Gut Bacteria May Inhibit Cancer Drugs – K Lant – Futurism

Therapy could stop superbugs on farms – P Ghosh – BBC News

SHU students travel to present phages research – P Parise – Setonian Online

June 9, 2017

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Effects of prebiotics on body fat and gut microbiota of children, a review on the phage community of the human gut, a metabolomics study of the rodent brain to analyze the influence of gut bacteria.

Pregnancy and early life

Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases – Sun Hwa Lee – Korean Journal of Pediatrics

Human vaginal microbiome

Association of vaginal dysbiosis and biofilm with contraceptive vaginal ring biomass in African women – Liselotte Hardy – PLOS ONE

Human gut microbiome

Age-Related Changes in the Composition of Gut Bifidobacterium Species – Kumiko Kato – Current Microbiology

Review: The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS – Heidi M Staudacher – Gut

Animal experiments

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut – H J Wisselink – Poultry Science

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls – Jean A Hall – PLOS ONE

The artificial sweetener acesulfame potassium affects the gut microbiome and body weight gain in CD-1 mice – Xiaoming Bian – PLOS ONE

Effects of different n-6 to n-3 polyunsaturated fatty acids ratio on reproductive performance, fecal microbiota and nutrient digestibility of gestation-lactating sows and suckling piglets – Jia Yin – Animal Science Journal

Nucleotide-binding oligomerization domain-containing protein 2 (Nod2) modulates T1DM susceptibility by gut microbiota – Yang-yang Li – Journal of Autoimmunity

Plant, root, and soil microbiome

Kinetic analysis of aerobic biotransformation pathways of a perfluorooctane sulfonate (PFOS) precursor in distinctly different soils – Lilan Zhang – Environmental Pollution

Plant breeding goes microbial – Zhong Wei – Trends in Plant Science

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover – Sebastian Elgueta – Journal of Environmental Science and Health, Part B

Probiotics/prebiotics

Prebiotic Reduces Body Fat and Alters Intestinal Microbiota in Children With Overweight or Obesity – Alissa C Nicolucci – Gastroenterology

Phages and viruses

Review: The Human Gut Phage Community and Its Implications for Health and Disease – Pilar Manrique – Viruses

Metabolomics

Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism – J R Swann – Journal of Pharmaceutical and Biomedical Analysis

More microbes

Multi-locus and ultra-long amplicon sequencing approach to study microbial diversity at species level using the MinION(TM) portable nanopore sequencer – Alfonso Benítez-Páez – bioRxiv

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species – Thomas M Nero – bioRxiv

Microbes in the news

Microbiology: Many forks make light work – ScienceDaily

Fungi awake bacteria from their slumber – ScienceDaily

Microbes on the market

Seres Completes Enrollment for SER-287 Phase 1b Clinical Trial in Patients with UC – Daniela Semedo – IBD News Today