Category Archives: Pregnancy and birth

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 23, 2016

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Today’s Microbiome Digest is dedicated to my sister Charlotte, who passed away last November. It would have been her birthday today.

Pregnancy and birth

Note: no mentioning of extraction controls, many of the Salter contaminants found, figures hard to read. Proceed with caution: Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid – Maria Carmen Collado – Scientific Reports

Human skin microbiome

Effects of a New Emollient-Based Treatment on Skin Microflora Balance and Barrier Function in Children with Mild Atopic Dermatitis – Pascale Bianchi – Pediatric Dermatology

Human gut microbiome

Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults – Theresa Wan-Chen Yap – PLOS ONE

Review: Molecular Insight into Gut Microbiota and Rheumatoid Arthritis – Xiaohao Wu – MDPI International Journal of Molecular Sciences

Animal models

Lingonberries reduce atherosclerosis in Apoe-/- mice in association with altered gut microbiota composition and improved lipid profile – Chrysoula Matziouridou – Molecular Nutrition & Food Research

News and views: Barrier regulation: tolerance stops at cell death – Johanna Pott – Nature Immunology

Animal microbiome

Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species – Stephanie N. Lawler – Frontiers in Microbiology

Flow cytometry analysis of the microbiota associated with the midguts of vector mosquitoes – Tibebu Habtewold – Parasites & Vectors

Plant, root, and soil microbiome

Distribution and diversity of bacterial communities and sulfate-reducing bacteria in a paddy soil irrigated with acid mine drainage – Han Wang – Journal of Applied Microbiology

PhD thesis: The lichen-associated microbiome: taxonomy and functional roles of lichen-associated bacteria – Margrét Auður Sigurbjörnsdóttir – University of Iceland

Air microbiome

The effect of dust storms on the atmospheric microbiome in the Eastern Mediterranean – Yinon Mazar – Environmental Science & Technology

Water and extremophile microbiome

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton – Francisco M. Cornejo-Castillo – Nature Communications

More microbiology

Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic Nematode Globodera pallida to Feed on Host-Derived Sucrose – Etienne G.J. Danchin – Molecular Biology and Evolution

Viruses and phages

Discovery of unfixed endogenous retrovirus insertions in diverse human populations – Julia Halo Wildschutte – PNAS

Virological factors that increase the transmissibility of emerging human viruses – Jemma L. Geoghegan – PNAS

Bioinformatics and metagenomics

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets – Sudhir Kumar – Molecular Biology and Evolution

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data – Jaime Huerta-Cepas – Molecular Biology and Evolution

Microbes in the news

Disease Detectives Find A Really Good Reason Not To Drink Date Palm Wine – Rae Ellen Bichell – NPR

Bacteria could be speeding up the darkening of Greenland’s ice – Tim Radford – The Guardian

Unlocking the Mechanics of the Urinary Tract Infection – Lina Zeldovich – The Atlantic

Transplant in training: Journey into the Microbiome! – Karen Gardner – The Frederick News-Post

Diversifying Your Microbiome – Academic Minute with Jack Gilbert – Inside Higher Ed

Methane-Eating Bacteria Could Be a Win-Win for Reducing Emissions, Impacts of Fish Farming – Hannah Furlong – Sustainable Brands

Artificial Sweeteners: A Wolf in Sheep’s Clothing? – David A. Johnson – Medscape

Paradigm shift: ‘We need to study lumps of bacteria’ – EurekAlert

Microbial diversity and ‘unique’ cheeses – Yufan Chen – Microbe Post

Old, deep and close to home: the places that scientists are looking for new drugs – Benjamin Thompson and Matt Hutchings- Microbe Post

The bacteria that grow better in SPACE: Tests reveal a certain strain develops faster in microgravity – but no-one knows why – Sarah Griffiths – Daily Mail

Windham schools to close for two days over intestinal bacteria – Jen Steer – Fox8 Cleveland

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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 21, 2016

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Skin microbiome and cutaneous function, gut microbiota of children in Brazil, donor effects in FMT, how the gut prevents inflammation through PGE2, airborne microalgae and fungi, and bugs hiding in fruits and vegetables.

General microbiome

Review: Investigating a holobiont: Microbiota perturbations and transkingdom networks – Renee Greer – Gut Microbes

Pregnancy and birth

The effect of neutral oligosaccharides on fecal microbiota in premature infants fed exclusively with breast milk: A randomized clinical trial – Amir-Mohammad Armanian – Journal of Research in Pharmacy Practice

Perinatal Microbiomes Influence on Preterm Birth and Preterms’ Health: Influencing Factors and Modulation Strategies – Ruiz, Lorena – Journal of Pediatric Gastroenterology & Nutrition

Review: Probiotics in early life: a preventative and treatment approach
Askhan Hashemi – Food & Function

Human skin microbiome

Review: Shaping of cutaneous function by encounters with commensals – Emma Barnard – The Journal of Physiology

Human respiratory microbiome

Relevant for CF research: Volatile Compounds Emitted by Pseudomonas aeruginosa Stimulate Growth of the Fungal Pathogen Aspergillus fumigatus – Benoit Briard – mBio

Human gut microbiome

Exclusive enteral nutrition in active pediatric Crohn disease: Effects on intestinal microbiota and immune regulation – Tobias Schwerd – Journal of Allergy and Clinical Immunology

Does the donor matter? Donor vs patient effects in the outcome of a next-generation microbiota-based drug trial for recurrent Clostridium difficile infection –
Arnab Ray – Future Microbiology

Gut microbiota differences in children from distinct socioeconomic levels living in the
same urban area in Brazil – Carolina Santos Mello – Journal of Pediatric Gastroenterology and Nutrition

Review: Practical Considerations and the Intestinal Microbiome in Disease: Antibiotics for IBD Therapy – Fedorak R.N. – Digestive Diseases

Editorial: Dietary metabolism, gut microbiota and acute heart failure – WH Wilson Tang – Heart

Animal models

Prostaglandin E2 constrains systemic inflammation through an innate lymphoid cell–IL-22 axis – Rodger Duffin – Science

Detection of peptidoglycan from the gut microbiota governs the lifespan of circulating phagocytes at homeostasis – Christopher B. Hergott – Blood

Intestinal Interleukin-17 Receptor Signaling Mediates Reciprocal Control of the Gut Microbiota and Autoimmune Inflammation – Pawan Kumar – Immunity

Lymphoid-Tissue-Resident Commensal Bacteria Promote Members of the IL-10 Cytokine Family to Establish Mutualism – Thomas C. Fung – Immunity

Rhubarb extract prevents hepatic inflammation induced by acute alcohol intake, an effect related to the modulation of the gut microbiota – Audrey M. Neyrinck – Molecular Nutrition & Food Research

Impact of Ethanol and Saccharin on Fecal Microbiome in Pregnant and Non-Pregnant Mice – Matthew T Labrecque – Journal of Pregnancy Child Health

Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community – Ilma Tapio – PLOS ONE

Review: The mouse gut microbiome revisited: From complex diversity to model ecosystems – Thomas Clavel – International Journal of Medical Microbiology

Review: Reversing Gut Damage in HIV Infection: Using Non-Human Primate Models to Instruct Clinical Research – Rosalie Ponte – EBioMedicine

Animal microbiome

Variability of the Sheep Lung Microbiota – Laura Glendinning – Applied and Environmental Microbiology

Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform – Si Hong Park – PLOS ONE

The Bacterial Community of Entomophilic Nematodes and Host Beetles – Sneha L. Koneru – Molecular Ecology

Plant, root, and soil microbiome

An Unusual Inverted Saline Microbial Mat Community in an Interdune Sabkha in the Rub’ al Khali (the Empty Quarter), United Arab Emirates – Christopher P. McKay – PLOS ONE

Effects of long term rice straw application on the microbial communities of rapeseed rhizosphere in a paddy-upland rotation system – Caijuan Peng – Science of the Total Environment

Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits –
L Bordez – Molecular Ecology

Arbuscular mycorrhizal fungi in Mimosa tenuiflora (Willd.) Poir from Brazilian semi-arid – Tancredo Augusto Feitosa de Souza – Brazilian Journal of Microbiology

The impact of tropical forest logging and oil palm agriculture on the soil microbiome – Binu M. Tripathi – Molecular Ecology

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

Decreasing Nitrogen Fertilizer Input Had Little Effect on Microbial Communities in Three Types of Soils – Hailing Yu – PLOS ONE

H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups – Sarah Piché-Choquette – PeerJ

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments – Lidianne L. Rocha – International Journal of Microbiology

Water and extremophile microbiome

An association network analysis among microeukaryotes and bacterioplankton reveals algal bloom dynamics – Shangjin Tan – Journal of Phycology

More, smaller bacteria in response to ocean’s warming? – Xosé Anxelu G. Morán – Proceedings of the Royal Society B

All of these are 16S rRNA gene amplicon based:
Profiling of microbial community of Odisha hot spring based on metagenomic sequencing – Archana Singh – Genomics Data
Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach – Archana Singh – Genomics Data
Structural insights of microbial community of Deulajhari (India) hot spring using 16s-rRNA based metagenomic sequencing – Archana Singh – Genomics Data
Metagenomic exploration of the bacterial community structure at Paradip Port, Odisha, India – Arnab Pramanik – Genomics Data

Air microbiome

Review: Airborne Microalgae: Insights, Opportunities, and Challenges – Sylvie V. M. Tesson – Applied and Environmental Microbiology

Airborne and Grain Dust Fungal Community Compositions Are Shaped Regionally by Plant Genotypes and Farming Practices – Loïc Pellissier – Applied and Environmental Microbiology

Waste and pollution microbiology

Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments – Emine Ertekin – Environmental Science & Technology

Managing microbial risks from indirect wastewater reuse for irrigation in urbanizing watersheds – Matthew Eric Verbyla – Environmental Science & Technology

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress – Daiana Lima-Morales – Applied and Environmental Microbiology

Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome – Daniel E. Ross – PLOS ONE

Sediment Bacterial Communities Associated with Anaerobic Biodegradation of Bisphenol A – Yuyin Yang – Microbial Ecology

Bioreactor microbiology

Nitrification at different salinities: Biofilm community composition and physiological plasticity – Blanca M. Gonzalez-Silva – Water Research

In vitro extraction and fermentation of polyphenols from grape seeds (Vitis vinifera) by human intestinal microbiota – Li Zhou – Food & Function

Food microbiology

Hiding in Fresh Fruits and Vegetables: Opportunistic Pathogens May Cross Geographical Barriers – Zahra S. Al-Kharousi – International Journal of Microbiology

Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food – Peng Chen – Genomics Data

More microbiology

Multispecies Swarms of Social Microorganisms as Moving Ecosystems – Eshel Ben-Jacob – Trends in Microbiology

A Deadly Path: Bacterial Spread During Bubonic Plague – Rodrigo J. Gonzalez – Trends in Microbiology

Correspondence: Bacterial Persistent Infection at the Interface between Host and Microbiota – Min Yue – Clinical Infectious Diseases

Microbes in the news

Immune study shows how gut keeps deadly infections at bay – Science Daily

Bacteria’s Achilles heel uncovered by single molecule chemistry – Phys.org

Tiny algae could block Metro Vancouver’s Roberts Bank container expansion. Migrating sandpipers depend on biofilm secreted by microscopic diatoms for fuel – Larry Pynn – Vancouver Sun

Systemic Antibody Responses To Oral Bacteria With Aging, University of Kentucky Study – BioSpace
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March 20, 2016

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Back in the PDT, so catching up with the literature.

Pregnancy and birth

In mice: The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Review: New techniques to characterise the vaginal microbiome in pregnancy – George L. Mendz – AIMS Microbiology

Perspective: The Placental Microbiome: A New Site for Policing Women’s Bodies – Saray Ayala – International Journal of Feminist Approaches to Bioethics

Review: Building a Beneficial Microbiome from Birth – Esther Castanys-Muñoz – Advances in Nutrition

Human oral microbiome

Microbiome associated with severe caries in Canadian First Nations children – EurekAlert

Comparative analysis of bacterial profiles in unstimulated and stimulated saliva samples – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

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

Helicobacter pylori Eradication Causes Perturbation of the Human Gut Microbiome in Young Adults – Theresa Wan-Chen Yap – PLOS ONE

FODMAPs alter symptoms and the metabolome of patients with IBS: a randomised controlled trial – Keith McIntosh – Gut

Tumour-associated and non-tumour-associated microbiota in colorectal cancer – Burkhardt Flemer – Gut
Review: Microbiota and lifestyle interactions through the lifespan – Simone Rampelli – Trends in Food Science & Technology

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanism and Application of Metabolomics – Xuyun He – Int J Mol Sci

Animal models

Effect of artesunate supplementation on bacterial translocation and dysbiosis of gut microbiota in rats with liver cirrhosis – Yun-Xia Chen – World Journal of Gastroenterology

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

Animal microbiome

Cuticular bacteria appear detrimental to social spiders in mixed but not monoculture exposure – Carl N. Keiser – Current Zoology

Review: Microbial diversity associated with ascidians: a review of research methods and application – Lei Chen – Symbiosis

Plant, root, and soil microbiome

Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity – Binu M. Tripathi – Frontiers in Microbiology

Spatial variability of microbial richness and diversity and relationships with soil organic carbon, texture and structure across an agricultural field – Muhammad Naveed – Applied Soil Ecology

Microbial community structure and nutrient dynamics in forest soils colonized by bracken fern (Pteridium aquilinum) – Manuel Aira – PeerJ Preprint

Evidence of horizontal gene transfer between obligate leaf nodule symbionts – Marta Pinto-Carbó – The ISME Journal

Bacteria-Soil-Plant Interaction: This Relationship to Generate can Inputs and New Products for the Food Industry – Jeremias Pakulski Panizzon – Rice Research

Microbial growth and community structure in acid mine soils after addition of different amendments for soil reclamation – R. Zornoza – Geoderma

Water and extremophile microbiome

Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy – Amy R. Smith – Geomicrobiology Journal

Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy – Emil S. Ruff – Frontiers in Microbiology

Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge – Xinxu Zhang – Frontiers in Microbiology

Built environment microbiology

Qualitative and Quantitative Analysis of Microbial Communities in Household Dishwashers in Germany – Britta Brands – Tenside Surfactants Detergents

Waste and pollution microbiology

Degradation of oxytetracycline and its impacts on biogas-producing microbial community structure – Halil Coban – Bioprocess and Biosystems Engineering

Diversity of arsenite oxidase gene and arsenotrophic bacteria in arsenic affected Bangladesh soils – Santonu Kumar Sanyal

Techniques

Example used in this review paper: kombucha (?): DNA metabarcoding of microbial communities for healthcare – Zaets I. Ye – Biopolym Cell

Next-Generation Sequencing in the Mycology Lab – Jan Zoll – Current Fungal Infection Reports

Metagenomics

Identification of virulence factors and antibiotic resistance markers using bacterial genomics – Sofiane Bakour – Future Medicine

Microbes in the news

Gut health: Stanford researchers explain how what’s in our bellies affects myriad health issues – Martha Ross – Contra Costa Times

Inflamed, noninflamed mucosal microbiota differ between patients with Crohn’s disease, UC – Healio

Video: Six Strange Things Bacteria Eat – Wall Street Journal

Bacteria in your mom’s gut may have influenced the way you fight off infections today
Katherine Ellen Foley – Quartz

New technique for rapidly killing bacteria using tiny gold disks and light – Nanowerk

Bacteria-powered Bio-Bots Avoid Obstacles on Way to Target – MedGadget

Pneumonia, middle ear infections might be prevented by diverse bacteria in gut microbiome – Emily Lunardo – Belmarra Health

Going viral: IU Southeast student, teacher discover a new type of virus
Student, professor find new bacteriophage in Ohio River – Jerod Clapp – News and Tribune

Brucellosis-causing bacteria could be dropped from bioterrorism list – Helenair

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March 17, 2016

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Metagenomics of Necrotizing Enterocolitis, sinus irrigation, variation in mice in German facilities, and bacteria vs phage.

Pregnancy and birth

The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants – Doyle V. Ward – Cell Reports

Human respiratory microbiome

Evaluation of bacterial transmission to the paranasal sinuses through sinus irrigation – Leah J. Hauser – International Forum of Allergy & Rhinology

Human gut microbiome

Fecal Microbiota Transplantation in Children: A Brief Review – Suchitra K Hourigan – Pediatric Research

Forum: Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota – Tom Konikoff – Trends in Microbiology

Commentary: Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections – Richard L. Gallo – Journal of the American Academy of Dermatology

Review: Low calorie sweeteners and gut microbiota – Kristian Daly – Physiology & Behavior

Animal models

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities – Philipp Rausch – International Journal of Medical Microbiology

Plant, soil, and root microbiome

Plant versus microbial controls on soil aggregate stability in a seasonally dry ecosystem – Joseph C. Blankinship – Geoderma

Soil microbial communities following bush removal in a Namibian savanna – Jeffrey S. Buyer – Soil

Monitoring benthic microflora in river bed sediments: a case study in the Anllóns River (Spain) – Diego Martiñá Prieto – Journal of Soils and Sediments

Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States – Erin A. Tripp – Journal of Biogeography

Viruses and phages

Classic Spotlight: Bacteria versus Phage—the Battle Rages! – Tina M. Henkin – Journal of Bacteriology

Techniques

Review: Confocal Microscopy Imaging of the Biofilm Matrix – Sebastian Schlafer – Journal of Microbiological Methods

Metabolomics

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

Review: Challenges of metabolomics in human gut microbiota research – Kirill S. Smirnov – International Journal of Medical Microbiology

Microbes in the News

Subset of E. coli bacteria linked to deadly disease in pre-term infants – Medical Xpress

Our gut microbiome is always changing; it’s also remarkably stable – Science Codex

Meeting report: Microbes in the City: Mapping the Urban Genome – New York Academy of Sciences

Viral Infections May Affect Cystic Fibrosis Patients’ Respiratory Microbiome, Study Says – Daniela Semedo – Lung Disease News

Diverse diets enrich gut microbes – Catharine Paddock – Medical News Today

Mother’s Microbiome Shapes Offspring’s Immunity – The maternal gut microbiome guides neo- and postnatal immune system development, a mouse study shows – Anna Azvolinsky – The Scientist

How bacteria get their magnetic compass – Robert Sanders – Berkeley News

Science, publishing, and career

Blogging for beginners – Andrew David Thaler – Science

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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 13, 2016

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General microbiome

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

Pregnancy and birth / Human vaginal microbiome

Review: The vaginal microbiota, host defense and reproductive physiology – Steven B Smith – The Journal of Physiology

Human gut microbiome

Review: Brain-Gut-Microbiota axis: Challenges for Translation in Psychiatry – John R. Kelly – Annals of Epidemiology

Editorial: The microbiome in celiac disease: Beyond diet-genetic interactions – Jose U. Scher – Cleveland Clinic Journal of Medicine
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

Heat-treated high-fat diet modifies gut microbiota and metabolic markers in apoe−/− mice – Nittaya Marungruang – Nutrition & Metabolism

Animal microbiome

Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee – Quinn S. McFrederick – Molecular Ecology

Plant, root, and soil microbiome

Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season – Dinggang Zhou – Frontiers in Plant Science

Succession of soil microbial communities and enzyme activities in artificial soils – Franziska Ditteric – Pedobiologia

Effect of copper and zinc on microbial tolerance to triclosan in two soil types – Gerty J. H. P. Gielen – Journal of Soils and Sediments

Microbial enzymes as an early warning management tool for monitoring mining site soils – Mohammad Wahsha – CATENA

Water and glacier microbiome

Bacterial communities potentially involved in iron-cycling in Baltic Sea and North Sea sediments revealed by pyrosequencing – Carolina Reyes – FEMS Microbiology Ecology

The Differing Biogeochemical and Microbial Signatures of Glaciers and Rock Glaciers – Timothy S. Fegel – Journal of Geophysical Research

Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon – Florent E. Angly – PeerJ

Infection microbiology

Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans – Salah Zangena – Scientific Reports

Viruses

RNA viruses as major contributors to Antarctic virioplankton – Jaclyn A Miranda – Environmental Microbiology

Review: Giant viruses of amoebas: an update – Sarah Aherfi – Frontiers in Microbiology

Microbial Ecology

Review: Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts – George Hajishengallis – Trends in Microbiology

Metagenomics and bioinformatics

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly – Paola Bonizzoni – Journal of Computational Biology

Microbes in the news

Cool Citizen Microbiology Project in Spain With Great Engagement – David Coil – Microbenet

Podcast: The Bacteria Behind Your Favorite Blues, Bries, and More – Science Friday

Science, publishing and career

Scientists who tweet: 3 Fred Hutch researchers talk about getting #science out into the world, 140 characters at a time – Mary Engel – Fred Hutch

This Student Adds A Woman In Science To Wikipedia Every Time She’s Harassed Online – Kelly Oakes – BuzzFeed

Bik’s Picks

Neandertals’ large lower thorax may represent adaptation to high protein diet – Miki Ben-Dor – American Journal of Physical Anthropology

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