Category Archives: Waste and pollution

April 5, 2016

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Differences in myelination and gene expression in prefrontal cortex between GF and conventional mice, migratory passerines, metagenomics of probiotics, and megaviromes.

Events

NAS Meeting: Microbiomes of the Built Environment: From Research to Application – David Coil – MicroBEnet

Human oral microbiome

Impact of age and sex on the composition and abundance of the intestinal microbiota in individuals with and without enteric infections – Pallavi Singh – Annals of Epidemiology

Review [PDF]: Oral Microbial Shift: Factors affecting the Microbiome and Prevention of Oral Disease – Namrata Dagli – Journal of Contemporary Dental Practice

Human reproductive tract microbiome

Review: Incorporating microbiota data into epidemiological models: Examples from vaginal microbiota research – Janneke van de Wijgert – Annals of Epidemiology

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

Human gut microbiome

Diversified mcr-1-Harbouring Plasmid Reservoirs Confer Resistance to Colistin in Human Gut Microbiota – Huiyan Ye – mBio

Animal models

Regulation of prefrontal cortex myelination by the microbiota – AE Hoban – Translational Psychiatry

Responses of fecal bacterial communities to resistant starch intervention in diabetic rats – Zhongkai Zhou – Starch

Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota – Ming-liang Chen – mBio

Commentary: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

Animal microbiome

Sample processing impacts the viability and cultivability of the sponge microbiome – Ana I. Esteves – Frontiers in Microbiology

Characterization of the gut microbiota of migratory passerines during stopover along the northern coast of the Gulf of Mexico – William B. Lewis – Journal of Avian Biology

Highlight: Microbes matter: herbivore gut endosymbionts play a role in breakdown of host plant toxins – Franziska Beran – Environmental Microbiology

Selective feeding by the giant barrel sponge enhances foraging efficiency – Steven E. McMurray – Limnology and Oceanography

PhD Thesis: Molecular investigation of Australian termites and their gut symbionts – Nurdyana Abdul Rahman – University of Queensland

Plant, root, and soil microbiome

Distance-dependent effects of pathogenic fungi on seedlings of a legume tree: impaired nodule formation and identification of antagonistic rhizosphere bacteria –  Lan Liu – Journal of Ecology

Bacterial community dynamics during ensiling of perennial ryegrass at two compaction levels monitored by terminal restriction fragment length polymorphism – K. Graf – Journal of Applied Microbiology

Microsite differentiation drives the abundance of soil ammonia oxidizing bacteria along aridity gradients – Manuel Delgado-Baquerizo – Frontiers in Microbiology

Not exactly microbes but sounded interesting: Do tropical rain forest soils have greater nematode diversity than High Arctic tundra? A metagenetic comparison of Malaysia and Svalbard – Dorsaf Kerfahi – Global Ecology and Biogeography

Use of two spatially separated plant species alters microbial community function in horizontal subsurface flow constructed wetlands – Mark Button – Ecological Engineering

Water microbiome

Spatio-temporal interdependence of bacteria and phytoplankton during a Baltic Sea spring bloom – Carina Bunse – Frontiers in Microbiology

Protist-bacteria associations: Gammaproteobacteria and Alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa – Jun Gong – Frontiers in Microbiology

Particulate matter stoichiometry driven by microplankton community structure in summer in the Indian sector of the Southern Ocean – M. Rembauville – Limnology and Oceanography

Waste and pollution microbiome

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases – Laura Terrón-González – Applied and Environmental Microbiology

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community – Christopher L. Hemme – mBio

Built environment microbiome

A novel, optical, on-line bacteria sensor for monitoring drinking water quality – Bo Højris – Scientific Reports

Food and probiotics microbiology

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing – Jennifer N. Patro – mSphere

Unravelling the effect of clostridia spores and lysozyme on microbiota dynamics in Grana Padano cheese: A metaproteomics approach – Alessio Soggiu – Journal of Proteomics

Viruses and phages / metagenomics

VIP: an integrated pipeline for metagenomics of virus identification and discovery – Yang Li – Scientific Reports

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics – Ali H. A. Elbehery – OMICS

Themed Issue of Current Opinion in Microbiology: Environmental microbiology/Megaviromes
Review: Giants among larges: how gigantism impacts giant virus entry into amoebae – Rodrigo Araújo Lima Rodrigues – Current Opinion in Microbiology
Review: Updating strategies for isolating and discovering giant viruses – Jacques Yaacoub Bou Khalil
Review, but not sure about what: Persistent virus and addiction modules: an engine of symbiosis – Luis P Villarreal

Metabolomics

In silico methods for linking genes and secondary metabolites: The way forward – Shradha Khater – Synthetic and Systems Biotechnology

Techniques and bioinformatics

It’s all relative: analyzing microbiome data as compositions – Gregory B. Gloor – Annals of Epidemiology

Not metagenomics but about a not-clearly defined 16S rRNA gene amplification pipeline. Not a good paper: Snapshot on a pilot metagenomic study for the appraisal of gut microbial diversity in mice, cat and men – Coline Plé – Gastroenterology Research and Practice

More microbiology

Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium – Jiajiao Li – Anaerobe

Cholesterol Analogs with Degradation-resistant Alkyl Side Chains Are Effective Mycobacterium tuberculosis Growth Inhibitors – Daniel J. Frank – The Journal of Biological Chemistry

Microbiology and art

This Artist Paints With Bacteria, And It’s Strangely Beautiful – Jacqueline Howard – Huffington Post

Microbes in the news

With a quote from me! Gut bacteria regulate nerve fibre insulation – Mo Costandi – The Guardian

Europe’s Microbiology Society’s Annual Conference 2016: the Twitter story – Microbepost

Antibiotic soap can alter a baby’s gut bacteria – Tim Sandle – Digital Journal

The fridge that detects bacteria in your food – NZ Herald

About COPD: Take a deep breath – your lung microbiome will appreciate it – GSK

Microbiome and the modern environment: a global drift toward dysbiosis? – Susan Prescott and Alan Logan – BioMed Central blog

Biofilm researcher: New Faces: Boo Shan Tseng: This Life Sciences professor is all about communities – University of Nevada, Las Vegas

Study by the University of Kaiserslautern: Viruses cause bacteria to produce pink pigments – AlphaGalileo

Promising new method inhibits TB–causing bacteria – Phys.org

Bacteria Hysteria

Do you know how clean your lean workout is? The DEADLY bacteria found in your gym mat – Kat Romero – Express

Bik’s Picks

Cellular telephone use during free-living walking significantly reduces average walking speed – Jacob E. Barkley – BMC Research Notes

So cool: The Cemetery as Archive: A 177-year-old cemetery is preparing to digitize millions of records that shed light on New York City’s shifting demographics – Jessica Leigh Hester

April 4, 2016

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Gut microbiome of Australian sea lions, Trichoderma fungi in endemic plants, and digging for microbial proof of Hannibal’s route over the alps.

Human vaginal microbiome

Comment: Translating the vaginal microbiome: gaps and challenges – Jacques Ravel – Genome Medicine

Human respiratory microbiome

Review: The lung microbiome: the perfect culprit for COPD exacerbations? – Carine Gomez – European Respiratory Journal

Animal models

Frogs: Short-term exposure to coal combustion waste has little impact on the skin microbiome of adult spring peepers, Pseudacris crucifer – Myra C. Hughey – Applied and Environmental Microbiology

Short bowel syndrome (SBS)-associated alterations within the gut-liver axis evolve early and persist long-term in the piglet model of short bowel syndrome – Prue M. Pereira-Fantini – Journal of Gastroenterology and Hepatology

Maternal Antibiotic Treatment Impacts Development of the Neonatal Intestinal Microbiome and Antiviral Immunity – Gabriela Gonzalez-Perez – The Journal of Immunology

Generation and Characterization of Indoor Fungal Aerosols for Inhalation Studies – Anne Mette Madsen – Applied and Environmental Microbiology

Correspondence: The premature invocation of a ‘gut-lung axis’ may obscure the direct effects of respiratory microbiota on pneumonia susceptibility – Robert P Dickson – Gut

Animal microbiome

Colony location and captivity influence the gut microbial community composition of the Australian sea lion (Neophoca cinerea) – Tiffany C. Delport – Applied and Environmental Microbiology

DGGE: Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca) – Zhirong Peng – World Journal of Microbiology and Biotechnology

Germs within Worms: Localization of Neorickettsia sp. within Life Cycle Stages of the Digenean Plagiorchis elegans – Stephen E. Greiman – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes – Jinping Zhang – World Journal of Microbiology and Biotechnology

Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens – Christin Zachow – Journal of Biotechnology

Water microbiome

Diverse and temporally-variable particle-associated microbial communities are insensitive to bulk seawater environmental parameters – Cheuk-Man Yung – Applied and Environmental Microbiology

Pollution and waste microbiology

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

Biofilm and Planktonic Bacterial and Fungal Communities Transforming High-Molecular-Weight Polycyclic Aromatic Hydrocarbons – Benjamin D. Folwell – Applied and Environmental Microbiology

Microbes and art

These petri dish “paintings” reveal the hidden beauty of bacteria – Julia Belluz – Vox

After Effects: A series of architectural scale models constructed with black paper and covered with flour and a layer of mould to create the effect of old abandoned buildings – Daniele Del Nero.

Microbes in the news

Scarlett Fever: A 19th-century disease is on the rise in the UK—and nobody knows why – Akshat Rathi – Quartz

The truth about Hannibal’s route across the Alps. How exactly did the Carthaginian general and his elephants reach Italy? Scientists have got their hands dirty to come up with an answer – Philip Ball – The Guardian

Gender differences in antibiotic prescribing in the community: a systematic review and meta-analysis – Wiebke Schröder – Journal of Antimicrobial Chemotherapy

Microbes Meet Cancer. Understanding cancer’s relationship with the human microbiome could transform immune-modulating therapies – Kate Yandell – The Scientist

Guts and Glory. An open mind and collaborative spirit have taken Hans Clevers on a journey from medicine to developmental biology, gastroenterology, cancer, and stem cells – Anna Azvolinsky – The Scientist

Science, pubilishing, and career

Medscape Physician Compensation Report 2016 – Carol Peckham – MedScape

Bik’s Picks

It turns out this planet has three suns in its sky – Rachel Feltman – Washington Post

April 2, 2016

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Yes, it is technically already April 3, but I only got to do the daily roundup late tonight, so I did not quite get it done in time. C-section and weight influence on infant colonization, dachshunds, crops selecting fungi, post-mortem microbial transmigration

Pregnancy and birth

Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome – Noel T. Mueller – Scientific Reports

Study provides evidence that “vaginal seeding” of infants born by caesarean partially restores microbiota – Amali Lokugamage – BMJ

Relationship between milk microbiota, bacterial load, macronutrients and human cells during lactation – Alba Boix-Amoros – Frontiers in Microbiology

Mode of Delivery Determines Neonatal Pharyngeal Bacterial Composition and Early Intestinal Colonization – David E. Brumbaugh – Journal of Pediatric Gastroenterology & Nutrition

Effect of Formula Containing Lactobacillus Reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section – Rodenas, Clara L. Garcia – Journal of Pediatric Gastroenterology & Nutrition

Human oral microbiome

Mucosal and salivary microbiota associated with recurrent aphthous stomatitis – Yun-ji Kim- BMC Microbiology

Assessment of oral malodor and tonsillar microbiota after gargling with benzethonium chloride – Yuki Iwamura – Journal of Oral Science

Potential screening and early diagnosis method for cancer: Tongue diagnosis – Shuwen Han – International Journal of Oncology

In vitro: A dual-species microbial model for studying the dynamics between oral streptococci and periodontal pathogens during biofilm development on titanium surfaces by flow cytometry – Anita Manti – Research in Microbiology

Human gut microbiome

Changes in fecal microbiota and metabolomics in a child with juvenile idiopathic arthritis (JIA) responding to two treatment periods with exclusive enteral nutrition (EEN) – Lillemor Berntson – Clinical Rheumatology

Renal Failure due to Excessive Intake of Almonds in the Absence of Oxalobacter formigenes – Yngvar Lunde Haaskjold – The American Journal of Medicine

Reanalysis of published data, no apparent new findings: Host genetics is associated with the gut microbial community membership rather than the structure – Peihua Zhao – Molecular BioSystems

Review: Modulatory Effects of Gut Microbiota on the Central Nervous System: How Gut Could Play a Role in Neuropsychiatric Health and Diseases – Shadi S Yarandi – Journal of Neurogastroenterology and Motility

Commentary: Can microbiota research change our understanding of neurodegenerative diseases? – Filip Scheperjans – Neurodegenerative Disease Management

Review: Microbes and the mind: emerging hallmarks of the gut microbiota–brain axis
– Kylynda C. Bauer – Cellular Microbiology

Animal models

Distinctly altered gut microbiota in the progression of liver disease – Guoxiang Xie – Oncotarget

Wolbachia confers sex-specific resistance and tolerance to enteric but not systemic bacterial infection in Drosophila – Radhakrishnan B Vasanthakrishnan – BioRxiv

Gut Microbiota and a Selectively Bred Taste Phenotype: A Novel Model of Microbiome-Behavior Relationships – Lyte, Mark – Psychosomatic Medicine

Periodontal dysbiosis linked to periodontitis is associated with cardio-metabolic adaptation to high-fat diet in mice – Maxime Branchereau – American Journal of Physiology Gastrointestinal and Liver Physiology

Protocol: The Gut Microbiome in the NOD Mouse – Jian Peng – Part of the series Methods in Molecular Biology

Animal microbiome

Fecal dysbiosis in miniature dachshunds with inflammatory colorectal polyps – Hirotaka Igarashi – Research in Veterinary Science

Plant, root, and soil microbiome

Differential response of ammonia-oxidizing archaea and bacteria to the wetting of salty arid soil – Yonatan Sher – Journal of Basic Microbiology

Selection of fungi by candidate cover crops – Maria-Soledad Benitez – Applied Soil Ecology

Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils – Ellen Latz – Scientific Reports

Water and extremophile microbiome

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau – Weigang Hu – Extremophiles

Seasonal and Spatial Changes of Planktonic Bacterial Communities Inhabiting the Natural Thermal Lake Hévíz, Hungary – Gergely Krett – Acta Microbiologica et Immunologica Hungarica

Microbiome of Death

Fluorescently labeled bacteria provide insight on post-mortem microbial transmigration –
Z.M. Burcham – Forensic Science International

Food microbiology

Review: Hygienic characteristics and microbiological hazard identification in horse and donkey raw milk – Giampaolo Colavita – Veterinaria Italiana

Waste and pollution microbiology

Microbial communities in riparian soils of a settling pond for mine drainage treatment – Miaochun Fan – Water Research

Metagenomic analysis shows diverse, distinct bacterial communities in biofilters among different marine recirculating aquaculture systems – Zhitao Huang – Aquaculture International

More microbiology

Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis – Sabrina Duranti – Scientific Reports

Metagenomics and bioinformatics

Not sure if this is a good approach; ignores variation between individual human microbiome strains: Reconstruction of bacterial and viral genomes from multiple metagenomes – Vineet K. Sharma – Frontiers in Microbiology

Metabolomics

Harnessing the power of microbial metabolism – Eduardo Santero – Current Opinion in Microbiology

Microbiology and art

BioArt: Joana Ricou shows the Beautiful Similarities of the Microbiome – Labiotech

Rap song: CosmosID Metagenomics: Exploring the Universe of Microbes – CosmosID – YouTube

Microbes in the news

Mythbusters: Human Microbiota – Caroline Ayinon – Yale Scientific

Introducing the “HomeGenome”. Not endorsing this. Exploring the Microcosm Within. Adventures and insights from the microbiome – Conan Milner – Epoch Times

April Fool’s Day microbiome jokes

Thanks to Microbiome Boost, Donuts May Be Beneficial: when paired with P. tursiops – Tim De Chant – PBS

A microbiology of the built environment April Fools’ joke – Jonathan Eisen – MicroBEnet

And of course my own selection: Human-derived microbial strains used for food and beverage production – Elisabeth Bik – Microbiome Digest

Science, publishing, and career

‘Lab Girl’ Is a Fierce, Uplifting, Must-Read Memoir – Hope Jahren is an acute observer, prickly, and funny as hell. – Elizabeth Royte – Elle

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 25, 2016

Posted on by

A minimal bacterial genome, gut microbes/TMAO/platelets, (pro)phages and genomes, Top 50 unidentified fungi, and Propionibacterium acnes as a contaminant.

General microbiome

Review: Speciation by Symbiosis: The Microbiome and Behavior – J. Dylan Shropshire – BioRxiv

Human gut microbiome
Research highlight: Gut microbes modulate platelet function and thrombosis risk – Irene Fernández-Ruiz – Nature Reviews Cardiology

Combination of human and mouse studies: Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk – Weifei Zhu – Cell

Animal microbiome

Comparison of Fecal Microbiota between German Holstein Dairy Cows with and without Left-Sided Displacement of the Abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Plant, root, and soil microbiome

Infection with a Shoot-Specific Fungal Endophyte (Epichloë) Alters Tall Fescue Soil Microbial Communities – Xavier Rojas – Microbial Ecology

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

Spatial and temporal variation of cultivable communities of co-occurring endophytes and pathogens in wheat – Morgane Comby – Frontiers in Microbiology

Plant Growth-Promoting Rhizobacteria Inoculation to Enhance Vegetative Growth, Nitrogen Fixation and Nitrogen Remobilisation of Maize under Greenhouse Conditions – Khing Boon Kuan – PLOS ONE

Microbial control of soil organic matter mineralisation responses to labile carbon in subarctic climate change treatments – Kathrin Rousk – Global Change Biology

Water microbiome

Effects of temperature and nutrients on changes in genetic diversity of bacterioplankton communities in a semi-closed bay, South Korea – Hyun Jung Kim – Marine Pollution Bulletin

Built environment microbiome

Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities – Kristian Brat – Polish Polar Research

Waste and pollution microbiome

Consistency between health risks and microbial response mechanism of various petroleum components in a typical wastewater-irrigated farmland – Juan Zhang – Journal of Environmental Management

Metagenomics and bioinformatics

DUDes: a top-down taxonomic profiler for metagenomics – Vitor C. Piro – Bioinformatics

Viruses

Genetic and life-history traits associated with the distribution of prophages in bacteria – Marie Touchon – The ISME Journal

Hyperexpansion of RNA Bacteriophage Diversity – Siddharth R. Krishnamurthy – PLOS Biology

Fungi

Top 50 most wanted fungi – Henrik Nilsson – MycoKeys

Book: Biology of Microfungi – Editors: De-Wei Li – Springer

Book: The Mycota: Environmental and Microbial Relationships – Editors: Irina S. Druzhinina, Christian P. Kubicek – Springer

Techniques

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples – Andries E. Budding – Journal of Clinical Microbiology

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing – Sarah Mollerup

More microbiology

531 kb (473 genes): Design and synthesis of a minimal bacterial genome – Clyde A. Hutchison III – Science

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv preprint

Microbes in the news

This man-made cell has the smallest genome ever — but a third of its genes are a mystery – Rachel Feltman – Washington Post

The Mysterious Thing About a Marvelous New Synthetic Cell – Ed Yong – The Atlantic

After 20 Year Quest, Biologists Create Synthetic Bacteria With No Extra Genes – Matthew Herper – Forbes

Scientists Create Tiniest Life Form Yet, Not Sure What It Is – Eric Roston – Bloomberg

Microbes can play games with the mind – Laura Sanders – Science News

SDSU researcher examines link between gut bacteria and metabolic disease – Adriana Millar – The Daily Aztec

What gut bacteria can teach us about cancer treatment: Studies probe link between gut bacteria and treatment effectiveness – Jenn Savedge – Mother Nature Network

Elizabethkingia: Senator seeks answers from CDC on mystery bacteria – Jonathan Stefonek – Daily Register

Study finds vast diversity among viruses that infect bacteria – EurekAlert

Bik’s Picks

Comb jelly ‘anus’ guts ideas on origin of through-gut – Amy Maxmen – Science

Funding Freeze Hits Natural History Museum Collections – Ed Yong – The Atlantic
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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 21, 2016

Posted on by

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

Posted on by

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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