Category Archives: Water microbiome

July 11, 2016

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Poor oral health associated with decreased chance of developing IBD, thumb-sucking associated with decreased chance of developing atopic sensitization, and the core actinobacteriome of rice plants.

Jobs

Senior Scientist intestinal health – Wageningen UR Livestock Research, The Netherlands

Human oral microbiome (sort of)

Inverse Association Between Poor Oral Health and Inflammatory Bowel Diseases – Weiyao Yin – Clinical Gastroenterology and Hepatology

Thumb-Sucking, Nail-Biting, and Atopic Sensitization, Asthma, and Hay Fever – Stephanie J. Lynch – Pediatrics

Human respiratory microbiome

Review: Airway Microbiota and the Implications of Dysbiosis in Asthma – Juliana Durack – Current Allergy and Asthma Reports

Review: Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Review: Communicating systems in the body: how microbiota and microglia cooperate – Daniel Erny – Immunology

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

Animal and bioreactor experiments

Dietary silver nanoparticles can disturb the gut microbiota in mice – Sybille van den Brule – Particle and Fibre Toxicology

Modelling Longitudinal Metabonomics and Microbiota Interactions in C57BL/6 mice fed a high fat diet – Ivan Montoliu – Analytical Chemistry

High-fiber and high-protein diets shape different gut microbial communities, which ecologically behave similarly under stress conditions, as shown in a gastrointestinal simulator – Massimo Marzorati – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Plant and insect microbial symbionts alter the outcome of plant-herbivore-parasitoid interactions: implications for invaded, agricultural and natural systems – Alison E Bennett – Journal of Ecology

Influences of plant type on bacterial and archaeal communities in constructed wetland treating polluted river water – Yan Long – Environmental Science and Pollution Research

Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice – Wenfeng Wang – Microbiological Research

Water microbiome

Comparative metagenome of a stream impacted by the urbanization phenomenon – Julliane Dutra Medeiros – Brazilian Journal of Microbiology

Drinking water systems

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Bioinformatics

An automated system for evaluation of the potential functionome: MAPLE version 2.1.0 – Hideto Takami – DNA Research

Microbes in the news

You Can Contract Fatal Bacteria Just By Sniffing – Angela Chen – Gizmodo
Deadly bug strikes in a day – New pathway discovered for bacteria – EurekAlert

Tiny bacteria-powered ‘windfarm’ for your phone? – Science Daily
Scientists show how bacteria can power micro-machines – Indiana Express

Antibiotic resistance discovered in the guts of ancient mummies – Andy Coghlan – New Scientist

Antibiotic-resistant bacteria have been around for centuries – Karen Graham – Digital Journal

Seres initiates first clinical trial of synthetic microbiome therapy for C. difficile – Healio

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 7, 2016

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Genetic variation and airway microbiome, Thai vegetarians, social wasps carry local yeast strains, classifying infections by host response, profiling of arbuscular mycorrhizal fungi.

Pregnancy and birth

Research Highlight: First steps in the infant gut microbiota – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Human respiratory microbiome

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome – Catherine Igartua – bioRxiv

Human gut microbiome

A Disease-associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – CMGH Cellular and Molecular Gastroenterology and Hepatology

Microbial community of healthy Thai vegetarians and non-vegetarians, their core gut microbiota and pathogens risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Animal experiments

Personality composition alters the transmission of cuticular bacteria in social groups – Carl N. Keiser – Biology Letters

Oat products modulate the gut microbiota and produce anti-obesity effects in obese rats – Ji-lin Dong – Journal of Functional Foods

Animal microbiome

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains – Leonardo Dapporto – Yeast

Spatial and temporal investigation of the microbiome of the Caribbean octocoral Erythropodium caribaeorum – Erin P McCauley – FEMS Microbiology Ecology

Bacterial and fungal symbionts of parasitic Dendroctonus bark beetles – Loïc Dohet – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture – Karl J. Romanowicz – FEMS Microbiology Ecology

High-resolution community profiling of arbuscular mycorrhizal fungi – Klaus Schlaeppi – New Phytologist

Mycorrhizal associations and soil properties of native Allanblackia stuhlmannii stands in the Eastern Usambara Mountains, Tanzania – P. Fransson – Annals of Applied Biology

Hierarchical neighbor effects on mycorrhizal community structure and function – Holly V. Moeller – Ecology and Evolution

Review: The role of plant-microbiome interactions in weed establishment and control – F. Trognitz – FEMS Microbiology Ecology

Water and extremophile microbiome

Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya – Anne Kelly Kambura – BMC Microbiology

Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic – Brandon T. Hassett – Environmental Microbiology

Metagenomics and bioinformatics

Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis – Jack W. E. Jeffries – Chemistry Select

Reaching saturation in 16S rRNA sequences: After All, Only Millions? – Rudolf Amann – mBio

More microbiology

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics – Timothy E. Sweeney – Science Translational Medicine

Press: A Blood Test To Determine When Antibiotics Are Warranted: Scientists can assay gene activity to distinguish between bacterial and viral infections – Alison F. Takemura – The Scientist

Editorial: Linking Ecosystem Function to Microbial Diversity – Anne E. Bernhard – Frontiers in Microbiology

Microbes in the news

Meet Angus, the C. difficile-sniffing dog trained to detect superbugs – CBC News

Researchers, farmers collaborate to prevent E. coli – Science Daily

How the bacterial protective shell is adapted to challenging environments – Phys.org

Could E.Coli be used to fight disease? Bacteria could transport next-generation vaccines, experts reveal – Daily Mail

Single microbe may restore social behaviors in mice – Ann Griswold – Spectrum

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

Discovery of new bacterium brings laurels to Palamuru University – The Hindu

July 6, 2016

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Two microbiology jobs, a Nature special on intestinal gut microbiota, coral dark spot syndrome, extremophiles from Yellowstone springs, and sugar-coating the envelope.

Jobs

Assembly Biosciences in San Francisco is looking for a Bioinformatics Scientist for supporting their microbiome programs. Contact Jared Kaleck at Klein Hersh for more info.

Nature Microbiology is looking for an Associate Editor, based in New York or London.

Events

4th Annual International Raising Clostridium difficile Awareness Conference and Health EXPO – September 20, 2016 – Atlanta

Human skin microbiome

Normal Skin Microbiota is Altered in Pre-clinical Hidradenitis Suppurativa – Hans Christian Ring – Acta Dermato-venereologica

The cutaneous microbiome and aspects of skin antimicrobial defense system resist acute treatment with topical skin cleansers – Aimee M. Two – Journal of Investigative Dermatology

Review: Bacterial and Viral Infections in Atopic Dermatitis: a Comprehensive Review – Peck Y. Ong – Clinical Reviews in Allergy & Immunology

Human urinary tract microbiome

Review: The urinary microbiota: a paradigm shift for bladder disorders? – Linda Brubaker – Current Opinion in Obstetrics & Gynecology

Human vaginal microbiome

Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis – Ki Ho Hong – Annals of Laboratory Medicine

Human gut microbiome

Fecal microbiota transplantation for recurrent Clostridium difficile infection in hematopoietic stem cell transplant recipients – B.J. Webb – Transplant Infectious Disease

The Esophageal Microbiome in Eosinophilic Esophagitis – Evan S. Dellon – Gastroenterology

Trimethylamine-N-oxide (TMAO) response to animal source foods varies among healthy young men and is influenced by their gut microbiota composition: a randomized controlled trial – Clara E. Cho – Molecular Nutrition & Food Research

Review: The Role of Gut Microflora and the Cholinergic Anti-inflammatory Neuroendocrine System in Diabetes Mellitus – Parth J. Parekh – Frontiers in Endocrinology

Review: Bifidobacteria and Their Role as Members of the Human Gut Microbiota – Amy O’Callaghan – Frontiers in Microbiology

Review: Navigating the Microbial Basis of Inflammatory Bowel Diseases: Seeing the Light at the End of the Tunnel – Laura E. Raffals – Gut and Liver

Animal and in vitro experiments

Composition of Gut Microbiota Influences Resistance of Newly Hatched Chickens to Salmonella Enteritidis Infection – Karolina Varmuzova – Frontiers in Microbiology

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

An Integrated Multi-Omics Approach Reveals the Effects of Supplementing Grass or Grass Hay with Vitamin E on the Rumen Microbiome and Its Function – Alejandro Belanche – Frontiers in Microbiology

Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers – Silvia Turroni – Frontiers in Microbiology

Animal microbiome

Composition and Functional Characterization of Microbiome Associated with Mucus of the Coral Fungia echinata Collected from Andaman Sea – Jhasketan Badhai – Frontiers in Microbiology

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

Temperature mediates continental-scale diversity of microbes in forest soils – Jizhong Zhou – Nature Communications

Molecular biosignatures reveal common benthic microbial sources of organic matter in ooids and grapestones from Pigeon Cay, The Bahamas – S. S. O’Reilly – Geobiology

Availability and function of arbuscular mycorrhizal and ectomycorrhizal fungi during revegetation of dewatered reservoirs left after dam removal – Andrew M. Cortese – Restoration Ecology

A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil – Pascal Weigold – Scientific Reports

Limited recovery of soil microbial activity after transient exposure to gasoline vapors – Jakub J. Modrzyński – Environmental Pollution

Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal community determine assemblages of the AMF spore-associated microbes – Bachir Iffis – Environmental Microbiology

Water and extremophile microbiome

Linking internal and external bacterial community control gives mechanistic framework for pelagic virus-to-bacteria ratios – Selina Våge – Environmental Microbiology

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing – Vera Thiel – Frontiers in Microbiology

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment – Louie Wurch – Nature Communications

Press: Scientists isolate, culture elusive Yellowstone microbe – Science Daily

Fungal and Prokaryotic Activities in the Marine Subsurface Biosphere at Peru Margin and Canterbury Basin Inferred from RNA-Based Analyses and Microscopy – Maria G. Pachiadaki – Frontiers in Microbiology

Unexpected biodiversity of ciliates in marine samples from below the photic zone – Jean-David Grattepanche – Molecular Ecology

Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia – Jaime Bibiloni-Isaksson – Environmental Microbiology

Bioreactor microbiology

Perspectives for microbial community composition in anaerobic digestion: From abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Other microbiology

Opinion: Sugar Coating the Envelope: Glycoconjugates for Microbe–Host Crosstalk – Hanne L.P. Tytgat – Trends in Microbiology

A Combinatorial Algorithm for Microbial Consortia Synthetic Design – Alice Julien-Laferrière – Scientific Reports

Bioinformatics and metagenomics – viruses and phages

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges – Katherine Bruder – Evolutionary Bioinformatics

Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer – Guillaume Bernard – Scientific Reports

Microbes in the news

Dear Science: How many germs are actually on a toilet seat — and should I care? – Rachel Feltman and Sarah Kaplan – Washington Post

‘Super bacteria’ discovered in Rio’s waters as Olympics near – Flora Charner – CNN
‘Super Bacteria’ Detected at Rio de Janeiro’s Beaches – Rosalie Chen – Time

Scientists Discover A Sponge Extract In Antarctica, Can Kill ‘SuperBug’ MRSA Bacterium – Science World Report

Training in microbiology, molecular biology concludes – The Tribune

Science, publishing, and career

The past, present and future of the PhD thesis – Nature

Let’s make peer review scientific – Drummond Rennie – Nature

Bik’s Picks

Warning: contains autoplay video with sound and light-flashes that might not be suitable for epileptics. Sneak peek: The ‘Game of Genomes’ is coming – sequencing Carl Zimmer’s genome – STAT 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

July 4, 2016

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Happy 4th! Since most folks in the US are firing up the BBQ today, here is a very short Digest. Make sure to read Alexandra Carmichael’s piece on the connection between microbes and Independence Day.

Human gut microbiome

Gut Microbiota Developments With Emphasis on Inflammatory Bowel Disease: Report From the Gut Microbiota for Health World Summit 2016 – Hester Eppinga – Gastroenterology

Review: Targeting the ecology within: The role of the gut–brain axis and human microbiota in drug addiction – Patrick D. Skosnik – Medical Hypotheses

Plant, root, and soil microbiome

Biogeographic distribution patterns of bacteria in typical Chinese forest soils – Zongwei Xia – Frontiers in Microbiology

A diverse soil microbiome degrades more crude oil than specialized bacterial assemblages obtained in culture – Terrence H. Bell – Applied and Environmental Microbiology

Crown galls of grapevine (Vitis vinifera) host distinct microbiota – Hanna Faist – Applied and Environmental Microbiology

Water microbiome

Environmental Breviatea harbour mutualistic Arcobacter epibionts – Emmo Hamann – Nature

Press: Research discovery may lead to new ways to treat bacterial disease. University researchers Marc Strous and Emmo Hamann part of international team exploring how microbes can be both friend and foe – Mark Lowey – UCalgary

Techniques

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy – Ting Luo – Applied and Environmental Microbiology

Microbes in the news

The microbes that mark Independence Day – Alexandra Carmichael – uBiome

Subway system laden with harmless bacteria, researchers say. ‘I wouldn’t recommend licking the seats any time soon,’ Harvard professor says – Amina Zafar – CBC News

Bacteria ‘gardeners’ farm algae to harvest when food runs out – Andy Coghlan – New Scientist

More flour recalled as the FDA doubles down on cookie dough warning – Ars Technica

Bacteria Hysteria

Your Cell Phone is Covered in Germs! 5 Tips to Keep It Clean – Ryan Reed – HGTV

July 2, 2016

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Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.

Human respiratory microbiome

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene

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

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Human gut microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology

Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community

Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties

Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville

Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology

Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology

Animal experiments

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports

Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines

Plant, root, and soil microbiome

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments

Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology

Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data

Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology

Built environment microbiome

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments

Techniques / Metabolomics

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology

Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B

Viruses and phages

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology

Microbes in the news

Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego

A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist

Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times

USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM

Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times

Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog

Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London

Science, publishing, and career

“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed

July 1, 2016

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NIH’s Lita Proctor writes about the Human Microbiome Project, oral microbiome among Cheyenne and Arapaho, Cystic Fibrosis, responses to resistant starch, the Swan Goose, sugarcane, litter decomposition.

General microbiome

Review: The National Institutes of Health Human Microbiome Project – Lita M. Proctor – Seminars in Fetal and Neonatal Medicine

Pregnancy and birth

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota – Rocio Martin – PLOS ONE

Human oral microbiome

Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology

Human respiratory microbiome

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline – Giovanni Bacci – PLOS ONE

Human skin microbiome

The skin microbiome is different in pediatric versus adult atopic dermatitis –
Baochen Shi – Journal of Allergy and Clinical Immunology

Just colony counts: Chlorhexidine avoids skin bacteria recolonization more than triclosan – Juan H. Macias – American Journal of Infection Control

Human gut microbiome

Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome

Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity – Alberto Caminero – Gastroenterology

Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms – Rafael Araos – Clinical Infectious Diseases

Nutrition and the Microbiome: Special Edition of the Annals of the New York Academy of Sciences
Review: Nutrition and the microbiome – Karin Moelling
Review: Nutrition meets the microbiome: micronutrients and the microbiota – Hans K. Biesalski

Letter: Microbiota and Alcoholic Liver Disease – Peng Chen – Alcoholism: Clinical and Experimental Research

Animal experiments

Sex differences and hormonal effects on gut microbiota composition in mice – Elin Org – Gut Microbes

Animal microbiome

Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides) – Wen Wang – Journal of Basic Microbiology

The gut microbiome of the sea urchin, Lytechinus variegatus from their natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles – Joseph A. Hakim – FEMS Microbiology Ecology

Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management – Min-Jung Lee – International Journal of Food Microbiology

Bacterial endosymbionts protect aphids in the field and alter parasitoid community composition – Lukas Rothacher – Ecology
Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection – Ephantus J. Muturi – Molecular Ecology

Plant, root, and soil microbiome

The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils – Fabian Bergkemper – Journal of Plant Nutrition and Soil Science

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza – Scientific Reports

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition – Witoon Purahong – Molecular Ecology

Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments – M. del R. Mora-Ruiz – FEMS Microbiology Ecology

Conference abstract: High diversity of enzymes in plant-associated microbiomes – Christina A. Müller – New Biotechnology

Review: Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground – Arjen Biere – Annual Review of Phytopathology

Unearthed! The Amazing Microbiome Exposed: Editor’s Note – Stephen L. Young – Bulletin of the Ecological Society of America
Unearthed! The Amazing Microbiome Exposed: The Arising Researcher – Marnie E. Rout
Unearthed! The Amazing Microbiome Exposed: The Established Researcher – John Klironomos

Water microbiome

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments – Benjamin J. Tully – Applied and Environmental Microbiology

Built environment microbiome

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches – W. Ahmed – Applied and Environmental Microbiology

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA – Lee F. Stanish – PLOS ONE

Microbes in space

Review: Venturing into new realms? Microorganisms in space – Christine Moissl-Eichinger – FEMS Microbiology Reviews

Techniques

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy – Aina E. F. Moen – BMC Research Notes

Microbes in the news

The North American Beaver: Castor canadensis : A look at our local Canadian friend’s microbes – Megan McGrath – Genotek’s The Microbiome Snapshot

Human Microbiome Market : Growth, Development, and Outlook 2014 – 2020 – SB Wire

uBiome Completely Re-Imagines Microbiome Experimentation with New Launch – PR Web

Bacteria prevents mosquitoes from spreading Zika, UW-Madison study says – Wisconsin State Journal

Study sheds more light on how bacteria rapidly causes infectious diseases – News Medical

Gut bacteria spotted eating brain chemicals for the first time – Andy Coghlan – New Scientist

Large Grant to Research on Bacteria in the Nose – Statens Serum Institute

Science, publishing, and career

Great and funny read: Some things you need to know about Google Scholar – Mark Dingemans – Ideophone

June 30, 2016

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Mycorrhizal fungi and CO2, pathogen defense in the gut, Mississippi River plume.

Animal experiments

Defensive Mutualism Rescues NADPH Oxidase Inactivation in Gut Infection – Gratiela Pircalabioru – Cell Host & Microbe

Press: Good gut relationships key in defence against pathogens – Medical Xpress

Plant, root, and soil microbiome

Mycorrhizal association as a primary control of the CO2 fertilization effect – César Terrer – Science

Press: Study finds that plant growth responses to high carbon dioxide depend on symbiotic fungi – EurekAlert

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns – Courtney A. Creamer – Journal of Geophysical Research

The interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances plant growth of Acacia gerrardii under salt stress – Abeer Hashem – Frontiers in Microbiology

Water and extremophile microbiome

Mississippi River plume enriches microbial diversity in the northern Gulf of Mexico – Olivia U. Mason – Frontiers in Microbiology

Editorial: Anthropogenic impacts on the microbial ecology and function of aquatic environments – Maurizio Labbate – Frontiers in Microbiology

Unanticipated geochemical and microbial community structure under seasonal ice cover in a dilute, dimictic Arctic lake – Ursel Schuette – Frontiers in Microbiology

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – Jacqueline Goordial – Environmental Microbiology

Metagenomics and bioinformatics

Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses – Kenneth G. Frey – Evolutionary Bioinformatics

Review: Reconstructing single genomes from complex microbial communities – Dongwan D. Kang – it-Information Technology

Review: A history of DNA sequence assembly – Eugene W. Myers Jr – it-Information Technology

Review: Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes – Miklós Bálint – FEMS Microbiology Reviews

Microbes in the news

Stanford undergrads cook up a biotech startup to develop new antibiotics for drug-resistant superbugs – Rosemary Mena-Werth – Stanford News

From the Evolution Conference, talk by Danielle Whittaker: Bacteria give bird its sexy smells – Patrick Monahan – Science

Australia’s Melbourne takes selfie of its microbiome – i4U News

The Microbiome and Bronchiolitis: An Unusual Pairing or Is It? – Lewis First – AAP Gateway

An Ounce of (Water) Prevention: microbial fuel degradation – Katherine Vanover – Fuel Market News

New study shows chronic fatigue isn’t just in your head. It may have to do with your gut – Ariana Eunjung Cha – Washington Post

Resistance to antibiotics and to immune system are interconnected in bacteria – EurekAlert

In times of great famine, microalgae digest themselves. AWI researchers decipher the connection between nutrient availability and algae growth – EurekAlert

Researchers develop effective strategy for disrupting bacterial biofilms – EurekAlert

How a germ catches a virus – Phys.org

Coming Soon: Gut Bacteria That Actually Cure Your Disease: The $34 billion probiotics market includes some dubious products. This crop looks different – Deena Shanker – Bloomberg

TV weatherman retracts story about toxic bacteria at Northwest Florida beaches – The Destin Log

Bik’s non-microbiology Picks

Former Relman lab member: NASA Astronaut Kate Rubins Prepares for First Trip to Space – Alison Thoet – ABC News

107 Nobel laureates sign letter blasting Greenpeace over GMOs – Joel Achenbach – Washington Post

The Academic Hermit – What are you going to do with your tool?: installation as the Frederick G. Novy Collegiate Professor of Microbiome Research at the University of Michigan – Pat Schloss

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