Category Archives: Food Microbiology

April 22, 2016

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General microbiome

Nutrigenomics, the Microbiome, and Gene-Environment Interactions: New Directions in Cardiovascular Disease Research, Prevention, and Treatment
A Scientific Statement From the American Heart Association – Jane F. Ferguson – Circulation: Cardiovascular Genetics

Human skin and eye microbiome

Commentary: Details Matter: Designing Skin Microbiome Studies – Heidi H. Kong – Journal of Investigative Dermatology

Defining the normal “core microbiome” of conjunctival microbial communities – Yusen Huang – Clinical Microbiology and Infection

Supplement with abstracts for the American Academy of Dermatology 74th Annual Meeting – Journal of the American Academy of Dermatology

Supplement with abstracts for the Society for Investigative Dermatology (SID 2016) Annual Meeting – Journal of Investigative Dermatology

Human gut microbiome

Strain-level dissection of the contribution of the gut microbiome to human metabolic disease – Chenhong Zhang – Genome Medicine

Review: Microbiome alterations in HIV infection a review – Brett Williams – Cellular Microbiology

Review? Does Gut Microbiota Affect Endothelial Functions in Chronic Kidney Disease Patients With Type 2 Diabetes Mellitus? – American Journal of Kidney Diseases

Commentary: The return of microbes – Didier Raoult – Clinical Microbiology and Infection

Review: Use your antibiotics wisely. Consequences to the intestinal microbiome – Jorge Cervantes – FEMS Microbiology Letters

Review: The Microbiome, Timing, and Barrier Function in the Context of Allergic Disease – Duane R. Wesemann – Immunity

Animal and in vitro models
Cigarette Smoke Attenuates the Nasal Host Response to Streptococcus pneumoniae and Predisposes to Invasive Pneumococcal Disease in Mice – Pamela Shen – Infection and Immunity

Susceptibility to Ticks and Lyme Disease Spirochetes Is Not Affected in Mice Coinfected with Nematodes – Denny Maaz – Infection and Immunity

Adherence of probiotic bacteria to human colon epithelial cells and inhibitory effect against enteric pathogens – In vitro study – Nowak Adriana – International Journal of Dairy Technology

Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior – Mar Gacias – eLIFE

Gut Microbiota Drive Autoimmune Arthritis by Promoting Differentiation and Migration of Peyer’s Patch T Follicular Helper Cells – Fei Teng – Immunity

Preview: Viral Safeguard: The Enteric Virome Protects against Gut Inflammation – Stephanie M. Karst – Immunity

Animal microbiome

Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate – Amrita Srivathsan – Frontiers in Zoology

Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India – S. S. Charan – Medical and Veterinary Entomology

Minireview: The Sponge Hologenome – Nicole S. Webster – mBio

Water and extremophile microbiome

Response of Antarctic cryoconite microbial communities to light – Elizabeth A. Bagshaw – Microbiology Ecology

Built environment microbiology
The Built Environment Is a Microbial Wasteland – Sean M. Gibbons – mSystems

Food microbiology

Assessment of the microbial diversity during an industrial-scale malting process by a polymerase chain reaction-denaturing gradient gel electrophoresis analysis – Ruilong Li – Journal of the Institute of Brewing (gotta love that name!)

Phages, viruses, and CRISPRs

The diversity-generating benefits of a prokaryotic adaptive immune system – Stineke van Houte – Nature

Microbes in the news
Your city’s microbiome is unique – Christina Procopiou – Newsweek

Human beings – and our offices – are crawling with microbes – Joanna Verran – The Conversation

About Jonathan Eisen: This microbiologist loves bugs, hates hype – and wants you to send him your cat’s poop – Rob Waters – STATnews

Close-up of a dust bunny – Holly Ganz – MicroBE.net

Looking Back, Looking Forward and Phage Hunters: A Q&A with the Student Commencement Speaker – Emily Hellewell – Brigham Young University

Do gut microbes shape our evolution? Researcher proposes that a host’s microbiota can steer its evolution in new directions – Science Daily

Pfizer, Roche Embrace The Microbiome, Leading $43M Bet On Second Genome – Luke Timmerman – Forbes

You’re Home to Trillions of Microbes That Affect Everything From Digestion to Depression – Sydney Lupkin – Vice

Pancreatic Cancer Risk Tied to Specific Mouth Bacteria – Infection Control Today

Science, publishing, and career
Due process in the Twitter age – Marcia McNutt – Science

Peer review: Troubled from the start – Alex Csiszar – Nature

Dirty room-mates make lab mice more useful. Housing lab mice with pet-shop mice gives them more human-like immune systems – Sara Reardon – Nature

UC Davis Storer Lecture series – since 1963 87% of speakers are male – Jonathan Eisen – The Tree of LIfe

April 13, 2016

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Thematic issue on effect of antibiotics on microbiomes, limited effect of probiotics on stool proteomics, culex mosquito development, ocean acidification, and new technique to determine microbial growth.

General microbiome

Thematic Issue: the effects of anthropogenic use of antibiotics on the microbiomes in various ecosystems and the implications for human health. Guest edited by Prof. Kornelia Smalla, the articles included in this issue are freely available to read til 11th May 2016. Environmental Dimension of Antibiotic Resistance – FEMS Microbiology Ecology
Review: Network-based metabolic analysis and microbial community modeling – Cesar Cardona – Current Opinion in Microbiology

Review: The importance of the microbiome in epidemiologic research – Blake M. Hanson – Annals of Epidemiology

Editorial: Microbiome: Eating for trillions – Derrick M. Chu – Nature

Pregnancy and birth

Preview: Another Reason to Thank Mom: Gestational Effects of Microbiota Metabolites – Seth Rakoff-Nahoum – Cell Host & Microbe

Review: The interplay of host immunity and environment on risk for bacterial vaginosis and associated reproductive health outcomes – Kerry Murphy – The Journal of Infectious Diseases

Human respiratory microbiome

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype – Leopoldo N. Segal – Nature Microbiology

Human gut microbiome

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults – Carolin A. Kolmeder – PLOS ONE

Review: The gut microbiota and metabolic disease: current understanding and future perspectives – T. Arora – Journal of Internal Medicine

Animal models

A Host-Produced Autoinducer-2 Mimic Activates Bacterial Quorum Sensing – Anisa S. Ismail – Cell Host & Microbe

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella – Fabian Rivera-Chávez – Cell Host & Microbe

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations – Alexander R. Moschen – Cell Host & Microbe

Animal microbiome

Culex pipiens Development Is Greatly Influenced by Native Bacteria and Exogenous Yeast – Leonardo M. Díaz-Nieto – PLOS ONE

Plant, root, and soil microbiome

Convergence of soil microbial properties after plant colonization of an experimental plant diversity gradient – Katja Steinauer – BMC Ecology

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus – Marta Alves – Scientific Reports

Relationship between presence of the desert shrub Haloxylon ammodendron and microbial communities in two soils with contrasting textures – Yanfeng Cao – Applied Soil Ecology

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil – Samiran Banerjee – Soil Biology and Biochemistry

Belowground response to drought in a tropical forest soil. I. Changes in microbial functional potential and metabolism – Nick Bouskill – Frontiers in Microbiology

Water and extremophile microbiome

Spatiotemporal Dynamics of Vibrio spp. within the Sydney Harbour Estuary – Nachshon Siboni – Frontiers in Microbiology

Assimilation of microbial and plant carbon by active prokaryotic and fungal populations in glacial forefields – Thomas Rime – Soil Biology and Biochemistry

Implications of Ocean Acidification for Marine Microorganisms from the Free-Living to the Host-Associated – Paul A. O’Brien – Frontiers in Marine Science

Waste and pollution microbiology

Shifts in microbial community structure and diversity in a MBR combined with worm reactors treating synthetic wastewater – Jia Liu – Journal of Environmental Sciences

Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine degraders in a former pesticide mixing site and a machinery washing area – James F. Douglass – Journal of Soils and Sediments

The effect of seasonality upon the development of lotic biofilms and microbial biostabilisation – Holger Schmidt – Freshwater Biology

Review: The importance of sewer biofilms – Henriette Jensen – Water

Food microbiology and functional foods

Lactobacillus plantarum TWK10 Supplementation Improves Exercise Performance and Increases Muscle Mass in Mice – Yi-Ming Chen – MDPI Nutrients

Investigation of the activity of the microorganisms in a Reblochon-style cheese by metatranscriptomic analysis – Christophe Monnet – Frontiers in Microbiology

Review: Prebiotics as a modulator of gut microbiota in paediatric obesity – A. C. Nicolucci – Pediatric Obesity

Techniques

Stable isotope probing with 18O-water to investigate microbial growth and death in environmental samples – Egbert Schwartz – Current Opinion in Biotechnology

Review: A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis – Aditi Sengupta – Agricultural & Environmental Letters

Microbial ecology

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning – Manuel Delgado-Baquerizo

Influence of dormancy on microbial competition under intermittent substrate supply: Insights from model simulations – Konstantin Stolpovsky – FEMS Microbiology Ecology

More microbiology

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis – Matt S. Conover – mBio

Biostatistics

Reinventing Biostatistics Education for Basic Scientists – Tracey L. Weissgerber – PLOS Biology

Microbes in the news

MSU professor Gemma Reguera making tiny innovations with a big impact – Erin F. Wasinger – Lansing State Journal

SCSU prof Elizabeth Lewis Roberts discovers fungus, bacteria help grass (really) – Anna Bisaro – New Haven Register

Probiotics for Livestock – Reducing Antibiotic Reliance – Alex Alexiev – MicroBEnet

Taking Cues From Human Nutrition To Reduce Antibiotic Use In Livestock – Amy Mayer – NPR

Why bacteria can’t get any bigger—or smaller – Elizabeth Pennisi – Science

Digestion of lignin in the gut – Science Daily

“Truly exciting”: Probiotic may increase muscle mass, energy & performance – Stephen Daniells – Nutraingredients

Breakthrough at Binghamton furthers development of bacteria-powered energy – The Engineer

Vibrio: Aggressive infectious bacteria species found in Sydney Harbour – Daisy Dumas – Sydney Morning Herald

Science, publishing, and career

Do interventions to reduce misconduct actually work? Maybe not, says new report – Alison McCook – Retraction Watch

$250 million, 300 scientists and 40 labs: Sean Parker’s revolutionary project to ‘solve’ cancer – Ariana Eunjung Cha – Washington Post

Science fairs are as flawed as my solar-powered hot dog cooker – Carl Zimmer – STATnews

The dark side of Guardian comments: part of a series on the rising global phenomenon of online harassment – the Guardian

How one lab challenged a grant rejection and won €5 million – Ewen Callaway – Nature

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 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 31, 2016

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A special mBio issue discussing the Holobiont concept, salivary microbiota in oral cancer, truffles, sinuses in germ-free mice, and Wolbachia in cave spiders.

General microbiome

Special Issue: The Holobiont Concept- mBio
Introduction to the Hologenome Special Series – Margaret McFall-Ngai
Microbes Drive Evolution of Animals and Plants: the Hologenome Concept – Eugene Rosenberg
Speciation by Symbiosis: the Microbiome and Behavior – J. Dylan Shropshire
Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts – Angela E. Douglas

Pregnancy and birth

Research Highlight: Baby steps towards the microbiome – Andrea Du Toit – Nature Reviews Microbiology

Oral microbiome

Changes in the salivary microbiota of oral leukoplakia and oral cancer – Xiaosheng Hu – Oral Oncology

Human respiratory microbiome

Tonsillar microbiota in children with PFAPA (periodic fever, aphthous stomatitis, pharyngitis, and adenitis) syndrome – M. V. Tejesvi – European Journal of Clinical Microbiology & Infectious Diseases

Conference abstract: Nasal Microbiome Composition Is Associated with Chitotriosidase (Chit1) Activity in Adult Hutterites – Catherine Igartua – Annals of the American Thoracic Society

Conference abstract: Gut Microbiota and Allergic Disease. New Insights
Susan V. Lynch- Annals of the American Thoracic Society

Human gut microbiome

Association between intestinal permeability and faecal microbiota composition in Italian children with beta cell autoimmunity at risk for type 1 diabetes – Claudio Maffeis – Diabetes/Metabolism Research and Reviews

Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection – Braden Millan – Clinical Infectious Diseases

Special issue with reviews: Gastric and Gut Microbiota in Health and Disease – Digestive Diseases

Animal models

Effect of a long-term high-protein diet on survival, obesity development and gut microbiota in mice – Pia Kiilerich – American Journal of Physiology

Differences in the paranasal sinuses between germ-free and pathogen-free mice – Ravi Jain – International Forum of Allergy & Rhinology

Effects of taurine on gut microbiota and metabolism in mice – Haining Yu – Amino Acids

Animal microbiome

Research Highlight: Microbiome ‘coral’ations – Ursula Hofer – Nature Reviews Microbiology

Classification of Wolbachia (Alphaproteobacteria, Rickettsiales): No evidence for a distinct supergroup in cave spiders – Michael Gerth – BioRxiv

Not a great title: Metagenomic bacterial community profiles of chicken embryo gastrointestinal tract by using T-RFLP analysis – L. A. Ilina – Doklady Biochemistry and Biophysics

Plant, root, and soil microbiome

Screening of soil bacteria as potential agents for drugs biodegradation: a case study with clofibric acid – Claudia Popa Ungureanu – Journal of Chemical Technology and Biotechnology

Metagenomes provide valuable comparative information on soil microeukaryotes –
Samuel Jacquiod – Research in Microbiology

The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales – Gian Maria Niccolò Benucci – Microbial Ecology

Bioreactor microbiology

The First Space-Related Study of a Kombucha Multimicrobial Cellulose-Forming Community: Preparatory Laboratory Experiments – O. Podolich – Origins of Life and Evolution of Biospheres

Food microbiology

Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques – Hana Šuranská – Folia Microbiologica

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening – Oylum Erkus – International Journal of Food Microbiology

Bioinformatics and metagenomics

Predicting microbial interactions through computational approaches – Chenhao Li – Methods

Microbes in the news

A Hidden Factor in Stroke Severity: The Microbes in Your Gut : A new study in mice demonstrates that manipulating the microbiome can influence the extent of brain damage caused by a stroke – Jordana Cepelewic – Scientific American

Pushing and Pulling on the Mosquito Microbiome – Kevin Bonham – Scientific American

Sampling an animal shelter – Holly Ganz – MicroBEnet

Intestinal Microbiome of Children with Cystic Fibrosis Promotes Gut Inflammation, Study Finds – Patricia Inacio – Cystic Fibrosis News Today
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March 29, 2016

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

Pregnancy and birth

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

Human respiratory microbiome (see also above)

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

Animal models

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

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

Animal microbiome

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

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

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

Plant, root, and snow microbiome

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

Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

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

Water, snow, and extremophile microbiome

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

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

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

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

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

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

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

Waste and pollution microbiome

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

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

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

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

Built environment microbiome

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

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

Food microbiome

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

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

Viruses and phages

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

More microbiology

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

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

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

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

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

Microbes in the news

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

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

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

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

What bacteria lurk in stable dust? – Horsetalk

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

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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March 24, 2016

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

General microbiome

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

Pregnancy and birth

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

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

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

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

Human skin microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

Microbes in blood

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

Animal models

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

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

Animal microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

Waste and pollution microbiology

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

Built environment microbiology

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

Forensic microbiology

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

Food microbiology

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

Computational modeling

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

Techniques

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

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

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

Proteomics

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

Microbes in the news

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

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

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

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

Science, publishing and career

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

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

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March 22, 2016

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

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

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

Infection, immunology, and transplantion microbiology

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

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

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

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

Human oral microbiome

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

Human eye and skin microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

Animal models

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

Cave microbiome

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

Built environment microbiology

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

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

Food microbiology

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

Bioinformatics, techniques, and metagenomics

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

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

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

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

Metagenomics and viruses

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

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

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

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

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

More microbiology

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

Microbes in the news

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

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

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

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

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

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

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

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

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

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

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

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

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

Blog posts by me:

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

Extreme environments at home – Elisabeth Bik – MicroBEnet

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March 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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