Category Archives: Transcriptomics Proteomics

July 12, 2016

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Two papers on plant/root/soil microbiomes of interest, analysis of transcriptional regulatory networks, and too much non-prescription antibiotic use  in the US.

Human vaginal microbiome

Review: Bacterial vaginosis: a critical analysis of current knowledge – D Nasioudis – BJOG

Human gut microbiome

Gut microbiome analysis in neuromyelitis optica reveals over-abundance of Clostridium perfringens – Bruce A.C. Cree – Annals of Neurology

Review: Gut Microbiota and Intestinal Decolonization of Pathogenic Microorganisms – De-Chang Chen – Chinese Medical Journal

Animal experiments

Human Gut-Derived Prevotella histicola Suppresses Inflammatory Arthritis in Humanized Mice – Eric V. Marietta – Arthritis & Rheumatology

Press: Gut bacteria can cause, predict and prevent rheumatoid arthritis – Science Daily

Gastric Bypass Surgery Reverses Diabetic Phenotypes in Bdnf-Deficient Mice – Shujun Jiang – American Journal of Pathology

Press: New study suggests potential role for gut microbiota in diabetes remission after bypass surgery – News Medical

Plant, root, and soil microbiome

Host genotype and age shape the leaf and root microbiomes of a wild perennial plant – Maggie R. Wagner – Nature Communications

Press: Breeding plants with more beneficial bacteria to feed the world won’t be simple, study says – Robin A. Smith – Phys.org

Soil inoculation steers restoration of terrestrial ecosystems – E. R. Jasper Wubs – Nature Plants

Soil microbes transplants could help restore damaged ecosystems – The dirt makes all the difference – Meaghan Lee Callaghan – PopSci

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil – Nicole K. Scharko – Environmental Science & Technology

Opinion: Plant microbiota affects seed transmission of phytopathogenic microorganisms – Matthieu Barret – Molecular Plant Pathology

Metagenomics and bioinformatics

A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data – Elizabeth T. Hobbs – Algorithms for Molecular Biology

Metagenome and Metatranscriptome Analyses Using Protein Family Profiles – Cuncong Zhong – PLOS Computational Biology

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights – Edoardo Pasolli – PLOS Computational Biology

Review: Metagenome-wide association studies: fine-mining the microbiome – Jun Wang – Nature Reviews Microbiology

Proteomics

An alignment-free ‘metapeptide’ strategy for metaproteomic characterization of microbiome samples using shotgun metagenomic sequencing – Damon H. May – Journal of Proteome Research

Bioreactor microbiology

A light-induced shortcut in the planktonic microbial loop – Robert Ptacnik – Scientific Reports

More microbiology

Non-prescription antimicrobial use in a primary care population in the United States: evidence for action – Roger Zoorob – Antimicrobial Agents and Chemotherapy

Press: Self-prescribing antibiotics is a big problem – American Society for Microbiology – EurekAlert

Transfer of DNA from Bacteria to Eukaryotes – Benoît Lacroix – mBio

Origins of pandemic clones from environmental gene pools – B. Jesse Shapiro – bioRxiv

UTSA professor’s study describes new strategies for investigating microbial outbreaks – EurekAlert

Microbes in the news

Railroad spanning Great Salt Lake helps MSU scientists understand origins of reef-like structures – Skip Anderson – Montana State University

The colon is defended from bacteria by a self-sacrificing sentinel cell – EurekAlert

July 9, 2016

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Bacteroidales from homeothermic animals, 136 microbial genomes from the Red Sea, corrosion of concrete sewers, and the microbiology lab in 2050 (still sexist!).

Pregnancy and birth

Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome – Zhanshan (Sam) Ma – Scientific Reports

Review: The Microbiome, Antibiotics, and Health of the Pediatric Population – Ravi S Misra- EC Microbiology

Human oral microbiome

Metagenomic Analysis of Sputum Microbiome as a Tool Towards Culture-independent Pathogen Detection of Patients with Ventilator-associated Pneumonia – Qiulong Yan – American Journal of Respiratory and Critical Care Medicine

Human respiratory microbiome

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients – Christian Munck – PLOS ONE

Association of sputum microbiota profiles with severity of community-acquired pneumonia in children – Melinda M. Pettigrew – BMC Infectious Diseases

Human gut microbiome

Review: Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease – Darrell W. Cockburn – Journal of Molecular Biology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Editorial: A Role for Chemists in Microbiome Research – Courtney C. Aldrich – ACD Infectious Diseases

Animal experiments

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection – Alison Morris – Microbiome

Animal microbiome

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals – Kate L. Ormerod – Microbiome

Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis – Bosheng Chen – Scientific Reports

Long-term effect of heavy-metal pollution on diversity of gastrointestinal microbial community of Bufo raddei – Wenya Zhang – Toxicology Letters

Plants, roots, and soil microbiome

Multiscale assemblage of an ectomycorrhizal fungal community: The influence of host functional traits and soil properties in a 10-ha miombo forest – David Bauman – FEMS Microbiology Ecology

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula) – Mahmoud W. Yaish – PLOS ONE

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis – Maya Ofek-Lalzar – FEMS Microbiology Ecology

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere

Water and extremophile microbiome

A catalogue of 136 microbial draft genomes from Red Sea metagenomes – Mohamed F. Haroon – Scientific Data

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples – Miguel I. Uyaguari-Diaz – Microbiome

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) – Marie-Ève Garneau – FEMS Microbiology Ecology

Built environment microbiome

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology

Bioreactors

The bioleaching potential of a bacterial consortium – Mauricio Latorre – Bioresource Technology

Biofilms

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – SpringerPlus

Bioinformatics and metagenomics

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis – Mitchell J. Brittnacher – PLOS ONE

Icarus: visualizer for de novo assembly evaluation – Alla Mikheenko – Bioinformatics

deBGA: read alignment with de Bruijn Graph-based seed and extension – Bo Liu – Bioinformatics

ConsPred – a rule-based (re-)annotation framework for prokaryotic genomes – Thomas Weinmaier – Bioinformatics

Proteomics

Review: Metaproteomic data analysis at a glance: advances in computational microbial community proteomics – Expert Review of Proteomics

Bik’s Picks

A typical day working in a laboratory in 2050: Are microbiologists becoming chemists and serene workers? – Daniele Sohier – Current Opinion in Food Science

Napa native on space mission showed early signs of promise – Jonathan Bloom – ABC News

 

 

July 5, 2016

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Circadian rhythm, resistant starch, mock communities, sea turtle microbiome, tea rhizosphere.

General microbiome

Review: The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock – Elizabeth A. C. Heath-Heckman – Integrative & Comparative Biology

Human oral microbiome

Microbial Ecosystem Analysis in Root Canal Infections Refractory to Endodontic Treatment – Luiz Carlos Feitosa Henriques – Journal of Endodontics

Human gut microbiome

Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions – Bijaya Upadhyaya – Scientific Reports

Press: Essential Science: Taking on metabolic disorders with starch – Tim Sandle – Digital Journal

Editorial: serologic microbial-associated markers to predict Crohn’s disease behaviour – A. G. Fraser – Alimentary Pharmacology & Therapeutics

Review: Microbiota and Liver – Kazumichi Abe – The Liver in Systemic Diseases

Animal experiments

A Role for Timp3 in Microbiota-Driven Hepatic Steatosis and Metabolic Dysfunction – Maria Mavilio – Cell Reports

Animal microbiome

A first insight into the gut microbiota of the sea turtle Caretta caretta – Khaled F. Abdelrhman – Frontiers in Microbiology

News and views: Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting? – A. Brune – Molecular Ecology

Bacterial communities of oceanic sea star (Asteroidea: Echinodermata) larvae – Madeline R. Galac – Marine Biology

Gut bacteria differentially affect egg production in the anautogenous mosquito Aedes aegypti and facultatively autogenous mosquito Aedes atropalpus (Diptera: Culicidae) – Kerri L. Coon – Parasites & Vectors

Review: Better with your parasites? Lessons for behavioural ecology from evolved dependence and conditionally helpful parasites – Kelly L. Weinersmith – Animal Behaviour

Plant, root, and soil microbiome

Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators – Pankaj Trivedi – Frontiers in Plant Science

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Yanchun Li – Journal of Applied Microbiology

Water and extremophile microbiome

Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities – S.L. Wilson – Journal of Biotechnology

The Ocean Microbiome: Metabolic Engine of the Marine Carbon Cycle – Elizabeth B. Kujawinski – Microbe

Biofilms

Relevant for Cystic Fibrosis: Temperate phages both mediate and drive adaptive evolution in pathogen biofilms – Emily V. Davies – PNAS

Press: Tiny viruses speed-up evolution of bacteria causing infections in cystic fibrosis patients – News Medical

Techniques

Droplet barcoding for massively parallel single-molecule deep sequencing –
Freeman Lan – Nature Communications

Transcriptomics

Comparative transcriptomics across the prokaryotic tree of life – Ofir Cohen – Nucleic Acids Research

Bioinformatics and metagenomics

PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets – Shareef M. Dabdoub – Scientific Reports

Optimization of 16S amplicon analysis using mock communities: implications for
estimating community diversity – Andrew Krohn – PeerJ

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data – Philip T. L. C. Clausen – Journal of Antimicrobial Chemotherapy

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies – Shalabh Thakur – BMC Bioinformatics

Editorial: Nucleic Acids Research annual Web Server Issue in 2016 – Nucleic Acids Research

June 29, 2016

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Two new papers on multiple sclerosis and breast tissue, cross-respiration, the Boston urban transit microbiome, and plastic debris.

Human respiratory microbiome

Review: The respiratory microbiome of HIV-infected individuals – MB Lawawni – Expert Review of Anti-infective Therapy

Human skin microbiome

The microbiota of breast tissue and its association with tumours – Camilla Urbaniak – Applied and Environmental Microbiology

Human gut microbiome

Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications

Review: Gut microbiota and hematopoietic stem cell transplantation: where do we stand? – D Zama – Bone Marrow Transplantation

Review: The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? – Roman M. Stilling – Neurochemistry International

Animal and in vitro experiments

A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration – Apollo Stacy – mBio

Press: Cross-respiration between oral bacteria leads to worse infections – EurekAlert

Microbiota-Regulated IL-25 Increases Eosinophil Number to Provide Protection during Clostridium difficile Infection – Erica L. Buonomo – Cell Reports

Animal microbiome

Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host – Yan Wang – Molecular Biology and Evolution

In barn swallows: Stress response, gut microbial diversity and sexual signals correlate with social interactions – Iris I. Levin – Biology Letters

Plant, root, and soil microbiome

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation – Natalie Christian – Microbial Ecology

Perspective: Soil immune responses – Jos M. Raaijmakers – Science

Water and extremophile microbiome

Microbes in mercury-enriched geothermal springs in western North America – Gill G. Geese – Science of The Total Environment

Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton – Cristina M. Herren – mSystems

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments – Marina N. Mato – Environmental Microbiology

Built environment microbiome

Commentary: Avoiding Pandemic Fears in the Subway and Conquering the Platypus – A. Gonzalez – mSystems

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems

Press: ‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – EurekAlert

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Food microbiology

Culture-independent bacterial community profiling of carbon dioxide treated raw milk – Raquel Lo – International Journal of Food Microbiology

Metagenomics and bioinformatics

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation – David Koslicki – mSystems

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – Microbial Genomics

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees – Maxime Hebrard – PLOS ONE

Proteomics and metabolomics

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses – Ernesto S. Nakayasu – mSystems

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria – Maria Maansson – mSystems

Techniques

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform – Fiona Fouhy – BMC Microbiology

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses – Lindsey A. Moser- mSystems

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Microbes in the news

Germs in the Subway Are the Harmless Kind – Nicholas Bakalar – New York Times

An Industrial Microbiologist Who Adds Biofuel to the Fire – Nandita Jayaraj – The Wire India

Interview of Faculty of Clinical Microbiology, Prof. Generalov Igor Ivanovich, at VSMU, Belarus – LinkedIn

 

June 28, 2016

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A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.

Events

IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer

Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer

Pregnancy and birth

Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine

Human gut microbiome

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports

Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily

Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases

Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology

Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology

Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology

A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal

Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry

Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer

Water and extremophile microbiome

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research

Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports

Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters

Metabolic networks and proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome

The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology

Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols

Viruses and phages

Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens

Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome

Microbial ecology and techniques

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS

Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily

High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances

Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution

Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology

Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology

Microbes in the news

Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News

Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune

Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical

June 14, 2016

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Breastfeeding protects against antibiotics’ effect in infants, pediatric gut microbiome after surgery, microbial contribution to regional wine characteristics, microbial hotspots on glacial surfaces, foodwebs in your gut, and much more!

Pregnancy and birth

Association of Early-Life Antibiotic Use and Protective Effects of Breastfeeding – 
Role of the Intestinal Microbiota – Katri Korpela – JAMA Pediatrics

Press: Antibiotics May Blunt Breast-Feeding’s Benefits – Infants given the drugs were prone to infections and obesity in childhood, researchers say – WebMD

Human gut microbiome

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease – Minna M. Wieck – Surgery

Press: Culture Crash: How Common Pediatric Diseases Affect the Healthy Intestinal Microbiome – Children’s Hospital Los Angeles

Systematic Review: Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis – Yanqiang Shi – PLOS ONE

Animal and bioreactor experiments

Vancomycin Treatment Alters Humoral Immunity and Intestinal Microbiota in an Aged Mouse Model of Clostridium difficile Infection – Edward van Opstal – Journal of Infectious Diseases

The structural alteration of gut microbiota in low-birth-weight mice undergoing accelerated postnatal growth – Jingjing Wang – Scientific Reports

MALDI-TOF: Investigation of the interactions between Chrysanthemum morifolium flowers extract and intestinal bacteria from human and rat – Jin-hua Tao – Biomedical Chromatography

Substrate-driven convergence of the microbial community in lignocellulose-amended enrichments of gut microflora from the Canadian beaver (Castor canadensis) and North American moose (Alces americanus) – Mabel Ting Wong – Frontiers in Microbiology

Animal microbiome
Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome – Julie L. Meyer – Frontiers in Microbiology

Plant, root, and soil microbiome

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics – Nicholas A. Bokulich – mBio

Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm – Daiva Domenech Tupinambá – Archaea

Effects of Frangula alnus on soil microbial communities and biogeochemical processes in Wisconsin forests – Joel P. Stokdyk – Plant and Soil

Species-specific effects of plant invasions on activity, biomass, and composition of soil microbial communities – Anna M. Stefanowicz – Biology and Fertility of Soils

Water and extremophile microbiome

Review: Biofilms on glacial surfaces: hotspots for biological activity – Heidi J Smith – NPJ Biofilms and Microbiomes

Press: MSU doctoral student publishes research on microbial biofilms and carbon cycling on glacial surfaces – Montana State University

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4,950 m, in Venezuelan Tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Large differences in bacterial community composition among three nearby extreme waterbodies of the high Andean plateau – Pablo Aguilar – Frontiers in Microbiology

The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu – Xianfang Fan – Archaea

Built environment microbiome / food microbiology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community – Stephan Thies – Scientific Reports

Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies – Agnieszka Piotrowska-Cyplik – Journal of the Science of Food and Agriculture

Metagenomics and bioinformatics

Linking comparative genomics and environmental distribution patterns of microbial populations through metagenomics – Tom O Delmont – bioRxiv

Species–function relationships shape ecological properties of the human gut microbiome – Sara Vieira-Silva – Nature Microbiology

Press: Unraveling the food web in your gut – The Flanders Institute for Biotechnology – EurekAlert

Protocol: A Brief Review on the Ecological Network Analysis with Applications in the Emerging Medical Ecology – Zhanshan (Sam) Ma – Part of the series Springer Protocols Handbook

Review: The evolution of genome mining in microbes – a review – Nadine Ziemert – Natural Product Reports

Transcriptomics, metabolomics

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information – Sandra E. Safo – arXiv

More microbiology

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity – Emanuele Bosi – PNAS

Microbes in the news

Bill Gates, Jennifer Doudna Will Take Podium at ASM Microbe – Ingrid Hein – Medscape

Insights into the ecology of the microbiome: dynamics of the gut, mouth and skin microbiomes of healthy subjects – Science Daily

Podcast: Profile Of A Scientist: Personalized Medicine, Gut Microbes And The Biology Of Space Travel, with Stanford biologist Mike Snyder – WBUR

WPI students may have discovered three new viruses in Worcester soil – Michael D. Kane – MassLive

Electronic sensor that tells dead bacteria from live by measuring ‘osmoregulation’ is potential future tool for medicine and food safety – Purdue University

Oral microbiome rich environment for study, product development, event attendees told – Hank Schultz – Nutraingredients

Take Care of Your Microbiome and Your Microbiome Will Take Care of You – Aaron M. Renn – Urbanophile

Science, publishing, and career

How to make your article easy to review – Part 4 – 25 tips from experienced reviewers on what to look out for before submitting your article – Elsevier

June 13, 2016

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Malassezia’s in horses’ ears, microbes in carnivorous plant pitchers, meta-analysis of arbuscular mycorrhizal fungi , and the metatranscriptome of an alkaline hot sulfur spring.

Pregnancy and birth

Early settlers – which E. coli strains do you not want at birth? – Thomas Secher – Am J Physiol Gastrointest Liver Physiol

Human gut microbiome

Intestinal Microbiota‐Generated Metabolite Trimethylamine‐N‐Oxide and 5‐Year Mortality Risk in Stable Coronary Artery Disease: The Contributory Role of Intestinal Microbiota in a COURAGE‐Like Patient Cohort – Vichai Senthong – Journal of the American Heart Association

Review: Gut microbiota, diet and obesity-related disorders – the good, the bad and the future challenges – Kevin J. Portune – Molecular Nutrition & Food Research

Animal experiments

Gut Microbiota are Linked to Increased Susceptibility to Hepatic Steatosis in Low Aerobic Capacity Rats Fed an Acute High Fat Diet – Matthew R Panasevich – Am J Physiol Gastrointest Liver Physiol

Animal microbiome

Don’t look a gift horse in the ear: Is Malassezia nana the main species in horses’ ear canal microbiome? – Ana Lúcia Aldrovandi – Brazilian Journal of Microbiology

Plant, root, and soil microbiome

Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity – Pattanop Kanokratana – Microbial Ecology

Riparian reforestation: are there changes in soil carbon and soil microbial communities? – J.E. Mackay – Science of The Total Environment

Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis – Megan A. Rúa – BMC Evolutionary Biology

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment – Adria L. Fernandez – Science of The Total Environment

Water and extremophile microbiome

Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment – Emily A. Walsh – Applied and Environmental Microbiology

Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism – Swetaleena Tripathy – Extremophiles

Temperature effects on net greenhouse gas production and bacterial communities in arctic thaw ponds – Karita Negandhi – FEMS Microbiology Ecology

Differences in the sensitivity of fungi and bacteria to season and invertebrates affect leaf litter decomposition in a Mediterranean stream – Juanita Mora-Gómez – FEMS Microbiology Ecology

Microbes in the news

Living Bacteria Can Now Store Data – George Dvorsky – Gizmodo

Note that the images in this article have no sources, and that the second image is showing mice data instead of human: The Bacteria In Your Gut And Cancer – Jack Hidary – Huffington Post

The pioneering dental laser that blasts away bacteria – and could help millions of Brits eradicate chronic gum disease without the need for antibiotics – Hilary Freeman – Daily Mail

Science, publishing, and career

The Mistrust of Science – Commenceent Address at CalTech – Atul Gawande

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 2, 2016

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Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News

May 24, 2016

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Endophytes in Miscanthus seeds, the microbes of Blood Pond Hell, microbes in indoor dust, and Dada2 sample inference from Illumina data.

General microbiome

Moonshot or mania? – Sally Adee looks behind the hype – New Scientist

Human gut microbiome

Research Highlight: Microbiota trigger inflammation – Ellen F. Carney – Nature Reviews Nephrology

Glycans affect DNA extraction and induce substantial differences in gut metagenomic studies – Emmanouil Angelakis – Scientific Reports

Microbiome of HIV-infected people – Grégory Dubourg – Microbial Pathogenesis

Review: The microbiota and immune response during Clostridium difficile infection – Erica L. Buonomo – Anaerobe

Animal experiments

Snapshot on a Pilot Metagenomic Study for the Appraisal of Gut Microbial Diversity in Mice, Cat, and Man – Coline Plé – Gastroenterology Research and Practice

Plant, root, and soil microbiome

The microbiomes and metagenomes of forest biochars – Genevieve L. Noyce – Scientific Reports

Endophytic bacteria in Miscanthus seed: implications for germination, vertical inheritance of endophytes, plant evolution and breeding – Naomi Cope-Selby – GCB Bioenergy

Impact of Faba Bean-Seed Rhizobial Inoculation on Microbial Activity in the Rhizosphere Soil during Growing Season – Anna Siczek – Int J Mol Sci

Evaluation of Strategies to Separate Root-Associated Microbial Communities: A Crucial Choice in Rhizobiome Research – Tim Richter-Heitmann – Frontiers in Microbiology

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time – Ngoc-Lan Nguyen – PLOS ONE

Water and extremophile microbiome

Estimating planktonic diversity through spatial dominance patterns in a model ocean – Alice Soccodato – Marine Genomics

Microbial community profiling of the Chinoike Jigoku (“Blood Pond Hell”) hot spring in Beppu, Japan: isolation and characterization of Fe(III)-reducing Sulfolobus sp. strain GA1 – Yusei Masakia – Research in Microbiology

Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea) – Peeter Laas – PLOS ONE

Fungal communities in sediments of subtropical Chinese seas as estimated by DNA metabarcoding – Wei Li – Scientific Reports

Built environment microbiology

Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study – Blake Hanson – Environmental Science: Processes & Impact

Microbiome Profiling of Drinking Water in Relation to Incidence of Inflammatory Bowel Disease – Jessica D Forbes – Canadian Journal of Microbiology

Infection microbiology

The scanning electron microscope in microbiology and diagnosis of infectious disease – Christine G. Golding – Scientific Reports

Bioinformatics

DADA2: High-resolution sample inference from Illumina amplicon data – Benjamin J Callahan – Nature Methods (OA by author)

MetaTrans: an open-source pipeline for metatranscriptomics – Xavier Martinez – Scientific Reports

An Introduction to Programming for Bioscientists: A Python-based Primer – Berk Ekmekci – Arxiv / PLOS

An Optimized Graph-Based Metagenomic Gene Classification Approach: Metagenomic Gene Analysis – Md Sarwar Kamal – Classification and Clustering in Biomedical Signal Processing

Complex heatmaps reveal patterns and correlations in multidimensional genomic data – Zuguang Gu – Bioinformatics

Unsupervised random forest: a tutorial with case studies – Nelson Lee Afanador – Journal of Chemometrics

Metagenomics

Review: The bright side of microbial dark matter: lessons learned from the uncultivated majority – Lindsey Solden – Current Opinion in Microbiology

Metabolomics

Review: Metabolomics of fecal samples: a practical consideration – Silke Matysik – Trends in Food Science & Technology

Viruses and phages

Targeted virus detection in next-generation sequencing data using an automated e-probe based approach – Marike Visser – Virology

Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens – Shin-Yi Lee Marzano – Journal of Virology

Viruses and bacteria in Th2 biased allergic airway disease – Feng Lan – Allergy

More microbiology

Biofilms: Microbial Shelters Against Antibiotics – Skander Hathroubi – Microbial Drug Resistance

Microbes in the news

Building An Antibiotic To Kill Bad Microbes While Sparing Good Ones – Madeline K. Sofia – NPR

A rallying call for microbiome science national data management – A National Microbiome Data Center is essential for enabling exploration of all the environmental genomic data – EurekAlert

Could Gut Microbiome Be the Holy Grail for Diabetes Treatment? – An Expert Weighs In at International Endocrinology Congress – Business Wire

AOBiome and its Consumer Division, Mother Dirt, Founding members of the Microbiome Coalition, Helps Launch of the National Microbiome Initiative – PR Newswire

Painful pooping may stop panda sex. A gut-wrenching tummy ache can throw cold water on pandas’ love life. Amy Middleton reports. – Amy Middleton – Cosmos Magazine