Category Archives: More Microbes

October 13, 2016

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Ethics and microbiome research, oversimplifying microbiome studies, viruses destroy archaea in the deep seafloor, Clostridium difficile in patients sharing hospital beds.

General microbiome

Perspective: Ethical issues in microbiome research and medicine – Rosamond Rhodes – BMC Medicine

Interview: Science communication: the dangers of oversimplifying microbiome studies – Interview with Lauren Freeman and Saray Ayala – Ben Johnson – NPJ Biofilms Community

Human gut microbiome

Preview: Making It Stick: A Compelling Case for Precision Microbiome Reconstitution – David Berry – Cell Host & Microbe

Preview: A Commensal Protozoan Strikes a Balance in the Gut – P’ng Loke – Cell Host & Microbe

Animal models

Intestinal microbiota could transfer host Gut characteristics from pigs to mice – H. Diao – BMC Microbiology

Plant, root, and soil microbiome

Review: How lichens impact on terrestrial community and ecosystem properties – Johan Asplund – Biological Reviews

Water (and coral) microbiology

Virus-mediated archaeal hecatomb in the deep seafloor – Roberto Danovaro – Science Advances

Press: Deep-Sea Viruses Destroy Archaea. Viruses are responsible for the majority of archaea deaths on the deep ocean floors, scientists show – Ruth Williams – The Scientist

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition – Sean P. McNally – Limnology and Oceanography

Food microbiology

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology

Techniques

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA – Daniel G. Mulcahy – PeerJ

Metagenomics

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties – C. Preston Neff – Cell Host & Microbe

Other microbiology

Division of labour in microorganisms: an evolutionary perspective – Stuart A. West – Nature Reviews Microbiology

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Microbes in the news

The Conversation Gut Series:

RI Hospital receives $500,000 CDC grant to research new approach for combating antibiotic resistance. Microbiome research will help prevent ongoing spread of multi-drug resistant bacteria – EurekAlert

Science, publishing, and career

How Are Scientists Using Social Media in the Workplace? – Kimberley Collins – PLOS ONE

5 retractions and a sack for Pfizer lead cancer researcher Min-Jean Yin – Leonid Schneider – For Better Science
Pfizer fires employee, requests five retractions – Alison McCook – Retraction Watch

Bik’s non-microbiology Picks

Genomics is failing on diversity – Alice B. Popejoy & Stephanie M. Fullerton – Nature
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations – Swapan Mallick – Nature

October 3, 2016

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Gut microbiota in a Belgian nursing home,  aspirin and antibiotics, and Enterococcus in fecal samples of wild marine species. Please note that the next couple of days won’t leave me much time to run literature searches after work-hours. I might publish less and shorter posts, but I hope to be back soon!

Pregnancy and birth

Review: Impact of Maternal Nutrition in Pregnancy and Lactation on Offspring Gut Microbial Composition and Function – Derrick M Chu – Gut Microbes

Human oral microbiome

Microbiome in the Apical Root Canal System of Teeth with Post-Treatment Apical Periodontitis – José F. Siqueira Jr, – PLOS ONE

Bacterial community of saliva in adults with and without periodontitis – Jianye Zhou – Int J Clin Exp Med

Human gut microbiome

Longitudinal survey of Clostridium difficile presence and gut microbiota composition in a Belgian nursing home – Cristina Rodriguez – BMC Microbiology

Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology – Yanfei Chen – Scientific Reports

Editorial: Disease-Associated Microbial Communities in Healthy Relatives: A Bacteria-Filled Crystal Ball? – Mark R. Frey – CMGH Cellular and Molecular Gastroenterology and Hepatology

Review: The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis – Michelle Prosberg – Scandinavian Journal of Gastroenterology

Animal models

Reduced metabolic activity of gut microbiota by antibiotics can potentiate the antithrombotic effect of aspirin – In Sook Kim – Biochemical Pharmacology

Bacterial Abscess Formation Is Controlled by the Stringent Stress Response and Can Be Targeted Therapeutically – Sarah C. Mansour – EBioMedicine

Press: New weapon for hard-to-treat bacterial infections – Science Daily

Animal microbiome

Enterococcus species diversity in fecal samples of wild marine species by real-time PCR – Aline Weber Medeiros – Canadian Journal of Microbiology

A Metabarcoding Survey on the Fungal Microbiota Associated to the Olive Fruit Fly – Antonino Malacrinò – Microbial Ecology
Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution – Vitor G. Faria – PLOS Genetics

Press: Evolution of a species also involves the bacteria it carries – Science Daily

Plant, root, and soil microbiome

Assemblages of fungi associated with cork oak forests in northwestern Tunisia – Mourad Ben Hassine Ben Ali – Nova Hedwigia

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments – Patrick J. Kearns – Nature Communications

Book chapter: Plant Growth-Promoting Bacteria: A Good Source for Phytoremediation of Metal-Contaminated Soil – Iqra Munir – Phytoremediation

Water and extremophile microbiome

Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu – Xianfang Fan – Frontiers in Microbiology

Seasonal Variation in an Acid Mine Drainage Microbial Community – Ryan Richard Auld – Canadian Journal of Microbiology

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea – Dapeng Xu – Journal of Eukaryotic Microbiology

Built environment microbiome

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden) – Kessy Abarenkov – MycoKeys

Bioaerosols in the Barcelona subway system – X. Triadó-Margarit – Indoor Air

Metagenomics, metatranscriptomics, and bioinformatics

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics – Christian Rinke – PeerJ

SAMSA: a comprehensive metatranscriptome analysis pipeline – Samuel T. Westreich – BMC Bioinformatics

More microbiology

Resveratrol suppresses NTHi-induced inflammation via up-regulation of the negative regulator MyD88 short – Carla S. Andrews – Scientific Reports

Press: Does red wine have health benefits? – Tim Sandle – Digital Journal
Resveratrol can help to reduce inflammation, study finds – Medical Xpress

Microbes in the news

Does gum disease have a link to cancer, dementia, stroke? – Suzanne Allard Levingston – Washington Post

From smart socks for diabetes to hand rehab: Health 2.0’s most interesting startups. DayTwo seeks to use insights from evaluating users’ microbiome to guide their diet choices – Stephanie Baum – MedCityNews

Graceleigh, Inc. Recalls Sammy’s Milk Baby Food Because of Possible Health Risk – FDA

September 30, 2016

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When does a probiotic stick around, microbial diversity in 12 French cheese varieties, effects of field conditions on fecal microbiota.

Events

Microbiome Drug Development Summit Europe – 24-26 January 2017, Paris, France

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – Jessica E. Koopman – Archives of Oral Biology

Review: Role of oral microbiome on oral cancers, a review – Pourya Gholizadeh – Biomedicine & Pharmatherapy

Human skin microbiome

Novel volatiles of skin-borne bacteria inhibit the growth of Gram-positive bacteria and affect quorum-sensing controlled phenotypes of Gram-negative bacteria – Marie Chantal Lemfack – Systematic and Applied Microbiology

Human gut microbiome

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome – María X. Maldonado-Gómez – Cell Host & Microbe

Press: A Probiotic That Actually Lasts. The bacteria in yogurts have largely failed to live up to their hyped health benefits, but there are other microbes that might – Ed Yong – The Atlantic

Animal microbiome

Consequences of coinfection with protective symbionts on the host phenotype and symbiont titres in the pea aphid system – Mélanie Leclair – Insect Science

Corals: Bacterial community diversity of the deep-sea octocoral Paramuricea placomus – Christina A. Kellogg – PeerJ

Plant, root, and soil microbiome

Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps – Tommaso Bardelli – Science of the Total Environment

Food microbiology

Highlighting the microbial diversity of 12 French cheese varieties – Eric Dugat-Bony – International Journal of Food Microbiology

Microbial ecology and more microbiology

Macroecology for microbiology – Jay T Lennon – PeerJ Preprint

Review: Fungal Super Glue: The Biofilm Matrix and Its Composition, Assembly, and Functions – Kaitlin F. Mitchell – PLOS Pathogens

Techniques

Effects of field conditions on fecal microbiota – Vanessa L. Hale – Journal of Microbiological Methods

A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing – Henrik Krehenwinkel – Methods in Ecology and Evolution

Microbes in the news

The cost of cheap drugs? Toxic Indian lake is ‘superbug hotspot’ – Zeba Siddiqui – Reuters

Effects of maternal stress on newborn health: An Interview with Dr. Connie Mulligan of the University of Florida – DNA Genotek

Gene-engineered gut bacteria successfully treat sick mice — and could treat humans someday – Leah Samuel – STAT News

Microbiology retreat showcases research – Anamika Veeramani – Yale Daily News

Science, publishing, and career

Working life: Doing science while black – Edward J. Smith – Science

September 28, 2016

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Twins, body fat, and bacteria, dietary zinc and C. diff infections, honey inhibits biofilm formation, microbial life in a Great Lake sinkhole.

Pregnancy and early life

Review: The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life -William B. Miller Jr. – Frontiers in Pediatrics

Human gut microbiome

Heritable components of the human fecal microbiome are associated with visceral fat – Michelle Beaumont – Genome Biology

Press: Body fat link to bacteria in faeces – BBC
How Gut Bacteria May Predict Belly Fat – Alice Park – Time

Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis – Kentaro Iwasawa – Gut

Commentary: Thinking with your stomach? Gut feelings on microbiome modulation of brain structure and function (Commentary on Luczynski et al.) – Anthony J. Hannan – European Journal of Neuroscience

Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection – Joseph P Zackular – Nature Medicine

Editorial: Devil in the detail: A closer look at childhood obesity and the gut microbiota – Michael W. Taylor – Environmental Microbiology

News and views: Culturing: Looking it up in our gut – Clarisse Marotz – Nature Microbiology

Animal microbiome

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice – Taichi A. Suzuki – PLOS ONE

Plant, root, and soil microbiome

Using a Control to Better Understand Phyllosphere Microbiota – Andrea R. Ottesen – PLOS ONE

Caves: Microbial contributions to subterranean methane sinks – J. T. Lennon – Geobiology

Diatom blooms and associated vegetation shifts in a subarctic peatland: responses to distant volcanic eruptions? – U. Kokfelt – Journal of Quaternary Science

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant – Gianna Pitsch – The Journal of Eukaryotic Microbiology

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi – Xihui Xu – PLOS ONE

Fungal Endophytes as a Metabolic Fine-Tuning Regulator for Wine Grape – Ming-Zhi Yang – PLOS ONE

Water and extremophile microbiome

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole – L. E. Kinsman-Costello – Geobiology

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments – Patrick J. Kearns – Nature Communications

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes – Jan-Hendrik Hehemann – Nature Communications

Proteomics

The impact of sequence database choice on metaproteomic results in gut microbiota studies – Alessandro Tanca – Microbiome

More microbiology

Diluted honey inhibits biofilm formation: potential application in urinary catheter management? – Somadina Emineke – Journal of Clinical Pathology

Press: Manuka honey may help prevent life-threatening urinary infections – Simon Hendel – The Conversation
Honey May Be a Natural Way to Beat Bacteria – Alexandra Sifferlin – Time

Personalized therapeutic cocktail of wild environmental phages rescues mice from A. baumannii wound infections – James M. Regeimbal – Antimicrobial Agents and Chemotherapy

Press: A Cocktail Of Wild Viruses Treats Bacterial Wound Infections In Mice – Alex Berezow – American Council on Science and Health

Microbes in the news

Chicago Shedd Aquarium Studies Microbes’ Effect on Sea Life – Illumina

The 3 Robs: NIH Funds Research to See if Gut Microbiomes of Hispanics/Latinos Influence Their Diabetes Risk – Albert Einstein College of Medicine

Antibiotic resistance can occur naturally in soil bacteria – Science Daily

Science, publishing, and career / Peer review

Author affiliation can bias peer review: Single-blind vs Double-blind Peer Review in the Setting of Author Prestige – Kanu Okike – JAMA

September 27, 2016

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Pediatric multiple sclerosis,  Hydra as a microbiome model, species from bat feces, textile wastewater, and sample preparation for metabolomics.

Events

HIV Microbiome Workshop 2016, November 17-18, 2016, NIH Campus, Bethesda, MD. Here is the program

Pregnancy and early life

Association of Chorioamnionitis with Aberrant Neonatal Gut Colonization and Adverse Clinical Outcomes – Kriti Puri – PLOS ONE

Human respiratory microbiome

Translational Aspects of the Human Respiratory Virome – Alicia B Mitchell – American Journal of Respiratory and Critical Care Medicine

Human skin and gut microbiome

The role of skin and gut microbiota in the development of atopic eczema – T. Marrs – British Journal of Dermatology

Associations between the gut microbiota and host immune markers in pediatric multiple sclerosis and controls – Helen Tremlett – BMC Neurology

Intestinal Dysbiosis and Yeast Isolation in Stool of Subjects with Autism Spectrum Disorders – Maria Rosaria Iovene – Mycopathologia

Interactions between Obesity Status and Dietary Intake of Monounsaturated and Polyunsaturated Oils on Human Gut Microbiome Profiles in the Canola Oil Multicenter Intervention Trial (COMIT) – Shuaihua Pu – Frontiers in Microbiology

Review: Diet Influence on the Gut Microbiota and Dysbiosis related to Nutritional Disorders – Maryam Tidjani Alou – Human Microbiome Journal

Review: Role of the Intestinal Microbiota in Host Responses to Stressor Exposure – A.R. Mackos – International Review of Neurobiology

Review: Exploring relationships between host genome and microbiome: new insights from genome-wide association studies – Muslihudeen A. Abdul-Aziz – Frontiers in Microbiology

Animal models

Vitamin D and allergic airway disease shape the murine lung microbiome in a sex-specific manner – Michael Roggenbuck – Respiratory Research

Perspective: Transitioning from microbiome composition to microbial community interactions: the potential of the metaorganism Hydra as an experimental model – Peter Deines – Frontiers in Microbiology

Animal microbiome

Bats: Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples – Faith M. Walker – PLOS ONE

Symbionts modify interactions between insects and natural enemies in the field – Jan Hrček – Journal of Animal Ecology

Plant, root, and soil microbiome

Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait – Kevin Panke-Buisse – Microbial Ecology

Effects of Artificial Soil Aeration Volume and Frequency on Soil Enzyme Activity and Microbial Abundance when Cultivating Greenhouse Tomato – Yuan Li – Soil Science Society of America Journal

Water and pollution microbiome

Degradation of crude oil in a contaminated tidal flat area and the resilience of bacterial community – Jaejin Lee – Marine Pollution Bulletin

Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants – Ken Meerbergen – MicrobiologyOpen

Metabolomics

Sample preparation procedures utilized in microbial metabolomics: an overview – Małgorzata Patejko – Journal of Chromatography B

More microbiology

The quest for the minimal bacterial genome – Esteban Martínez-García – Current Opinion in Biotechnology

Microbes in the news

Inaugural lecture will explore some microbes’ invisible war on humans – University of Kansas

 

September 26, 2016

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Bifidobacteria, pathogens in oysters, root exudate cocktails.

Human mouth microbiome

Novel strategy to detect and locate periodontal pathogens: The PNA-FISH technique – Luzia Mendes – Microbiological Research

Human gut microbiome

Bifidobacteria—Insight into clinical outcomes and mechanisms of its probiotic action – Amrita Sarkar – Microbiological Research

Animal experiments

Response of germ-free mice to colonization with O. formigenes and altered Schaedler flora – Xingsheng Li – Applied and Environmental Microbiology

Animal microbiome

The contribution of marine aggregate-associated bacteria to the accumulation of pathogenic bacteria in oysters: an agent-based model – Andrew M. Kramer – Ecology and Evolution

The Relative Abundance and Transcriptional Activity of Marine Sponge-Associated Microorganisms Emphasizing Groups Involved in Sulfur Cycle – Sigmund Jensen – Microbial Ecology

Plant, root, and soil microbiome

Root exudate cocktails: the link between plant diversity and soil microorganisms? – Katja Steinauer – Ecology and Evolution

Wastewater and pollution microbiology
Bacterial community analysis of an industrial wastewater treatment plant in Colombia with screening for lipid-degrading microorganisms – Lina Marcela Silva-Bedoya – Microbiological Research

Functional characterization and unique diversity of genes and microorganisms involved in arsenite oxidation from the tailings of a realgar mine – Xian-Chun Zeng – Applied and Environmental Microbiology

More microbes

Forum: Bacteria Are Smartphones and Mobile Genes Are Apps – J. Peter W. Young – Trends in Microbiology

Microbes in the news

How the Air Force Will Attack Its Tiniest Enemy: Plane-Corroding Bacteria – Eric Tegler – Popular Mechanics

Tiny Bacteria Are Eating America’s Fighter Jets – David Tracy – Foxtrotalpha

Body fat link to bacteria in faeces – BBC

Prof Emphasizes Importance of Microbiomes in Regulating Human Health – Shruti Juneha – The Cornell Daily Sun

Does this 25 year-old hold the key to winning the war against superbugs? – Nicola Smith – Telegraph.co.uk

Kissing chickens is bad for your health, CDC warns – Karin Brulliard – Washington Post

September 24, 2016

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Eye microbiome, malnutrition and rotavirus, edible insects, vineyard management, and drones.

Human eye / skin microbiome

Impact of Microbiota on Resistance to Ocular Pseudomonas aeruginosa-Induced Keratitis – Abirami Kugadas – PLOS Pathogens

Press (scroll to halfway the page to read this item): Lab chat: Eye bacteria and contact lenses  – Megan Thielking – STAT News

Human gut microbiome

Malnutrition Is Associated with Protection from Rotavirus Diarrhea: Evidence from a Longitudinal Birth Cohort Study in Bangladesh – Hans Verkerke – Journal of Clinical Microbiology

Animal models

Immunosuppression, peripheral inflammation and invasive infection from endogenous gut microbiota activate retinal microglia in mouse models – Victoria Maneu – Microbiology and Immunology

Animal microbiome

Phenological asynchrony between host plant and gypsy moth reduces insect gut microbiota and susceptibility to Bacillus thuringiensis – Vyacheslav V. Martemyanov – Ecology and Evolution

Plant, root, and soil microbiome

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management – Kayla N. Burns – Soil Biology and Biochemistry

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter – Ruibo Sun – Environmental Microbiology

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak – Gregory J. Pec – New Phytologist

Water microbiome

Dense water plumes modulate richness and productivity of deep sea microbes – Gian Marco Luna – Environmental Microbiology

Food microbiology

The microbiota of marketed processed edible insects as revealed by high-throughput sequencing – Cristiana Garofalo – Food Microbiology

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota – Linhuan Wu – Food Microbiology

Techniques

Detection of food and skin pathogen microbiota by means of an electronic nose based on metal oxide chemiresistors – Estefanía Núñez Carmona – Sensors and Actuators B: Chemical

A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms – Bin Li – Journal of Mass Spectrometry

Microbial ecology

The biogeography of kin discrimination across microbial neighbourhoods – Susanne A. Kraemer – Molecular Ecology

More microbiology

Microbes can fly: Drone Transport of Microbes in Blood and Sputum Laboratory Specimens – Timothy K. Amukele – Journal of Clinical Microbiology

Microbes in the news

New CDC Report Shows One Quarter of Contact Lens-related Eye Infections Due to Improper Use, Modifiable Factors – PR Web

Extremely rare US leprosy case found in California elementary school student – Andrew Dalton – STAT News

How Can Science Benefit from Microbes on the ISS? – Jessica F – Nature World News

New Research Indicates Alzheimer’s and Other Neurodegenerative Diseases Are Contagious – PR Newswire

Deadly Viruses and Bacteria Mistakenly Shipped 21 Times – R. Jeffrey Smith – The Daily Beast

Science, publishing, and career

Meet the world’s top peer reviewer: Jonas Ranstam – Ivan Oransky and Adam Marcus – STAT News

September 22, 2016

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Jobs at Second Genome, endohyphal bacteria in fungi on tropical seeds and leaves, designing buildings to house our germs.

Jobs and events

Second Genome (San Francisco, CA) is hiring.

Southern California Microbiome Symposium – Connections to the Environment and Health – Sept 23, UC Irvine

Human gut microbiome

Review: Current Hypothesis for the Relationship between Dietary Rice Bran Intake, the Intestinal Microbiota and Colorectal Cancer Prevention – Winnie K. W. So – MDPI Nutrients

Animal models

Temporal Development of Gut Microbiota in Triclocarban Exposed Pregnant and Neonatal Rats – Rebekah C. Kennedy – Scientific Reports

Animal microbiome

Parasitic Infection by Pseudocapillaria tomentosa is Associated with a Longitudinal Restructuring of the Zebrafish Gut Microbiome – Christopher A Gaulke – bioRxiv

Biology, Pest Status, Microbiome and Control of Kudzu Bug (Hemiptera: Heteroptera: Plataspidae): A New Invasive Pest in the U.S. – Anirudh Dhammi – International Journal of Molecular Sciences

Plant, root, and soil microbiome

A Hardy Plant Facilitates Nitrogen Removal via Microbial Communities in Subsurface Flow Constructed Wetlands in Winter – Penghe Wang – Scientific Reports

Diversity, Specificity, and Phylogenetic Relationships of Endohyphal Bacteria in Fungi That Inhabit Tropical Seeds and Leaves – Justin P. Shaffer – Frontiers in Ecology and Evolution

More microbiology

Nuclear pore-like structures in a compartmentalized bacterium – Evgeny Sagulenko – bioRxiv

Review: Molecular microbiology methods for environmental diagnosis – T. Bouchez – Environmental Chemistry Letters

Self-healing cementitious materials based on bacteria and nutrients immobilized respectively – Huaicheng Chen – Construction and Building Materials

Techniques

An Enteric Micromotor Can Selectively Position and Spontaneously Propel in the Gastrointestinal Tract – Jinxing Li – ACS Nano

Microbes in the news

Black Slime Is Coating World Monuments—And That May Be Good – Michelle Z. Donahue – National Geographic

Designing Buildings to House Our Favorite Germs – Melissa Pandika – Ozy

Very cool talks: Lake Arrowhead Microbial Genomes #LAMG16: Day 3 – David Coil – MicroBEnet

Prairies Yield Clues for Antibiotic Resistance – AgResearch Magazine

Genetically Engineered Bacteria Can Grow Food, Forks on Mars – Jacqueline Ronson – Inverse.com

CosmoCrops! – The 2016 winners of the Nordic Mini-Jamboree! – Copenhagen University iGEM
UW Medical Center takes action after finding bacteria in medical devices – Coral Garnick – BizJournals

Gut bacteria explain insects’ tolerance to a toxic diet – Science Daily

A field guide to dangerous bacteria – Tabletopwhale

Science, publishing, and career

The natural selection of bad science – Paul E. Smaldino – Royal Society Open Science

Press: The Inevitable Evolution of Bad Science – Ed Yong – The Atlantic

Salaries: Reality check: A feeling that good performance is not adequately rewarded is pervading the research world – Chris Woolston – Nature Careers

September 21, 2016

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Secretor status of mother affects infant’s gut microbiota development, differences between lean and obese kids, effect of ozone levels on plant microbiomes.

Pregnancy and early life

Mothers Secretor Status Affects Development of Childrens Microbiota Composition and Function: A Pilot Study – Paula Smith-Brown – PLOS ONE

Press: Research reveals importance of breast milk gene for toddler gut bacteria – University of Queensland

Human vaginal microbiome

Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota – Christina Gill – PLOS ONE

Human urinary tract microbiome

Review: Urinary incontinence: Making sense of the urinary microbiota in clinical urology – Gregor Reid – Nature Reviews Urology

Human gut microbiome

Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease – G. Hoarau – mBio

Role of Gut Microbiota and Short Chain Fatty Acids in Modulating Energy Harvest and Fat Partitioning in Youth – Martina Goffredo – Journal of Clinical Endocrinology & Metabolism

Press: Gut bacteria differ between obese and lean youth – MedicalXpress
Fat Flora? Gut Bacteria Differ in Obese Kids – Christopher Wanjek – LiveScience

Conference poster: Unique Gut Microbiome Triggers Ankylosing Spondylitis, Research Hints – Nancy A. Melville – Medscape

Review: The Microbiome: a Revolution in Treatment for Rheumatic Diseases? – James T. Rosenbaum – Current Rheumatology Reports

Review: Gut Instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration – Timothy G. Dinan – The Journal of Physiology

Animal models

Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis – Marlies Meisel – The ISME Journal

Animal microbiome

In situ visualization of bacterial populations in coral tissues: pitfalls and solutions – Naohisa Wada – PeerJ

Plant, root, and soil microbiome

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice – Yoshiaki Ueda – PLOS ONE

Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang – Rajal Debnath – Frontiers in Plant Science

Does cryptic microbiota mitigate pine resistance to an invasive beetle-fungus complex? Implications for invasion potential – Chihang Cheng – Scientific Reports

Microbial Community Dynamics and Response to Plant Growth-Promoting Microorganisms in the Rhizosphere of Four Common Food Crops Cultivated in Hydroponics – C. Sheridan – Microbial Ecology

Review: The Plant Microbiota: Systems-Level Insights and Perspectives – Daniel B. Müller – Annual Review of Genetics

Water microbiome

Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River basin, Yangtze River Delta – Wei Cai – Wter Science & Technology

Metagenomics and bioinformatics

Metagenomics as a preliminary screen for antimicrobial bioprospecting – Soha Al-Amoudi – Gene

TreeScaper: visualizing and extracting phylogenetic signal from sets of trees – Wen Huang – Molecular Biology and Evolution

Techniques

Microbial community analysis using MiSeq sequencing in a novel configuration fluidized bed reactor for effective denitrification – Phatchariya Rungkitwatananukul – Bioresource Technology

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq – Catherine M. Burke – PeerJ

More microbiology

A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time – Josef C. Uyeda – PLOS ONE

Microbes in the news

The Perks of Manipulating the Microbiome: Probiotics, poop pills and … – Lynne Peeples – Gastroenterology & Endoscopy News

About paper that came out in June: The Breast Has Its Own Microbiome—and the Mix of Bacteria could Prevent or Encourage Cancer – Knvul Sheikh – Scientific American

Plants take it all in to deal with bacteria – Science Daily

Purdue scientists have bright idea for detecting harmful bacteria in food products – Purdue University

UCR professor discovers bacterial connection between wild bees and flowers – Som Chaturvedi – The Highlander (belongs to this paper)

Microbes and money

Skin Microbiome Company Mother Dirt Launches First-Ever Biome-Friendly Moisturizer
AOBiome’s consumer division expands skin product line to complement signature AO+Mist – PR Newswire

Science, publishing, and career

Sad outcome of survey: “Although the majority of department chairs value educational scholarship, only a minority perceive value in faculty blogging effort”. Does Academic Blogging Enhance Promotion and Tenure? A Survey of US and Canadian Medicine and Pediatric Department Chairs – Christian Blake Cameron

September 20, 2016

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A review of antibiotics’ effect on the human microbiome, the pig gut microbiome, microbiome of Green Design, expanding Unifrac, and GutCheck, the Microbiome Game.

General human microbiome

Review: Antibiotic use and microbiome function – Manuel Ferrer – Biochemical Pharmacology

Human respiratory microbiome

Taxa of the Nasal Microbiome Are Associated with Influenza-Specific IgA Response to Live Attenuated Influenza Vaccine – Hannah M. Salk – PLOS ONE

Changes in the bacterial microbiome of patients with chronic rhinosinusitis after endoscopic sinus surgery – Ravi Jain – International Forum of Allergy & Rhinology

Human gut microbiome

Gastric microbiota in the functional dyspepsia patients treated with probiotic yogurt – Hirohiko Nakae – BMJ Open Gastroenterology

Animal microbiome

A reference gene catalogue of the pig gut microbiome – Liang Xiao – Nature Microbiology

Press: Gut Microbial Genes Profiled in Pigs From Diverse Breeds, Locations – Genome Web

The Prevalence of Canine Oral Protozoa and Their Association with Periodontal Disease – Niran Patel – The Journal of Eukaryotic Microbiology

Functional diversity of ant-associated bacterial communities – A. A. Dymova – Biology Bulletin

Plant, root, and soil microbiome

Can inoculation with living soil standardize microbial communities in soilless potting substrates? – Petra Bukovská – Applied Soil Ecology

Effects of saline water irrigation and fertilization regimes on soil microbial metabolic activity – Li -Juan Chen – Journal of Soils and Sediments

More on the Centralia coal mine fire (see yesterday’s post): Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire – Taylor K Dunivin – PeerJ Preprint

Water and extremophile microbiome

Metagenomics as a preliminary screen for antimicrobial bioprospecting – Soha Al-Amoudi – Gene

Built environment microbiome

The Microbiome of Green Design: Sustainable building practices may have unforeseen consequences for microbial communities and human health – Carolyn Beans – BioScience

More microbiology

Cat-Scratch Disease in the United States, 2005–2013 – Christina A. Nelson – Emerging Infectious Diseases

Press: Don’t Kiss That Kitty: Cat-Scratch Fever Is Making People Sicker – Erin Ross – NPR

Bioinformatics and proteomics

Strategies to improve usability and preserve accuracy in biological sequence databases – Johan Bengtsson-Palme – Proteomics

Expanding the UniFrac Toolbox – Ruth G. Wong – PLOS ONE

MetaStorm: A Public Resource for Customizable Metagenomics Annotation – Gustavo Arango-Argoty – PLOS ONE

Microbes in the news

Gut Check: The Microbiome Game – MoBio
Gut Check: The Microbiome Game now available for purchase – David Coil – MicroBEnet

Antibiotic Resistant Bacteria and the World’s Peril: The U.N. General Assembly is taking on a danger that threatens the health of our entire species – Laurie Garrett – Scientific American

Scientists uncover a clever ranking strategy bacteria use to fight off viruses – NewsWire Rockefeller

Oetzi Iceman Update: Bacteria Found In Mummy’s Stomach May Lead To Cancer Research – Janice Williams – International Business News

Stone Age mummy still revealing secrets, 25 years on – Simon Sturdee – Phys.org

Lake Arrowhead Microbial Genomics #LAMG16 Report: Day 1 – David Coil – MicroBEnet