Category Archives: Built Environment Microbiology

April 1, 2016 (the serious one)

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Make sure to check out my special April 1st post about the creative use of human-derived microbes in food and beverage production. Today’s serious update is about a twin study on oral microbiota and the effects of host genetics and smoking, microbes in floral nectar along an urbanization gradient, plankton biogeography among alpine lakes, and classification of metagenomics data.

General microbiome

Review: Compositional Data Analysis of the Microbiome: Fundamentals, Tools, and Challenges – Matthew C.B. Tsilimigras – Annals of Epidemiology

Review: Gut Microbiotas and Host Evolution: Scaling Up Symbiosis – Michael Shapira – Trends in Ecology and Evolution

Pregnancy and birth

Conference abstract: Neonatal microbiota in health and disease – P. Panigrahi – International Journal of Infectious Diseases

Human oral microbiome

Analysis of the association between host genetics, smoking, and sputum microbiota in healthy humans – Mi Young Lim – Scientific Reports

Human cervical microbiome

Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia – Sang-Soo Seo – Clinical Nutrition

Human gut microbiome

Review: The effect of NOD2 on the microbiota in Crohn’s disease – Mackenzie L Lauro – Current Opinion in Biotechnology

Animal models

Prebiotics and Bioactive Milk Fractions Affect Gut Development, Microbiota and Neurotransmitter Expression in Piglets – Kirsten Berding – Journal of Pediatric Gastroenterology & Nutrition

Isolation of Lactobacillus reuteri from Peyer’s patches and their effects on sIgA production and gut microbiota diversity – Panpan Wang – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Ectomycorrhizal fungal richness declines toward the host species’ range edge – Richard A. Lankau – Molecular Ecology

Diversity and temporal dynamics of the epiphytic bacterial communities associated with the canopy-forming seaweed Cystoseira compressa (Esper) Gerloff & Nizamuddin – Francesco Paolo Mancuso – Frontiers in Microbiology

Do rhizosphere priming effects enhance plant nitrogen uptake under elevated CO2? –
Ming Nie – Agriculture, Ecosystems & Environment

Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer – Andrew B. Moyes – New Phytologist

Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient – Jacek Bartlewicz – BMC Ecology

Water and pollution microbiome

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns – Sabine Filker – Molecular Ecology

Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current – Martina A Doblin – PeerJ preprint

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water – Alexander H. Frank – Environmental Microbiology

Chemical multi-contamination drives benthic prokaryotic diversity in the anthropized Toulon Bay – Benjamin Misson – Science of The Total Environment

Phylogenetic clustering of fungal communities in human-disturbed streams – H. Mykrä – Ecosphere

Built environment microbiome

Changes in bacterial composition of biofilm in a metropolitan drinking water distribution system – R. P. Revetta – Journal of Applied Microbiology

Food microbiology

Biodiversity and technological-functional potential of lactic acid bacteria isolated from spontaneously fermented quinoa sourdoughs – L. Ruiz Rodríguez – Journal of Applied Microbiology

Bioreactor microbiology

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system – Daan R. Speth – Nature Communications

An exploratory study on the influence orange juice on gut microbiota using a dynamic colonic model – Ana Luiza Rocha Faria Duque – Food Research International

Bioinformatics and metagenomics

FOCUS2: agile and sensitive classification of metagenomics data using a reduced database – Genivaldo Silva – BioRxiv

Microbial Ecology

Microbial diversity arising from thermodynamic constraints – Tobias Großkopf – The ISME Journal

Techniques

Genetic circuit design automation: Programming circuitry for synthetic biology –
Alec A. K. Nielsen – Science

Review: Exploring the Secretomes of Microbes and Microbial Communities Using Filamentous Phage Display – Dragana Gagic – Frontiers in Microbiology

Microbes in the news

Your Cat’s Poop Might Help Save Lives: KittyBiome – Lisa Richman – Catster

Pine Bacteria Getting a Closer Look From Scientists – Lorena Anderson – UC Merced

Episode 2: Peek inside a lab trying to create living medicine — from bugs in your gut – Carl Zimmer – STAT News

Poop paper flushed due to possible sample contamination – Shannon Palus – Retraction Watch

About the minimal cell: Breakthrough in synthetic biology is far from ‘playing God’ – New Scientist

Commense Advances Microbiome Platform Targeting Early Childhood Health – Businesswire

New research supports previous findings in the placental microbiome – Baylor College of Medicine

Forensic microbiology from an entomological perspective – SFAM – Microbe Blog
New Potent Nanodrug to Combat Antibiotic-Resistant Infections – University of Arkansas

Vedanta Biosciences Announces License Agreement with RIKEN and other Japanese Institutions for New Immune Boosting Microbiome Technology – Pipeline Review

Brewers Claim They’ve Made Ice-Cold Beer With Vaginal Bacteria; In Theory It Works – Dana Dovey – Medical Daily

Beer brewed with vaginal bacteria is the draft we didn’t ask for – Justina Huddleston – She Knows

Scientists create ‘programming language for bacteria’ – BT.com

‘Listeria on Rye’? Many U.S. Deli Meat Slicers Cut Corners on Cleanliness – Health Day

Retail Deli Slicer Cleaning Frequency — Six Selected Sites, United States, 2012 – Laura G. Brown – CDC Morbidity and Mortality Weekly Report (MMWR)

Science, publishing, and career

Life in the lab, book review of “Lab Girl” by Hope Jahren – Meg Lowman – Science

How to Make Psychology Studies More Reliable – Ed Yong – The Atlantic

Hilda Bastian: She speaks — and draws — truth to scientific power – Karen Weintraub – STAT news

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March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 29, 2016

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Microbiota and stroke outcome, viruses and FMT, Arctic polar deserts, sex and dorm rooms (aren’t you curious?).

Pregnancy and birth

A Study of the Infant Nasal Microbiome Development over the First Year of Life and in Relation to Their Primary Adult Caregivers Using cpn60 Universal Target (UT) as a Phylogenetic Marker – Shelley W. Peterson – PLOS ONE

Human respiratory microbiome (see also above)

Pharyngeal carriage of Neisseria species in the African meningitis belt – Kanny Diallo – Journal of Infection

Human gut microbiome

Commensal microbiota affects ischemic stroke outcome by regulating intestinal γδ T cells – Corinne Benakis – Nature Medicine

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation – Christel Chehoud – mBio

Correlation between diet and gut bacteria in a population of young adults – Lino Mayorga Reyes – International Journal of Food Sciences and Nutrition

Fecal Microbiota Transfer in Patients With Chronic Antibiotic-Refractory Pouchitis – Andreas Stallmach – American Journal of Gastroenterology

Review: Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications – S. Woloszynek – International Review of Cell and Molecular Biology

Review: Metabolic role of lactobacilli in weight modification in humans and animals – Fatima Drissi – Microbial Pathogenesis

Editorial: The Dawning of Microbiome Remediation for Addressing Antibiotic Resistance – Alison Laufer Halpin – Clinical Infectious Diseases

Review: Beyond Antibiotics: New Therapeutic Approaches For Bacterial Infections – Alan R. Hauser – Clinical Infectious Diseases

Correspondence: The Microbiome: A Biological Mechanism Underpinning the Social Gradient of Musculoskeletal Conditions? – Sharon L Brennan-Olsen – Journal of Bone and Mineral Research

Animal models

Effects of chlorpyrifos on the gut microbiome and urine metabolome in mouse (Mus musculus) – Yanping Zhao – Chemosphere

The Effect of Antibiotics on Associated Bacterial Community of Stored Product Mites – Jan Kopecky – PLOS ONE

Animal microbiome

Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species – Ming-Ming Su – PLOS ONE

Microbial Diversity and Parasitic Load in Tropical Fish of Different Environmental Conditions – Philipp Hennersdorf – PLOS ONE

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

Plant, root, and snow microbiome

Diversity and distribution of the endophytic bacterial community at different stages of Eucalyptus growth – Paulo Sérgio Balbino Miguel – Antonie van Leeuwenhoek

Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book: Microbial-mediated Induced Systemic Resistance in Plants
Editors: Devendra K. Choudhary, Ajit Varma – Springer

Water, snow, and extremophile microbiome

Microbial communities in a High Arctic polar desert landscape – Clare M. McCann – Frontiers in Microbiology

Responses of methanogenic and methanotrophic communities to warming in varying moisture regimes of two boreal fens – Krista Peltoniemi – Soil Biology and Biochemistry

Oligotyping and metagenome analyses reveal a high-resolution recurrence that frames potential ecological strategies of North Sea bacterioplankton – M. Chafee – Annual DOE JGI Genomics of Energy & Environment Meeting

Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities – Luis N. Morgado – Global Change Biology

Patterns and variability in geochemical signatures and microbial activity within and between diverse cold seep habitats along the lower continental slope, Northern Gulf of Mexico – Marshall Bowles – Deep Sea Research Part II: Topical Studies in Oceanography

Surface waters in northern Tanzania harbor fecal coliform and antibiotic resistant Salmonella spp. capable of horizontal gene transfer – Beatus Lyimo – African Journal of Microbiology Research

Book chapter: Planktonic Bacterial Communities in Mountain Lake Ecosystems – Masanori Fujii – Structure and Function of Mountain Ecosystems in Japan

Waste and pollution microbiome

Biodegradation of dispersed Macondo crude oil by indigenous Gulf of Mexico microbial communities – Jian Wang – Science of The Total Environment

The effects of various land reclamation scenarios on the succession of soil Bacteria, Archaea, and fungi over the short and long term – Junjian Li – Frontiers in Ecology and Evolution

Illumina MiSeq sequencing reveals long-term impacts of single-walled carbon nanotubes on microbial communities of wastewater treatment systems – Yuanyuan Qu – Bioresource Technology

Predictive functional profiling using marker gene sequences and community diversity analyses of microbes in full-scale anaerobic sludge digesters – Jing Gao – Bioprocess and Biosystems Engineering

Built environment microbiome

Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants – Julia C Luongo – Indoor Air

Microbiological characterization of stable resuspended dust – Nora Kováts – Int J Occup Med Environ Health

Food microbiome

Reducing bias in complex microbial community analysis in shrimp based on propidium monoazide combined with PCR-DGGE – Fei Zhao – Food control

A simple and rapid method for detecting living microorganisms in food using laser speckle decorrelation – Jonghee Yoon – arXiv

Viruses and phages

A strange endocytobiont revealed as largest virus – P Scheid – Current Opinion in Microbiology

More microbiology

A generalized spatial measure for resilience of microbial systems – Ryan S. Renslow – Frontiers in Microbiology

Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes – Felipe L. Pereira – Genomics

In Vitro Selection of RNA-cleaving DNAzymes for Bacterial Detection – Wenqing Zhang – Methods

Architectural transitions in Vibrio cholerae biofilms at single-cell resolution – Knut Drescher – PNAS

Book: New Weapons to Control Bacterial Growth – Editors: Tomas G. Villa, Miguel Vinas – Springer

Microbes in the news

How bacteria, fungi, and mold are finding a home in high-end kitchens
Scientists and chefs find flavor through fermentation – Lindsey J. Smith – The Verge

Could bugs in the gut offer clues for reducing the severity of stroke? – Eric Boodman – STAT news

Microbial cocktails join fecal transplants in IBD treatment trials –
Mark Ratner – Nature Biotechnology News

The Fridge Laser That Detects Bacteria Crawling All Over Food – Rachel Metz – Technology Review

What bacteria lurk in stable dust? – Horsetalk

Humans use ‘sticky molecules’ to hang on to good bacteria in the gut – Stuart Gillespie – University of Oxford

Clostridium botulinum: New Details Emerge on a Notorious Bird-Killing Bacteria – Matt Soniak – Audubon

Swiss study finds E. coli bacteria in ice cubes – The Local

How Dirty Are Public Restrooms, Really? – Stephanie Pappas – Live Science

Gut Microbes Can Evolve From Foe to Friend—And Do It Fast – Ed Yong – National Geographic

Oyster research could lead to food safety strategies – Cookson Beecher – Food Safety News

Why a healthy gut may be the secret to a lean, healthy body – Jennifer Landa – Fox News

Does the 5-Second Rule When You Drop Food Really Work? Here’s What Science Says – Jessica Eggert – Science.Mic

Science, publishing, and career

The seagull of science: Google’s bold bid to transform medicine hits turbulence under a divisive CEO – Charles Piller – STAT news

Andrew Kern on PLoS: Things aren’t what they seem – Storify

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March 24, 2016

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Two papers on antibiotics in early childhood and obesity, diabetic foot ulcers, vertebrate animal microbiomes, cattle hides, kimchi, human archaeological remains, and high inter-center variability in microbiome results.

General microbiome

Review: Stress as a Normal Cue in the Symbiotic Environment – Julia A. Schwartzman – Trends in Microbiology

Pregnancy and birth

Administration of Antibiotics to Children Before Age 2 Years Increases Risk for Childhood Obesity – Frank I. Scott – Gastroenterology

Antibiotic Exposure During the First 6 Months of Life and Weight Gain During Childhood – Jeffrey S. Gerber – JAMA

Editorial: From Bottles to Diapers: How Manipulating and Exploring the Microbiome Is Defining Newborn Care – Jill L. Maron – Clinical Therapeutics

Research highlight: Gut microbiota dysbiosis precedes NEC – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Human skin microbiome

One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers – Karen Smith – BMC Microbiology

Human gut microbiome

Colonic Mucosal Epigenome and Microbiome Development in Children and Adolescents – R. Alan Harris – Journal of Immunology Research

Defining the microbial transcriptional response to colitis through integrated host and microbiome profiling – Nicholas Edward Ilott – The ISME Journal

Targeting colorectal cancer-associated bacteria: a new area of research for personalized treatments – T. Faïs – Gut Microbes

Relative Abundance in Bacterial and Fungal Gut Microbes in Obese Children: A Case Control Study – Borgo Francesca – Childhood Obesity

Review: Can attention to the intestinal microbiota improve understanding and treatment of anorexia nervosa? – Jacquelyn Carr – Expert Review of Gastroenterology & Hepatology

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: FoMenTing Change? – Flaviano S. Martins – Digestive Diseases and Sciences

Review: Does the Microbiome Cause B27-related Acute Anterior Uveitis? – James T. Rosenbaum – Ocular Immunology and Inflammation

Microbes in blood

The prognostic significance of bacterial DNA in patients with decompensated cirrhosis and suspected infection – Tony Bruns – Liver International

Animal models

The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy – Gut Microbes

TLR4-Dependent Secretion by Hepatic Stellate Cells of the Neutrophil-Chemoattractant CXCL1 Mediates Liver Response to Gut Microbiota – Amélie E. Bigorgne – PLOS ONE

Animal microbiome

Vertebrate bacterial gut diversity: size also matters – Jean-Jacques Godon – BMC Ecology

Larval growth rate is associated with the composition of the gut microbiota in the Glanville fritillary butterfly – L. Ruokolainen – Oecologia

Host origin and tissue-microhabitat shaping the microbiota of the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – FEMS Microbiology Ecology

Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides – Jessica Chopyk – Microbiome

Plant, root, and soil microbiome

High Diversity Revealed in Leaf Associated Protists (Rhizaria: Cercozoa) of Brassicaceae – Sebastian Ploch – The Journal of Eukaryotic Microbiology

Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe – Jing Zhang – Scientific Reports

Spatial and seasonal influences on culturable endophytic mycobiota associated with different tissues of Eugenia jambolana Lam. and their antibacterial activity against MDR strains – Manila Yadav – BMC Microbiology

Response of enzyme activities and microbial communities to soil amendment with sugar alcohols – Huili Yu – Microbiology Open

Bioprospecting plant-associated microbiomes – Christina A. Müller – Journal of Biotechnology

Water and extremophile microbiome

Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters – Christoph Reitschuler – Antonie van Leeuwenhoek

Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics – Alexandra Meziti – Environmental Microbiology

Heterotrophic Proteobacteria in the vicinity of diffuse hydrothermal venting – Dimitri Meier – Environmental Microbiology

Waste and pollution microbiology

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates – Vrutika Patel – BMC Microbiology

Built environment microbiology

Diversity of ribosomal 16S DNA- and RNA-based bacterial community in an office building drinking water system – Jenni Inkinen – Journal of Applied Microbiology

Forensic microbiology

Complications in the study of ancient tuberculosis: Presence of environmental bacteria in human archaeological remains – Romy Müller – Journal of Archaeological Science

Food microbiology

Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable – Young Joon Oh – Antonie van Leeuwenhoek

Computational modeling

Host Selection of Microbiota via Differential Adhesion – Kirstie McLoughlin – Cell Host & Microbe

Techniques

The real cost of sequencing: scaling computation to keep pace with data generation – Paul Muir – Genome Biology

Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability – Andreas Hiergeist –
International Journal of Medical Microbiology

Genotyping bacterial and fungal pathogens using sequence variation in the gene for the CCA-adding enzyme – Paul Franz – BMC Microbiology

Proteomics

Review: Tackling probiotic and gut microbiota functionality through proteomics – Lorena Ruiz – Journal of Proteomics

Microbes in the news

Can we model how viruses move between species? – Nancy Mendoza – Microbe Post

The Virus That Could Cure Alzheimer’s, Parkinson’s, and More – Jon Palfreman – PBS

Report: Laminate wood flooring risk was underestimated by CDC – Jonathan Eisen – MicroBEnet

Microbiota profiles in patients with colorectal cancer differ from healthy individuals – Healio

Science, publishing and career

Set up a ‘self-retraction’ system for honest errors, says Daniele Fanelli – Nature

Incorporating Primary Scientific Literature in Middle and High School Education – Sarah C. Fankhauser – ASM Science

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March 22, 2016

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Eye microbiota and contact lenses, leaf-cutter ant dumps, bacteria help with platinum transformation, metagenomics from a Swedish cave, extreme habitats at home, bacteria on board the ISS, a special issue on Megaviromes, and a recipe for Poop Peeps.

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

Effect of Infant Formula Containing a Low Dose of the Probiotic Bifidobacterium lactis CNCM I-3446 on Immune and Gut Functions in C-Section Delivered Babies: A Pilot Study – L. Baglatzi – Clinical Medicine Insights: Pediatrics

Infection, immunology, and transplantion microbiology

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia – P. Gyarmati – Scientific Reports

Rifaximin preserves intestinal microbiota balance in patients undergoing allogeneic stem cell transplantation – D Weber – Bone Marrow Transplantation

Gut microbiome–derived metabolites modulate intestinal epithelial cell damage and mitigate graft-versus-host disease – Nathan D Mathewson – Nature Immunology

Crosstalk between microbiota, pathogens and the innate immune responses – Claudia Günther – International Journal of Medical Microbiology

Human oral microbiome

Commentary: Microbiota-derived metabolites modulate tissue homeostasis: relevance to the oral cavity? – Hervé Le Moual – Oral Diseases

Human eye and skin microbiome

Changes in the Eye Microbiota Associated with Contact Lens Wearing – Hakdong Shin – mBio

Human vaginal microbiome

Improvement and automation of a real-time PCR assay for vaginal fluids – E. De Vittori – Forensic Science International

Human gut microbiome

Conference report: Talking about cross-talk: the immune system and the microbiome: A report on the first EMBO conference entitled “Next Gen Immunology—From Host Genome to the Microbiome: Immunity in the Genomic Era”, Feb 2016 – David Zeevi – Genome Biology

Review: An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease? – Burman S. – Digestive Diseases

Review: Gut Microbiota: The Brain Peacekeeper – Chunlong Mu – Frontiers in Microbiology

Review [PDF]: The intestinal microbiota and its role in human health and
disease – Keiko Kataoka – The Journal of Medical Investigation

Editorial: The microbiome as a possible target to prevent celiac disease – Maureen M Leonard – Expert Review of Gastroenterology & Hepatology

Animal models

Mice: Arthritis-induced alveolar bone loss is associated with changes in the composition of oral microbiota – Jôice Dias Corrêa – Anaerobe

Chickens: Dietary High Fluorine Alters Intestinal Microbiota in Broiler Chickens – Qin Luo – Biological Trace Element Research

Tilapia: Abrupt suspension of probiotics administration may increase host pathogen susceptibility by inducing gut dysbiosis – Zhi Liu – Scientific Reports

Animal microbiome

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability – Gina R. Lewin – PLOS ONE

Plant, root, and soil microbiome

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity – Paul Carini – bioRxiv

Biological role in the transformation of platinum-group mineral grains – Frank Reith – Nature Geoscience

Associations between ectomycorrhizal fungi and bacterial needle endophytes in Pinus radiata: implications for biotic selection of microbial communities – Megan A. Rúa – Frontiers in Microbiology

Functional composition of plant communities determines the spatial and temporal stability of soil microbial properties in a long-term plant diversity experiment – Tanja Strecker – Oikos

No synergistic effects of water and nitrogen addition on soil microbial communities and soil respiration in a temperate desert – Yan Gui Su – CATENA

The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests – Nicholas P. Rosenstock – New Phytologist

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass – Erin E. Nuccio – Ecology

Temporal distance decay of similarity of ectomycorrhizal fungal community composition in a subtropical evergreen forest in Japan – Shunsuke Matsuoka – FEMS Microbiology Ecology

Review: The Functioning of Rhizosphere Biota in Wetlands – a Review – Amir Neori – Wetlands

Water and extremophile microbiome

Experimental evidence that microbial activity lowers the albedo of glaciers – M. Musilova – Geochemical Perspectives Letters

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor – William D. Orsi – Environmental Microbiology Reports

Cave microbiome

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante’s Cave, Northern Sweden – Marie Lisandra Zepeda Mendoza – PLOS ONE

Built environment microbiology

Microbial diversity of extreme habitats in human homes – Amy M. Savage – PeerJ preprint

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A. Coil – PeerJ

Food microbiology

Isolation and identification of biocellulose-producing bacterial strains from Malaysian acidic fruits – Wen Yi W. V – Letters in Applied Microbiology

Bioinformatics, techniques, and metagenomics

Strain-level microbial epidemiology and population genomics from shotgun metagenomics – Matthias Scholz – Nature Methods

Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions – Shengqin Wang – Journal of Theoretical Biology

A framework for inferring biological communities from environmental DNA – Andrew Olaf Shelton – Ecological Applications

Review: Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money – Antony T. Vincent – Journal of Microbiological Methods

Metagenomics and viruses

A Next-Generation Sequencing Data Analysis Pipeline for Detecting Unknown Pathogens from Mixed Clinical Samples and Revealing Their Genetic Diversity – Yu-Nong Gong – PLOS ONE

Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics – Daniel Wüthrich – Virology

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets – Oskar E. Karlsson – PLOS ONE

Special issue of Current Opinion in Microbiology: Megaviromes
Review: Giant viruses come of age – Matthias G Fischer
Review: Giant viruses and the origin of modern eukaryotes – Patrick Forterre

To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life – Patrick Forterre – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

More microbiology

The mystery of plague in medieval Iceland – Chris Callow – Journal of Medieval History

Microbes in the news

HT: Tomer Altman: Poop Peeps: Today we’re going to make Poop Peeps. Marshmallow Peeps that are shaped like the poop emoji.– Matthew Cetta – Nomageddon

Elizabethkingia, the rare and deadly bacteria that’s sickening people in the Midwest, explained – Julia Belluz – Vox

Forest resilience; can microbes help combat climate change issues faster than genetic adaptations? – Armand Séguin

Controversial New Push to Tie Microbes to Alzheimer’s Disease. A journal article says herpes virus and Lyme disease bacteria are behind the mind-robbing illness, but not all researchers are convinced – Melinda Wenner Moyer – Scientific American

Bacteria Are Revolutionizing Biotech–Here’s Why We Need To Talk About It – Catherine Feuillet – Forbes

Contact Lenses Fill Your Eyes With Bacteria – Mandy Oaklander – Time

Killing Bacteria With Gold Nanodisks And Light – Jennifer Hicks – Forbes

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

Top Science Fair Projects Put Stream Data, Bacteria to Work – Dan Swanson – News Channel Nebraska

The Daily Startup: Startups Look to ‘New Frontier’ of Microbiomes to Fight Disease – Wall Street Journal

The Human Microbiome Handbook – Edited by Jason Tetro, Emma Allen-Vercoe

New Bioinformatic Approach Enables Strain-Level Microbial Profiling From Metagenomic Data – Genome Web

Ulcerative Colitis Improves in Multidonor Fecal Transplant Trial – Damian McNamara – MedScape

Blog posts by me:

New papers, March 22, 2016 – Elisabeth Bik – MicroBEnet

Extreme environments at home – Elisabeth Bik – MicroBEnet

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March 16, 2016

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Events

Strategies & Techniques for Analyzing Microbial Population Structures (STAMPS) Course 8/3-8/13 – MicroBEnet

Human skin microbiome

An in Vitro Model for the Human Cutaneous Microbial Ecosystem – Danique A. van der Krieken – Acta Dermato-Venereologica

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – I.M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory tract microbiome

High genetic diversity of Staphylococcus aureus strains colonising the nasopharynx of Gambian villagers before widespread use of pneumococcal conjugate vaccines – Chinelo Ebruke – BMC Microbiology

Human gut microbiome

Note: data segregate according to study: Gene expression profiling gut microbiota in different races of humans – Lei Chen – Scientific Reports

Review: A healthy gastrointestinal microbiome is dependent on dietary diversity – Mark L. Heiman

Review: Gut Microbiota and Obesity: Potential Therapeutic Targets and Probiotic 
Nicole D. White – American Journal of Life Sciences

Animal models

Fuzhuan tea consumption imparts hepatoprotective effects and alters intestinal microbiota in high saturated fat diet-fed rats – Michelle T. Foster – Molecular Nutrition & Food Research

Long-term effects of early life microbiota disturbance on adaptive immunity in laying 
K. Simon – Poultry Science

Rapid evolution of microbe-mediated protection against pathogens in a worm host –
Kayla C King – ISME Journal

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats
Hongxing Han – Scientific Reports

Animal microbiome

Genomic Analysis of Companion Rabbit Staphylococcus aureus – Mark A. Holmes – PLOS ONE

Plant, root, and soil microbiome

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants – Tao Ding – PLOS ONE

Water and extremophile microbiome

Ecosystem function decays by fungal outbreaks in Antarctic microbial mats – David Velázquez – Scientific Reports

Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters – Richard A. Haugland – Journal of Microbiological Methods

Built environment microbiome

Potentially harmful secondary metabolites produced by indoor Chaetomium species on artificially and naturally contaminated building materials – I. Došen – Indoor AIr

Food microbiology

Helicobacter pylori in bottled mineral water: genotyping and antimicrobial resistance properties – Reza Ranjbar – BMC Microbiology

Effects of Temperature on Bacterial Communities and Metabolites during Fermentation of Myeolchi-Aekjeot, a Traditional Korean Fermented Anchovy Sauce – Ji Young Jung – PLOS ONE

Viruses and phages

The Formulation of Bacteriophage in a Semi Solid Preparation for Control of Propionibacterium acnes Growth – Teagan L. Brown – PLOS ONE

News & Views: Microbial oceanography: Viral strategies at sea – T. Frede Thingstad – Nature

Lytic to temperate switching of viral communities – B. Knowles – Nature

Microbial Ecology

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla – Judith Zimmerman – Molecular Ecology

Bioinformatics

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to 
Yanming Zhang – Nucleic Acids Research

Techniques

The US Culture Collection Network lays the foundation for progress in preservation of valuable microbial resources – Kevin McCluskey – Phytopathology

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

A modified micro chamber agar spot slide culture technique for microscopic examination of filamentous fungi – Peralam Yegneswaran Prakash – Journal of Microbiological Methods

Microbes in the news

uBiome is World’s First Company to Appoint Citizen-Scientist-in-Residence – PR Web

Incredible images reveal bacteria motor parts in unprecedented detail – Science Codex

Ancient Bacteria With Photosynthesis Were Much More Common Than Previously Thought, Study Finds – Catherine Griffin – HNGN

Viral Remnants Help Regulate Human Immunity: Endogenous retroviruses in the human genome can regulate genes involved in innate immune responses – Jyoti Madhusoodanan – The Scientist

Plastic That Mimics Insect Wings Kills Bacteria, University of California, Irvine Study – Biospace

Early heavy metal exposure can cause permanent changes to gut microbiome and cause a host of diseases – Dave Mihalovic – SOTT

Slice of PLOS: Bacteria’s Social Media – Lauren Richardson – PLOS ONE

“Unsurprisingly, Perlmutter has his critics.” Neurologist David Perlmutter gets to the guts of brain health with surprising advice – SMH.com

Opinion: A Mother’s Microbes: On “vaginal seeding” and the challenge of evidence-based parenting – Rob Knight and Jack Gilbert – The Scientist

Australian Scientists Discover How Gut Bacteria May Prevent Stomach Cancer – MSN

Reduction in dietary diversity impacts richness of human gut microbiota – Science Codex
http://www.nature.com/articles/srep23075

Press might be overinterpreting Mouse seminal microbiome study:
Scientists discover microbiome that may be responsible for male reproductive disorders – EurekAlert

Seminal work. How unruly data led MU scientists to discover a new microbiome – Roger Meissen – Decoding Science

Microbiome: This Type Of Bacteria May Increase Risk Of Reproductive Disorders – Kathleen Lees – HNGN

Science, publishing, and career

Handful of Biologists Went Rogue and Published Directly to Internet – Amy Harmon

Peer-Led Team Learning Helps Minority Students Succeed – Julia J. Snyder – PLOS Biology

Video parody: PloS ANNA VS ELSAvier – For The First Time – Luisa Hugerth -YouTube

Bik’s Picks

A Month in Mammoth. Two sleep researchers braved the subterranean environment of a Kentucky cave to see if they could train their bodies to abandon the cyclical rhythms of the 24-hour day – The Scientist

Night Night, Flipper – Watch underwater footage of a dolphin sleeping in the wild – The Scientist

Scientists Find That Getting Multiple Tattoos Strengthens Your Immune System – Kelly Tatera – Science Explorer

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March 15, 2016

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Intrapartum antibiotics and newborn gut microbiota, the seminal fluid microbiome, and xenobiotic metabolism by gut microbes.

General microbiome

Review: The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo – Therapeutic Advances in Gastroenterology

Pregnancy and birth

Evaluation of the effects of intrapartum antibiotic prophylaxis on newborn intestinal microbiota using a sequencing approach targeted to multi hypervariable 16S rDNA regions – Irene Aloisio – Applied Microbiology and Biotechnology

Human respiratory microbiome

Neonatal Gastrointestinal and Respiratory Microbiome in Cystic Fibrosis: Potential Interactions and Implications for Systemic Health – Juliette C. Madan – Clinical Therapeutics

Review: Host-microbiome interactions in acute and chronic respiratory infections – Steven Taylor – Cellular Microbiology

Human reproductive tract microbiome

Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status – Angela B. Javurek – Scientific Reports

Human gut microbiome

Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection – Caroline Vincent – Microbiome

Upper Versus Lower Gastrointestinal Delivery for Transplantation of Fecal Microbiota in Recurrent or Refractory Clostridium difficile Infection: A Collaborative Analysis of Individual Patient Data From 14 Studies – Luis Furuya-Kanamori – Journal of Clinical Gastroenterology

Similar depletion of protective Faecalibacterium prausnitzii in psoriasis and Inflammatory Bowel Disease, but not in Hidradenitis Suppurativa – Hester Eppinga – Journal of Crohn’s and Colitis

Review: The role of the gastrointestinal tract and microbiota on uremic toxins and chronic kidney disease development – David Briskey – Clinical and Experimental Nephrology

Review: The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism – Peter Spanogiannopoulos – Nature Reviews Microbiology

Animal microbiome

Vertebrate hosts as islands: dynamics of selection, immigration, loss, persistence and potential function of bacteria on salamander skin – Andrew H. Loudon – Frontiers in Microbiology

Plant, root, and soil microbiome

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure – Felix Beulig – Nature Microbiology

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms – Jaejoon Jun – Scientific Reports

Bacterial Community Succession in Pine-Wood Decomposition – Anna M. Kielak – Frontiers in Microbiology

Cave microbiome

MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot – Surajit De Mandal – Environmental Science and Pollution Research

Water microbiome

Bacterial diversity and distribution in seven different estuarine sediments of Poyang Lake, China – Ping Sheng – Environmental Earth Sciences

Built environment microbiology

Detection of Balamuthia mandrillaris DNA in the storage case of contact lenses in Germany – Carsten Balczun – Parasitology Research

Viruses and phages

Characterization of Viral Communities of Biting Midges and Identification of Novel Thogotovirus Species and Rhabdovirus Genus – Sarah Temmam – MDPI Viruses

Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa – Joshua O. Amimo – Archives of Virology

Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition – Matthieu Galtier – Environmental Microbiology

Review: Mutualistic viruses and the heteronomy of life – Thomas Pradeu – Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences

Microbial Ecology

Engineering microbial consortia for controllable outputs – Stephen R Lindemann – ISME Journal

Review: The Anthropocene: a conspicuous stratigraphical signal of anthropogenic changes in production and consumption across the biosphere – Mark Williams – Earth’s Future

Book, all chapters written by Thomas CG Bosch and David J Miller. Not free of plagiarism and self-citing: The Holobiont Imperative: Perspectives from Early Emerging Animals – Springer

Bioinformatics and metagenomics

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data – Melanie Schirmer – BMC Bioinformatics

Microbes in the news

Bacterial biofilms in hospital water pipes may show pathogenic properties – Phys.org

Developed in Prince William, ISOThrive feeds human microbiome – Potomac Local

The first Truth is already not true: 3 Truths and a Lie About the Microbiome. Stick to the science if you want a healthy gut. – Megan Meyer – US News

The microbial death clock – Kai Kupferschmidt – Science
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March 14, 2016

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Happy Pi day! I’m currently in Europe, so today is just 14-3 here. But microbiomes are everywhere, so here we go with bacterial vaginosis in Africa, biofilms of streams and hospital shower hoses, and fungi in Chinese oil-shale mines.

Human vaginal microbiome

Can one size fit all? Approach to bacterial vaginosis in sub-Saharan Africa – Zenda Woodman – Annals of Clinical Microbiology and Antimicrobials

Human gut microbiome

Review: The diet-microbiota-metabolite axis regulates the host physiology – Takahiro Yamada – Journal of Biochemistry

Plant, root, and soil microbiome

No difference in the competitive ability of introduced and native Trifolium provenances when grown with soil biota from their introduced and native ranges – Natasha Shelby – AOB Plants

Water microbiome

Review: The ecology and biogeochemistry of stream biofilms – Tom J. Battin – Nature Reviews Microbiology

Built environment microbiome

Characterization of biofilms developing on hospital shower hoses and implications for nosocomial infections – Maria J. Soto-Giron – Applied and Environmental Microbiology

Pollution and waste microbiology

Fungal diversity in major oil-shale mines in China – Shaoyan Jiang – Journal of Environmental Sciences

More microbiology

How pneumococci lose their capsule – Andrea Du Toit – Nature Reviews Microbiology

Microbes in the news

Airplane lavatories that clean themselves? It’s happening – Karla Cripps – CNN

Self-Cleaning Airplane Toilets Are A Crappy Idea – Martin Rivers – Forbes

Fighting back from bacterial meningitis – Paul Sisson – San Diego Union Tribune

Artists create living paintings from glow-in-the-dark bacteria – Geraldine Cremin – Mashable

Deadly disease outbreak in Wisconsin baffles public health officials – Keren Landman – STAT news

Wisconsin Bacterial Infection: A Case Of The Rare Elizabethkingia – Xbox360

Is fermented food a recipe for good gut health? – Philippa Roxby – BBC

Stanford chemists develop an ultra-sensitive test for cancers, HIV – Bjorn Carey – Stanford News

Fake drugs in Nigeria: Imprisonment of 2:1 microbiology graduate – National Mirror Online

How Does Salmonella Get on Pistachios? – Linda Larsen – Food Poisoning Bulletin

How Gut Bacteria Are Shaking Up Cancer Research – Makiko Kitamura – Bloomberg

Science, publishing, and career

About Kate Rubins, who worked in our lab: Napa astronaut prepares for space station journey: four-month mission aboard ISS- Howard Yune – Napa Valley Register

The Subtle Ways Gender Gaps Persist in Science – Paul Voosen – Chronicle

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March 5, 2016

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Lung microbes in Cystic Fibrosis, microbiota of reindeer, strawberry phyllosphere, and microbes in raindust.

Pregnancy and birth

Dynamics of Gut Microbiota According to the Delivery Mode in Healthy Korean Infants – Eun Lee- Allergy Asthma Immunol Res.

Review: Respiratory Microbiome of New-Born Infants – David J. Gallacher – Frontiers in Pediatrics

Review: Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features – Silvia Arboleya – Annual Review of Food Science and Technology

Review: Maternal microbiome – A pathway to preterm birth – Angela E. Vinturache – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease – Deborah A. Hogan – PLOS ONE

Human oral microbiome

Levels of Candidate Periodontal Pathogens in Subgingival Biofilm – R.R.D.S Oliveira – Journal of Dental Research

Human gut microbiome

Effects of plant stanol ester consumption on fasting plasma oxy(phyto)sterol concentrations as related to fecal microbiota characteristics – Sabine Baumgartner – The Journal of Steroid Biochemistry and Molecular Biology

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients – Forbes, Jessica D. – Inflammatory Bowel Diseases

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis – Ohad Manor – Scientific Reports

Research highlight: Growth impairment in undernourished children – Claire Greenhill – Nature Reviews Endocrinology

Review: Elucidating the role of the host genome in shaping microbiome composition – Emily R. Davenport – Gut Microbes

Review: The Microbiome: A Key Regulator of Stress and Neuroinflammation – Kieran Rea – Neurobiology of Stress

Review: The Brain-Gut-Microbiome Axis: What Role Does it Play in Autism Spectrum Disorder? – Ruth Ann Luna – Current Developmental Disorders Reports

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: The human gut microbiome and its dysfunctions through the meta-omics prism – Stanislas Mondot – Annals of the New York Academy of Sciences

Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Effects of environmental temperature on the gut microbial communities of tadpoles – Kevin D. Kohl – Environmental Microbiology

Apple-Derived Pectin Modulates Gut Microbiota, Improves Gut Barrier Function, and Attenuates Metabolic Endotoxemia in Rats with Diet-Induced Obesity – Tingting Jiang – MDPI Nutrients

The effects of fecal microbial transplantation on microbiome and immunity in SIV-infected macaques – Tiffany Hensley-McBain – Journal of Virology

Soy Protein Compared with Milk Protein in a Western Diet Increases Gut Microbial Diversity and Reduces Serum Lipids in Golden Syrian Hamsters – Dustie N Butteiger – Journal of Nutrition

Review: The interplay between intestinal bacteria and host metabolism in health and disease: lessons from Drosophila melanogaster – Adam C. N. Wong – Disease Models & Mechanisms

Animal microbiome

New Insights into the Microbiota of the Svalbard Reindeer Rangifer tarandus platyrhynchus – Sylwia Zielińska – Frontiers in Microbiology

Geographically conserved microbiomes of four temperate water tunicates – Patrick L. Cahill – Environmental Microbiology Reports

Twenty five new viruses associated with the Drosophilidae (Diptera) – Claire L Webster – bioRxiv

Plant, root, and soil microbiome

Soil Microbial Community Interactions Under Tillage Systems in Australia – Vivian A. Rincon-Florez – Plant, Soil and Microbes

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Dispersal of Bacillus subtilis and its effect on strawberry phyllosphere microbiota under open field and protection conditions – Feng Wei – Scientific Reports

Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities – Christopher J. Barnes – Frontiers in Microbiology

Elevation gradient of soil bacterial communities in bamboo plantations – Yu-Te Lin – Botanical Studies

Soil microbial functional capacity and diversity in a millet-shrub intercropping system of semi-arid Senegal – S. Diakhaté – Journal of Arid Environments

Bioaugmentation of microbes to restore coastal wetland plants to protect land from coastal erosion – Regina Bledsoe – International Biodeterioration & Biodegradation

Review: Nutrient scavenging activity and antagonistic factors of non-photobiont lichen-associated bacteria: a review – M. Auður Sigurbjörnsdóttir – World Journal of Microbiology and Biotechnology

Water, rain, and extremophile microbiome

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin – Silke Langenheder – Environmental Microbiology Reports

Comparative summer dynamics of surface cyanobacterial communities in two connected lakes from the west of Ireland – N. Touzet – Science of The Total Environment

Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean – Ghida Nouhad Itani – Scientific Reports

Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific – Sarah K. Hu – FEMS Microbiology Ecology

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge – Julie L. Meyer – Scientific Reports

Biodigester microbiology

This one sounded wrong: Microbial diversity in an anaerobic digester with biogeographical proximity to geothermal active region – Rishi Mahajan – Environmental Technology

Food microbiology

Impact of mulches and growing season on indicator bacteria survival during lettuce cultivation – Aixia Xu – International Journal of Food Microbiology

Built environment microbiology

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center – Aaron J. Prussin II – PLOS ONE

Bioweathering Potential of Cultivable Fungi Associated with Semi-Arid Surface Microhabitats of Mayan Buildings – Benjamín O. Ortega-Morales – Frontiers in Microbiology

Microbiome of death

Review: The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death – Gulnaz T. Javan – Frontiers in Microbiology

Waste and pollution microbiology

Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils – Juan Ramos-Garza – Canadian Journal of Microbiology

Review: Understanding the development of environmental resistance among microbes: A Review – Jatin Srivastava – CLEAN – Soil, Air, Water

Review: Microbial communities, processes and functions in acid mine drainage ecosystems – Lin-xing Chen – Current Opinion in Biotechnology

Infection microbiology

Absence of Serological Evidence of Rickettsia spp., Bartonella spp., Ehrlichia spp. and Coxiella burnetii Infections in American Samoa – Colleen Lau – Ticks and Tick-borne Diseases

Comparison between a Broad-Range Real-Time and a Broad-Range End-Point PCR Assays for the Detection of Bacterial 16S rRNA in Clinical Samples – Mariam Meddeb – Annals of Clinical & Laboratory Science

Metagenomics and bioinformatics

Capturing the most wanted taxa through cross-sample correlations – Mathieu Almeida – The ISME Journal

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
Gabriele Andrea Lugli – FEMS Microbiology Letters

Sequence techniques

Microbial Ecology in the Era of Next Generation Sequencing – Surajit De Mandal – Omics: Next Generation: Sequencing & Applications

Microbial Ecology

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? – Emily B. Graham – Frontiers in Microbiology

Microbes in the news

Would you try to vaginally “seed” your baby’s microbiome after a C-section – Jonathan Eisen – The Tree of Life

Science, publishing, and career

This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter – Andrew David Thaler – Southern Friend Science

The “Creator” paper, Post-pub Peer Review, and Racism Among Scientists – Dr24hours – Complex Roots

UC reclassifies master’s degrees, charges elevated tuition – Nanette Asimov – SF Chronicle

She Wanted to Do Her Research. He Wanted to Talk ‘Feelings.’ – A. Hope Jahren – NY Times

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March 3, 2016

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Gut microbiome of Indian Nicobarese tribe, CDI patients’ stories about life before and after stool transplants, cryptic species in Nematoda, and similar fungi at opposite poles.

Pregnancy and birth

Review: The Developing Microbiome of the Preterm Infant – Mara E. DiBartolomeo – Clinical Therapeutics

Gut colonization by aerobic microorganisms is associated with route and type of nutrition in premature neonates – Ülle Parm – Nutrition Research

Human oral microbiome

Influence of a triclosan toothpaste on periodontopathic bacteria and periodontitis progression in cardiovascular patients: a randomized controlled trial – G. J. Seymour – Journal of Periodontal Research

Human respiratory microbiome

Review: Microbes and asthma: Opportunities for intervention – Hermelijn H. Smits – Journal of Allergy and Clinical Immunology

Understanding Persistent Bacterial Lung Infections: Clinical Implications Informed by the Biology of the Microbiota and Biofilms – Alexa A. Pragman – Clinical Pulmonary Medicine

Human gut microbiome

Elucidating the richness of bacterial groups in the gut of nicobarese tribal community – Perspective on their lifestyle transition – Maile Anwesh – Anaerobe

Resistant potato starches (type 4 RS) exhibit varying effects on laxation with and without phylum level changes in microbiota: A randomised trial in young adults – W.J. Dahl – Journal of Functional Foods

Recommended: Fecal microbiota transplantation for recurrent Clostridium difficile infection: The patient experience – Amy L. Pakyz – American Journal of Infection Control

Analysis of Gut Microbiome Reveals Significant Differences Between Men with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls – Daniel A. Shoskes – The Journal of Urology

RiMINI – the influence of rifaximin on minimal hepatic encephalopathy (MHE) and on the intestinal microbiome in patients with liver cirrhosis: study protocol for a randomized controlled trial – Christian Schulz – BMC Trials

Editorial: Dysbiosis in fungal microbiota in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Models of microbiome research

Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

Effect of breast feeding time on physiological, immunological and microbial parameters of weaned piglets in an intensive breeding farm – G.R. García – Veterinary Immunology and Immunopathology

Animal microbiome

Prevalence of potential nitrogen-fixing, green sulfur bacteria in the skeleton of reef-building coral Isopora palifera – Shan-Hua Yang – Limnology and Oceanography

An investigation of the microbiota in uterine flush samples and endometrial biopsies from dairy cows during the first 7 weeks postpartum – Lif Rødtness Vesterby Knudsen – Theriogenology

Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability – S Derycke – Molecular Ecology

Hologenome analysis of two marine sponges with different microbiomes – Taewoo Ryu – BMC Genomics

Plant, root, and soil microbiome

Land use change in the Amazon rainforest favors generalist fungi – Rebecca C Mueller – Functional Ecology

Drivers of phosphorus limitation across soil microbial communities – Petr Čapek – Functional Ecology

Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures – Guixiang Zhou – Scientific Reports

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Frontiers in Microbiology

Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions – María Laura Pérez – World Journal of Microbiology and Biotechnology

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches – Steven D. Leavitt – Scientific Reports

Rhizosphere competence of wild-type and genetically-engineered Pseudomonas brassicacearum is affected by the crop species – Stacey Blouin Bankhead – Phytopathology

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study – Katrina L. Callender – PLOS ONE

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs – A. Ö. C. Dupont – Environmental Microbiology

Water and extremophile microbiome

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome – Shunyan Cheung – Journal of Plankton Research

Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic – Filipa Cox – Ecology Letters

Food microbiology

Salmonella in Shell Eggs: Mechanisms, Prevention and Detection – Seockmo K – Omics Journal of Nutrition & Food Sciences

Intensive aquaculture selects for increased virulence and interference competition in bacteria – Lotta-Riina Sundberg – Proceedings of the Royal Society B

Application of electrolyzed oxidizing water in production of radish sprouts to reduce natural microbiota – Chunling Zhang – Food Control

Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions, seasonality and their spoilage potential – Nuwan R. Vithanage – International Dairy Journal

Microbiological characteristics of fresh tofu produced in small industrial scale and identification of specific spoiling microorganisms (SSO) – Franca Rossi – LWT – Food Science and Technology

Built Environment and Waste Microbiome

The efficacy of disinfectants in the decontamination of dental unit water lines: an in vitro laboratory study – Mrudula Patel – BDJ Open

Review: Bacterial communities in full-scale wastewater treatment systems – Agnieszka Cydzik-Kwiatkowska – World Journal of Microbiology and Biotechnology

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds – Mohd Faidz Mohamad Shahimin – Science of The Total Environment

Microbes in space

Two older papers that showed up in my PubMed alert today:
Review: The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond – Wilfred F.M. Röling – Astrobiology
Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions – Andrew C. Schuerger – Astrobiology

Phages and viruses

Diversity of phage infection types and associated terminology: the problem with “Lytic or Lysogenic” – Zack Hobbs – FEMS Microbiology Letters

Techniques

Effect of Freezing Conditions on Fecal Bacterial Composition in Pigs – Barbara U. Metzler-Zebeli – MDPI Animals

Microbes in the news

Astronaut Scott Kelly back on earth, Northwestern profs celebrate – Chicago Sun Times

Microbial Manifesto: The Global Push to Understand the Microbiome (Kavli Roundtable) – Alan Brown – Live Science

‘Gut’ bacteria may help put a kink in family obesity cycle – Science Codex

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