Monthly Archives: July 2015

July 31, 2015

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Microbiome antibodies prevented an HIV vaccine from working, effect of antibiotics during rhinosinusitis, microbiome and tuberculosis, how mussels get colonized, and a fruit based nutrient bar’s effect on human metabolism.

Human respiratory microbiome

The Microbiome at the Pulmonary Alveolar Niche: How It Affects the Human Innate Response against Mycobacterium tuberculosis – Alexander J. Adami – Tuberculosis

The effect of antibiotics on the microbiome in acute exacerbations of chronic rhinosinusitis – Mark A. Merkley – International Forum of Allergy & Rhinology

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Human gut microbiome

Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies – Wilton B. Williams – Science

Not microbiota, but of interest: Go with the Flow: Regional gastrointestinal transit and pH studied in 215 healthy volunteers using the wireless motility capsule: influence of age, gender, study country and testing protocol – Y. T. Wang – Alimentary Pharmacology & Therapeutics

Commentary: You Lose Some, You Win Some: Weight Loss Induces Microbiota and Metabolite Shifts – Elisabeth M. Bik – EBioMedicine

Review: The role of the gut microbiota in metabolic health – Aafke W. F. Janssen and Sander Kersten – The FASEB Journal

Microbiome models

MyD88 Adaptor-Dependent Microbial Sensing by Regulatory T Cells Promotes Mucosal Tolerance and Enforces Commensalism – Sen Wang – Immunity

Commentary: A Toolbox for Microbiome Engineering – Mohamed S. Donia – Cell Systems

Animal microbiome

The nasopharyngeal microbiota of feedlot cattle that develop bovine respiratory disease – Devin B. Holman – Veterinary Microbiology

Adapted to change: the rapid development of symbiosis in newly settled, fast-maturing chemosymbiotic mussels in the deep sea – Laming Sven R – Marine Environmental Research

Plant, soil, and root microbiology

Roots from distinct plant developmental stages are capable of rapidly selecting their own microbiome without the influence of environmental and soil edaphic factors – Jun Yuan – Soil Biology and Biochemistry

Environmental Filtering of Microbial Communities in Agricultural Soil Shifts with Crop Growth – Sarah K. Hargreaves – PLOS ONE

Interactions between a plant growth-promoting rhizobacterium and smoke-derived compounds and their effect on okra growth – Heino B. Papenfus – Journal of Plant Nutrition and Soil Science

Food microbiology

Diversity and dynamics of antibiotic-resistant bacteria in cheese as determined by PCR denaturing gradient gel electrophoresis – Ana Belén Flórez – International Journal of Food Microbiology

Proteomics and metabolomics

A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation – Alessandro Tanca – Data in Brief

A multicomponent nutrient bar promotes weight loss and improves dyslipidemia and insulin resistance in the overweight/obese: chronic inflammation blunts these improvements – Joyce C. McCann – The FASEB Journal

Microbes in the news

Gut microbiome may have interfered with experimental HIV vaccines – Rachel Tompa – Fred Hutch

Vacation souvenirs can be crappy, but rarely are they actual crap: Ilana Brito, the Biologist Who Flew to Fiji for Feces – Rachel Becker – Ozy

Science, publishing, and career

Why not have a life? I only stay late if I’m actually doing an experiment – Gary McDowell – Science

Bik’s Picks

Deadly Fungus Could Threaten U.S. Salamanders – Stephanie Pappas – Discover / LiveScience

Plants send out stress signals just like animals, scientists find – Robert Gebelhoff – Washington Post

Vaccine Success Holds Hope For End To Deadly Scourge Of Ebola – Kate Kelland – Huffington Post

The world’s best whiskey is being sent into space for the sake of science – Gabriel Fisher – Quartz

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July 30, 2015

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Correct vocabulary of microbiome research, microbiome during mosquito development, microbes on Granada’s Royal Chapel stone, and microbes in Atacama desert.

General microbiome

About the proper use of “16S”, “microbiome”, and “microbiota”, and why “microflora” is not correct. Note Elies: But “microbiota” is a plant too!
The vocabulary of microbiome research: a proposal – Julian R. Marchesi – Microbiome

Human oral microbiome

Host response mechanisms in periodontal diseases – Nora Silva – Journal of Applied Oral Science

Human respiratory microbiome

The airway microbiome in patients with severe asthma: Associations with disease features and severity – Yvonne J. Huang – The Journal of Allergy and Clinical Immunology

Human gastric microbiome

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome – DeAnna E. Beasley – PLOS ONE

Microbiome models

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets – Nirupama Benis – BMC Genomics

Animal microbiome

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology

Review: The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals – A. Rodrigues Hoffmann – Veterinary Pathology

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi affect plant community structure under various nutrient conditions and stabilize the community productivity – Gaowen Yang – Oikos

Complementarity in both plant and mycorrhizal fungal communities are not necessarily increased by diversity in the other – Cameron Wagg – Journal of Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing –
Youwei Hong – Canadian Journal of Microbiology

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil – Abdullah M. Al-Sadi – BMC Microbiology

Mineralogy: Geochemical evidence of microbial activity within ooids – Mara R. Diaz – Sedimentology

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments – Isabel C. Romero – Journal of Marine Science and Engineering

Inexplicable Arsenic: Human Dimensions of Soil, Water, Food and Microbial
Resources – Ramakrishnan B – Journal of Environmetnal and Analytical Toxicology

Water microbiome

Structure of the archaeal community in the Black Sea photic zone – A. Y. Merkel – Microbiology

Review: Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes – Thomas Mock – Global Change Microbiology

Extremophiles

Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert – Maria Cecilia Rasuk – Microbial Ecology

Thesis: Microbial Ecology, Biogeochemistry, and Signatures of Life at Low Temperature in Arctic Thermokarst Lake Sediments and High Sierra Snow Fields – Matheus Carnevali, Paula B – University of Nevada, Reno

Waste and built environment microbiology

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters – Samik Bagchi – PLOS ONE

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada – Fadwa Jroundi – PLOS ONE

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil – Juliana Alves Resende – Microbial Ecology

Metagenomics and bioinformatics

deFUME: Dynamic exploration of functional metagenomic sequencing data – Eric van der Helm – BMC Research Notes

Microbial Ecology

An Economic Framework of Microbial Trade – Joshua Tasoff – PLOS ONE

Microbes in the news

Kingdoms are so 20th century: The tree of life gets a makeover: Schoolroom kingdoms are taking a backseat to life’s supergroups – Susan Milius – Science News

Soil-Dwelling Fungus Rode Joplin Tornado to Unexpected Human Home – Jennifer Frazer – Scientific American

Agave extracts show ability to shift gut microbiota: Ingredion study – Stephen DANIELLS – Nutraingredients

Bacterial Find Sheds Light on Digestive Issues, Diabetes, Obesity – American Crystallographic Association

Water At Some Olympic Venues In Rio de Janeiro Reportedly Contain Virus Levels On Par With Raw Sewage – Brad Brooks and Jeny Barchfield – Huffington Post

LASA students developing bacteria to improve carbon monoxide detectors – Calily Bien – KXAN

Bik’s Picks

A tragic death leaves just four northern white rhinos living and little hope for the species – Rachel Feltman – Washington Post

‘Once in a Blue Moon’ Happens on Friday — Why? – Geoff Gaherty – Discovery

How did you get that job: designing a parachute for NASA’s Mars rover – Elizabeth Lopatto – The Verge

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July 29, 2015

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Pack hunting by soil amoeba, microbiota of meconium and uterus, transcriptomics of oral phages, no differences in antibiotic resistance gene content in organic or regular pigs, and effects of IBD associated microbes on mouse physiology.

General microbiome

Editorial: News Feature: Microbes on the mind – Helen H. Shen – PNAS

Microbiome of pregnancy and birth

Note: just one sample was PCR positive: First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota – Richard Hansen – PLOS ONE

Understanding the Biologic Therapies of Probiotics, Prebiotics, and Synbiotics: Exploring Current Evidence for Use in Premature Infants for the Prevention of Necrotizing Enterocolitis – Asmerom, Mussie – Journal of Perinatal & Neonatal Nursing

Human oral microbiome

Transcriptome analysis of bacteriophage communities in periodontal health and disease – Tasha M. Santiago-Rodriguez – BMC Genomics

Human respiratory microbiome

Paired analysis of the microbiota of surface mucus and whole-tissue specimens in patients with chronic rhinosinusitis – Raymond J.T. Kim – International Forum of Allergy & Rhinology

Human genital microbiome

Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the 16S rRNA gene – Hans Verstaelen – PeerJ

Human skin microbiome

Review: Regulation of T cell immunity in atopic dermatitis by microbes: the Yin and Yang of cutaneous inflammation – Tilo Biedermann – Frontiers in Immunology

Human gut microbiome

Ruminococcal cellulosomes: molecular Lego to deconstruct microcrystalline cellulose in human gut – Gurvan Michel – Environmental Microbiology

Influence of galacto-oligosaccharide mixture (B-GOS) on gut microbiota, immune parameters and metabonomics in elderly persons – Jelena Vulevic – British Journal of Nutrition

Review: Microbiome influences on allergy in mice and humans – Benjamin J Marsland – Current Opinion in Immunology

Editorial: Gut microbiota: Microbiota and neuroimmune signalling—Metchnikoff to microglia – John F. Cryan & Timothy G. Dinan

Review: A Survey on the Developmental Intestinal Microbiota Research in China: the history, funding, and frontiers of gut bacteria – Hui Min Chen – Journal of Digestive Diseases

Editorial: Stool microbiome changes in VEGF-TKI-induced diarrhoea – Nature Reviews Urology

Models of microbiome research

Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice – Thomas W Hoffmann – ISME Journal

The Role of Curcumin in Modulating Colonic Microbiota During Colitis and Colon Cancer Prevention – Rita-Marie McFadden – Inflammatory Bowel Diseases

Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneumonia –
Stefanie Gauguet – Infection and Immunity

Oral Administration of P. gingivalis Induces Dysbiosis of Gut Microbiota and Impaired Barrier Function Leading to Dissemination of Enterobacteria to the Liver – Mayuka Nakajima – PLOS ONE

Fecal microbiota transplantation and bacterial consortium transplantation have comparable effects on the re-establishment of mucosal barrier function in mice with intestinal dysbiosis – Ming Li – Frontiers in Microbiology

Symbiotic maple saps minimize disruption of the mice intestinal microbiota after oral antibiotic administration – Riadh Hammami – International Journal of Food Sciences and Nutrition

Animal microbiome

Characterization of Antibiotic Resistance Gene Abundance and Microbiota Composition in Feces of Organic and Conventional Pigs from Four EU Countries – Lenka Gerzova – PLOS ONE

Symbiotic bacteria enable olive fly larvae to overcome host defences – Michael Ben-Yosef – Royal Society Open Science

Plant, root, and soil microbiome

Not sure where to file this one under, but pretty cool: Pack hunting by a common soil amoeba on nematodes – Stefan Geisen – Environmental Microbiology

Anaerobic degradation pathway of the novel chiral insecticide Paichongding and its impact on bacterial communities in soils – Zhiqiang Cai – Journal of Agricultural and Food Chemistry

Metagenomics and bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metabolomics and Proteomics

Effects of Dietary Different Doses of Copper and High Fructose Feeding on Rat Fecal Metabolome – Xiaoli Wei – Journal of Proteome Research

Science, publishing, and career

Let’s Make Gender Diversity in Data Science a Priority Right from the Start – Francine D. Berman – PLOS Biology

Microbes in the news

What are ‘eye crusties’ made of? uBiome asking for participants to use their eye kit

Bacteria Hysteria

Germaphobes look away! Your gym bag might contain high levels of bacteria usually found in faeces – Irish Examiner

Bik’s Picks

A Skeleton, a Catholic Relic, and a Mystery About American Origins – Adrienne Lafrance – The Atlantic

The confounding case of the missing carbon – Michael Casey – CBS News

Washington Is Finally Getting What It Deserves As It Sinks Into The Sea – Kate Sheppard – Huffington Post

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July 28, 2015

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A review of the human hand microbiome, microbiome and anxiety in mouse models, diabetes, bacteria in thrombolites, how plants recruits microbial symbionts, towards a standard in microbial genome annotation, and an article about the lab of Jill Banfield.

Microbiome of pregnancy and birth

Prevalence of oral Candida in the first year of life – C. Stecksén-Blicks – Mycoses

Cross-colonization of infants with probiotic organisms in a neonatal unit – L. Hickey – Journal of Hospital Infection

Human oral microbiome

Periodontal microbiota and phospholipases: The Oral Infections and Vascular Disease Epidemiology Study (INVEST) – Adrien Boillot – Atherosclerosis

Review: Alterations of the oral microbiota and oral clinical findings in dry mouth – Y. Hayashi – Journal of Oral Biosciences

Human skin and eye microbiome

Review of Human Hand Microbiome Research – Sarah L. Edmonds-Wilson – Journal of Dermatological Research

Correspondence: Harnessing the microbiome in glaucoma and uveitis – Ankur Gupta – Medical Hypotheses

Human respiratory microbiome

High diversity of non-sporulating moulds in respiratory specimens of immunocompromised patients: should all the species be reported when diagnosing invasive aspergillosis? – Dea Garcia-Hermoso – Mycoses

 

Human gut microbiome

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment – Xuan Zhang – Nature Medicine

A tough pill to swallow (perspective): Ready for Oral Fecal Microbiota Pill in Clinical Practice? – Timothy Nguyen – The Journal for Nurse Practitioners

Review: The human gut microbiota and virome: potential therapeutic implications – Emidio Scarpellini – Digestive and Liver Disease

Review: Intestinal Immunity and Gut Microbiota as Therapeutic Targets for Preventing Atherosclerotic Cardiovascular Diseases – Tomoya Yamashita – Circulation Journal

Microbiome models

Microbiota and host determinants of behavioural phenotype in maternally separated mice – G. De Palma – Nature Communications

Microbiota regulates type 1 diabetes – Michael P Burrows – PNAS

Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon – Noortje Ijssennagger – PNAS

Intestinal inhibition of Atg7 prevents tumour initiation through a microbiome-influenced immune response and suppresses tumour growth – Jonathan Lévy – Nature Cell Biology

Lactulose increases bacterial diversity and modulates the swine faecal microbiome as revealed by 454-pyrosequencing – Jong Pyo Chae – Animal Feed Science and Technology

Dynamic Metabonomic and Microbiological Response of Rats to Lincomycin Exposure: An Integrated Microbiology and Metabonomics Analysis – Manna Lin – RSC Advances

Green propolis modulates gut microbiota, reduces endotoxemia and expression of TLR4 pathway in mice fed a high-fat diet – Aline Rissetti Roquetto – Food Research International

Changes in the Swine Gut Microbiota in Response to Porcine Epidemic Diarrhea Infection – Hyeon-Woo Koh – Microbes and Environments

Review: Interrelatedness Between Dysbiosis in the Gut Microbiota Due to Immunodeficiency and Disease Penetrance of Colitis – Avijit Ray – Immunology

Animal microbiome

Experimental studies of microbial populations and incidence of zoonotic pathogens in the faeces of red deer (Cervus elaphus) – Sebastian Gnat – Letters in Applied Microbiology

Yeast microbiota of natural cavities of manatees (Trichechus inunguis and T. manatus) in Brazil and its relevance for animal health and management in captivity – José J.C. Sidrim – Canadian Journal of Microbiology

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches – Yukihiro Kinjo – Microbes and Environments

Prokaryotic microbiota in the digestive cavity of the jellyfish Cotylorhiza tuberculata – Sara Cortés-Lara – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling – J. M. Mobberley – Scientific Reports

Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden – Hanna Millberg – Fungal Ecology

Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant – Nicola J. Day – Journal of Ecology

Fungal colonization of the rooting system of the early land plant Asteroxylon mackiei from the 407-Myr-old Rhynie Chert (Scotland, UK) – Christine Strullu-Derrien – Botanical Journal of the Linnean Society

Alder trees enhance crop productivity and soil microbial biomass in tea plantations – P.E. Mortimer – Applied Soil Ecology

Perspective: Plant genotype, microbial recruitment and nutritional security – Jai S. Patel – Frontiers in Plant Science

I don’t always have symbionts, but when I do, I prefer alphaproteobacteria: Endemic Mimosa species from Mexico prefer alphaproteobacterial rhizobial symbionts – Cyril Bontemps – New Phytologist

Conference abstract: Changes in rhizosphere microbiome from halotolerant tomato are correlated with physiological and biochemical parameters of oxidative stress in plants – Radu Liviu Sumalan – Journal of Biotechnology

Review: Root associated bacteria – Friends or enemies? A review – Gabriela Mihalache – Memoirs of the Scientific Sections of the Romanian Academy

Analysing the effect of soil organic matter on bacterial communities using T-RFLP fingerprinting: different methods, different stories? – A. Blaud – Biology and Fertility of Soils

Water microbiome

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties – Bei-bei Chai – Journal of Environmental Biology

Extremophiles

Review: Microbial communities and primary succession in high altitude mountain environments – Sonia Ciccazzo – Annals of Microbiology

Metagenomics and bioinformatics

FastQFS – A tool for evaluating and filtering paired-end sequencing data generated from high throughput sequencing – Rahul Sharma – Mycological Progress

Toward a standard in structural genome annotation for prokaryotes – H. James Tripp – Standards in Genomic Sciences

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria – Cindy Shi – SciTech Connect

Microbial Ecology

Socially mediated induction and suppression of antibiosis during bacterial coexistence
Monica I. Abrudan – PNAS

Microbes in the news

About work in the lab of Jill Banfield: At Tiny Scales, a Giant Burst on Tree of Life – Kevin Hartnett – Quanta Magazine

Swan song for antibiotics? Can phage therapy and gene editing fill the gap? – Nicholas Staropoli – Genetic Literacy Project

Metagenomic Study Finds Differences in Oral, Gut Microbiomes of Rheumatoid Arthritis Patients – Genome Web

Your Burger Is Full of Living Things, Even If It’s Vegetarian – Maddie Stone – Gizmodo

Title incorrect, it’s a Yersinia, but different species: A Species Of Bacteria That Causes Bubonic Plague And Other Disease In Salmon May Also Be Able To Treat Cancer – Lecia Bushak – Medical Daily

Bacteria in gut profiling secret to healthy weight – Peta Bee – The Australian

Bacteria to protect Appenzeller cheese from fakes – Anand Chandrasekhar – SwissInfo

Grandparents largely to blame for China’s spiking childhood obesity, Microbiota treatment sees dramatic results in obese children – RJ Whitehead – FoodNavigator

Bik’s Picks

Reception of odors and repellents in mosquitoes – Anandasankar Ray – Current Opinion in Neurobiology

570 Sea Turtle Hatchlings Are Released Into Atlantic Ocean – Getty Images

Everything you need to know about lactose intolerance – with maps! – New Scientist

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July 27, 2015

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Microbiome webinar tomorrow, female urinary microbiota, listening to our gut, bacteria on plastic in the North Sea, quantifying food spoilage, and “less is more” when it comes to dog poop.

Events

Tomorrow: Microbiome, Antibiotics and Human Disease – Cell Press Webinar July 28, at noon EST

Genome Science 2015 – September 7-9, University of Birmingham, UK

Human urinary tract microbiome

The Female Urinary Microbiota in Urgency Urinary Incontinence – Meghan M. Pearce – American Journal of Obstetrics and Gynecology

Human gut microbiome

Low urinary indoxyl sulfate levels early after ASCT reflect a disrupted microbiome and are associated with poor outcome – Daniela Weber – Blood

Review: Listening to Our Gut: Contribution of Gut Microbiota and Cardiovascular Risk in Diabetes Pathogenesis – Daniel Li – Current Diabetes Reports

Animal microbiome

Less is More—Optimization of DNA Extraction from Canine Feces – Christina D. Lindquist – Journal of Forensic Sciences

Review: Prebiotics and gut microbiota in chickens – Mohsen Pourabedin – FEMS Microbiology Letters

Topographical mapping of the rainbow trout (Oncorhynchus mykiss) microbiome reveals a diverse bacterial community in the skin with antifungal properties – Liam Lowrey – Applied and Environmental Microbiology

Plant, root, and soil microbiome

PGPR enhanced phytoremediation of petroleum contaminated soil and rhizosphere microbial community response – Jinyu Hou – Chemosphere

Water microbiome

Bacterial community profiling of plastic litter in the Belgian part of the North Sea –
Caroline A. De Tender – Environmental Science & Technology

The Dynamics of the bacterial diversity in the redox transition and anoxic zones of the Cariaco Basin assessed by parallel tag sequencing – Maria J. Rodriguez-Mora – FEMS Microbiology Ecology

Characterization of para-nitrophenol degrading bacterial communities in river water using functional markers and stable isotope probing – Agnieszka Kowalczyk – Applied and Environmental Microbiology

Review: Slow Microbial Life in the Seabed – Bo Barker Jørgensen – Annual Review of Marine Science

Food microbiology

Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores – Paulo de Boer – Microbiome

Microbes in the news

Microbial Me: Interview with Jack Gilbert – Lydialyle Gibson – The University of Chicago Magazine

We Want the Funk: The Ups and Downs of Wild Microbes in Beer – Kaitlyn Keller – PLOS Blogs

Chinese scientists discover therapy to child obesity – XinhuaNet

Is your milk off? This 3D-printed ‘smart’ bottle cap will know – Duncan Geere – TechRadar

The Bacteria Solution: A cosmetics startup knows that live microbes are the secret to healthier skin. Will anyone believe that? – Caroline Winter – Bloomberg Businessweek

Bacteria Hysteria

With “shocking” video (but I was entertained): How clean is YOUR car? Deadly bugs such as E.coli and found lurking on steering wheels and handbrakes caused by people eating and drinking on the move – Kate Pickles – Daily Mail

Microbes and Art

Video: Invisible You – The Human Microbiome: Rogan Brown tells the story behind his work ‘Cut Microbe’, an intricate paper sculpture based on a single bacteria form. – On permanent display at Eden Project in Cornwall, UK.

Bik’s Picks

Increasing prevalence of autism is due, in part, to changing diagnoses – Penn State Science

Oil droplets turn cells into tiny lasers. Injecting single cells with spheres of fluorescent dye could open new research and treatment avenues using light – Allie Wilkinson – Nature

Why Lake Tahoe is so blue (and how to measure it) – Kelsey Warner – CS Monitor

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July 25, 2015

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Extracting DNA from the soil under a cadaver, metabolomics of periodontitis, HLA haplotypes and microbiome, and microbes using ancient carbon from melting permafrost.

Microbiome of pregnancy and health

Gut Bifidobacterium microbiota in one-month-old Brazilian newborns – Łukasz Grześkowiak – Anaerobe

Microbiome of death

Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations – Sheree J. Finley – Australian Journal of Forensic Sciences

Human oral microbiome

Editorial: Targeting specific bacteria in the oral microbiome – Jorge Frias-Lopez – Trends in Microbiology

The human salivary microbiome exhibits temporal stability in bacterial diversity – Simon J. S. Cameron – FEMS Microbiology Ecology

Association of Synergistetes and Cyclodipeptides with Periodontitis – J.T. Marchesan – Journal of Dental Research

Human urinary tract microbiome

Article in Russian: Microbial communities on kidney stones – YM Romanova – Mol Gen Mikrobiol Virusol

Human gut microbiome

The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study – Johannes R. Hov – PLOS ONE

Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru – Lindsey O’Neal – Anaerobe

Crohn-associated microbial communities from colonic mucosal biopsies in patients of the western Mediterranean – Roberto Vidal – Systematic and Applied Microbiology

Human eye microbiome

Bacteria Colonizing the Ocular Surface in Eyes With Boston Type 1 Keratoprosthesis: Analysis of Biofilm-Forming Capability and Vancomycin Tolerance – Sarmad H. Jassim – Investigative Ophthalmology & Visual Science

Microbiome models

Persistent hyperglycemia modulates gut immune function and microbiota in rats – Katsuya Mori – Journal of Intensive Care

Animal microbiome

16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo – S.S. Paul – Anaerobe

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology

Plant, root, and soil microbiome

Fungal colonization of the rooting system of the early land plant Asteroxylon mackiei from the 407-Myr-old Rhynie Chert (Scotland, UK)- Christine Strullu-Derrien – Botanical Journal of the Linnean Society

Soils, microbes, and forest health: A qualitative analysis of social and institutional factors affecting genomic technology adoption – Sara E. Crann – Technology in Society

Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations – Sheree J. Finley – Australian Journal of Forensic Sciences

Water microbiome

Spatial patterns of benthic bacterial communities in a large lake – Li-Xiang Liu – International Review of Hydrobiology

Extremophile microbiome

Utilization of ancient permafrost carbon in headwaters of Arctic fluvial networks – Paul J. Mann – Nature Communications

Waste water and bioreactor microbiology

Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing – Yogananda Maspolim – Journal of Environmental Sciences

Influence of co-substrate on textile wastewater treatment and microbial community changes in the anaerobic biological sulfate reduction process – Kashif Rasool – Journal of Hazardous Materials

Metabolic networks

Metabolic interactions in microbial communities: untangling the Gordian knot – Olga Ponomarova – Current Opinion in Microbiology

Association of Synergistetes and Cyclodipeptides with Periodontitis – J.T. Marchesan – Journal of Dental Research

Microbes in the news

If the sea is dirty, the sand is worse. Beach sand contains more fecal bacteria than seawater – Megan Scudellari – Boston Globe

Bacteria Hysteria

The Best Way To Clean Your Purse From All That Dirty Bacteria – Madelyn Chung – Huffington Post Canada

Breast milk containing bacteria for sale on Craigslist in Upstate – Gabrielle Komorowski – WYFF4

Bik’s Picks

What San Diego Scientists Are Discovering About Dolphins And Diabetes – Megan Burke – KPBS

Bid to save dolphins in polluted Ganges – Nirmala Ganapathy – Straits Times

 

The SnotBot: Patrick Stewart Backs Drones That Collect Whale Snot – Keith Wagstaff – NBC News

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July 24, 2015

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A review about small molecules produced by human microbiota, layers of microbial life in Dead Sea sediments, fungus making “hair ice”, exploring deep microbial life in the sea, and bacterial diversity at the North Pole.

Events

3rd Microbiome R&D and Business Collaboration Forum: USA, San Diego, September 10-11, 2015

WAO Symposium on Food Allergy & the Microbiome – 5-6 December 2015, Miami, FL

Microbiome reviews

Small molecules from the human microbiota – Mohamed S. Donia, Michael A. Fischbach – Science

Editorial: Microbiota-induced T cells block allergic inflammation – Yvonne Bordon – Nature Reviews Immunology

Perspective: Promise and pragmatism in clinical microbiome research – Nadim J. Ajami – Mini-Reviews in Medicinal Chemistry

Review: The Role of Intestinal Microbiota in Graft versus Host Disease – no authors listed – Mini-Reviews in Medicinal Chemistry

Editorial: Protective role of gut microbial SCFAs – Ellen F. Carney – Nature Reviews Nephrology

Human oral microbiome

In vitro work: Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

Human gut microbiome

Agave Inulin Supplementation Affects the Fecal Microbiota of Healthy Adults Participating in a Randomized, Double-Blind, Placebo-Controlled, Crossover Trial – Hannah D Holscher – Journal of Nutrition

Plant, root, and soil microbiome

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea – C. Thomas – Geobiology

Evidence for biological shaping of hair ice – D. Hofmann – Biogeosciences

Water and extremophile microbiome

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor – F. Inagaki – Science

Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs – Samia Amarouche-Yala – Extremophiles

Bacterial diversity in snow on North Pole ice floes – Aviaja L. Hauptmann – Extremophiles

Identifying the sources of nitrate contamination of groundwater in an agricultural area (Haean basin, Korea) using isotope and microbial community analyses – Heejung Kim – Science of the Total Environment

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages – Haiwei Luo – Molecular Biology and Evolution

Built environment microbiome

Microbiological characterization of 3193 French dwellings of Elfe cohort children – S. Rocchi – Science of The Total Environment

Metagenomics and bioinformatics

For plant/animal assemblages, but might be of interest: cati: an R package using functional traits to detect and quantify multi-level community assembly processes – Adrien Taudiere – Ecography

Metabolomics and proteomics

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation – Rafael Bargiela – Proteomics

Microbes in the news

‘It’s like going to Pluto and seeing McDonald’s: ‘These microbes live more than 2 kilometers below the sea floor off the coast of Japan – Mitch Leslie – Science

It takes a village… to ward off dangerous infections? New microbiome research suggests so – MedicalXpress

Pathogenic microbiome bacteria change shape to adapt to nasopharyngeal environment – American Microbiome Institute

Rotting Fungus Creates Beautiful, Glistening ‘Hair Ice’ – Elizabeth Goldbaum – LiveScience

Not endorsing this one, full of errors and false claims: Discovery of Microbiome “Third Brain” Confirmed by Scientific Research in Japan – BusinessWire

Science, publishing, and career

New life for old bones: inventing ways to apply the DNA sequencing revolution to tissues ravaged by time. – Elizabeth Culotta – Science

Songwriting and science: Pitching songs, however, has taught me a few practical lessons about pitching papers and grant proposals: – C. Neal Stewart Jr. – Science

Bik’s Picks

Comparisons of life-history parameters between free-ranging and captive killer whale (Orcinus orca) populations for application toward species management – Todd R. Robeck – Journal of Mammalogy

Kiwi genome provides insights into evolution of a nocturnal lifestyle – Diana Le Duc – Genome Biology

A medical-toxicological view of tattooing – Peter Laux – The Lancet

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July 23, 2015

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Proteobacteria in gut dysbiosis, microbes on seagrass, viral dark matter, metabolic ups and downs in the biofilm, bacteria/whiskey/copper, The Brown Lagoon, and I’ll see you in the gut.

Human gut microbiome

Review: Proteobacteria: microbial signature of dysbiosis in gut microbiota – Na-Ri Shin – Trends in Biotechnology

DGGE: Equol status and changes in faecal microbiota in menopausal women receiving long-term treatment for menopause symptoms with a soy-isoflavone concentrate – Lucía Guadamuro – Frontiers in Microbiology

Microbiome models

Editorial with a clever title. Like. Escaping Negative Selection: ILC You in the Gut – Adam M. Farkas – Immunity

Maraviroc modifies gut microbiota composition in a mouse model of obesity: a plausible therapeutic option to prevent metabolic disorders in HIV-infected patients – Patricia Perez-Matute – Rev Esp Quimioter

Plants, roots, and soil microbiome

Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals – A. Schmalenberger – Scientific Reports

Cultivation-dependent analysis the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea (sic) – Yu-Feng Jiang – Ecotoxicology

Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417 – Roeland L. Berendsen – BMC Genomics

Water microbiome

Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin – Perrine Cruaud – Frontiers in Marine Science

Assessment of Zooplankton Community Composition along a Depth Profile in the Central Red Sea – John K. Pearman – PLOS ONE

Waste and bioreactor microbiology

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage – Susanne G. Langer – Microbial Biotechnology

Effects of Calamagrostis epigejos, Chamaenerion palustre and Tussilago farfara on nutrient availability and microbial activity in the surface layer of spoil heaps after hard coal mining – Anna M. Stefanowicz – Ecological Engineering

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition – Franziska S. Hanschen – PLOS ONE

Assessing hog lagoon waste contamination in the Cape Fear Watershed using Bacteroidetes 16S rRNA gene pyrosequencing – Ann M. Arfken – Applied Microbiology and Biotechnology

Bacterial community structure and predicted alginate metabolic pathway in an alginate-degrading bacterial consortium – Akihisa Kita – Journal of Bioscience and Bioengineering

Metagenomics and bioinformatics

Viral dark matter and virus-host interactions resolved from publicly available microbial genomes – Simon Roux – eLIFE

Conference abstract: MetaFast: fast reference-free graph-based comparison of shotgun
metagenomic data – Sergey V. Kazakov

Microbial Ecology

Metabolic co-dependence gives rise to collective oscillations within biofilms – Jintao Liu – Nature

Neutral Models of Microbiome Evolution – Qinglong Zeng – PLOS Computational Biology

Fitness cost of antibiotic susceptibility during bacterial infection – Damien Roux – Science Translational Medicine

New Paradigms in Sepsis: From Prevention to Protection of Failing Microcirculation –
J. Hawiger – Journal of Thrombosis and Haemostasis

Helicobacter pylori eradication for the prevention of gastric neoplasia – Alexander C Ford – Cochrane Library

Microbes in the news

Mutations that make bacteria resistant to antibiotics might also make them deadlier – Arielle Duhaime-Ross – The Verge

Bacteria are many things, but selfish isn’t one of them, scientists say – Robert Gebelhoff – Washington Post

Ulcer-causing bacteria may be key to stomach cancer: A combination of antibiotics and a drug reducing the production of gastric acid can eliminate the bacteria – Stephen Feller – UPI

Project aims to use probiotic bacteria to protect algal crops and increase ecosystem resilience – Lawrence Livermore National Laboratory

Bacteria makes copper from whisky waste – Tereza Pultarova – E&T Institution for Engineering and Technology

Bik’s Picks – reptile edition

HT Ed Yong: No Motherhood Yet for 100-Year-Old Turtle – John R. Platt – Scientific American

Turns Out Boa Constrictors Might Not Actually Suffocate Their Prey – Hilary Hanson – Huffington Post

A Fossil Snake With Four Legs – Ed Yong – National Geographic
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July 22, 2015

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Disappearance of intestinal diversity with Westernization, microbial responses in the Namib Desert after “wetting events”, how fast do ocean bacteria grow, irradiation of oral microbiota, and paying $8 to read 2 sentences.

Human gut microbiome

Antibiotic Exposure and Juvenile Idiopathic Arthritis: A Case–Control Study – Daniel B. Horton – Pediatrics

Bile diversion to the distal small intestine has comparable metabolic benefits to bariatric surgery – Charles Robb Flynn – Nature Communications

Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory bowel disease – S. K. Hourigan – Alimentary Pharmacology & Therapeutics

Review: Gut Microbiome: Westernization and the Disappearance of Intestinal Diversity – Nicola Segata – Current Biology

Models of microbiome research

Dual zinc transporter systems in Vibrio cholerae promote competitive advantages over gut microbiome – Ying Sheng – Infection and Immunity

Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

You have to pay $8 to read the remaining 2 sentences of this In Brief: Engineered microbes treat experimental hyperammonemia – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Review: The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution – Andreas Brune and Carsten Dietrich – Annual Review of Microbiology

Plant, root, and soil microbiome

Effects of silver sulfide nanomaterials on mycorrhizal colonization of tomato plants and soil microbial communities in biosolid-amended soil – Jonathan D. Judy – Environmental Pollution

Phylogenic diversity and tissue specificity of fungal endophytes associated with the pharmaceutical plant, Stellera chamaejasme L. revealed by a cultivation-independent approach – Hui Jin – Antonie van Leeuwenhoek

Water regime history drives responses of soil Namib Desert microbial communities to wetting events – Aline Frossard – Scientific Reports

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility – Acacio Aparecido Navarrete – Antonie van Leeuwenhoek

Water microbiome

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms – Marine Landa – The ISME Journal

Review: Growth Rates of Microbes in the Oceans – David L. Kirchman – Annual Review of Marine Science

Metagenomics, bioinformatics

Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data – Will Rowe – PLOS ONE

Protective tunicate endosymbiont with extreme genome reduction – Jan-Christoph Kehr – Environmental Microbiology

Metabolomics

Microbial Urease in Health and Disease – Diego Mora – PLOS Pathogens

Techniques

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae) – Anush Kosakyan – European Journal of Protistology

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets – Guoqin Yu – PLOS ONE

Bacteria in the news

Fungi—key to tree survival in warming forest – Phys.org

Story behind the paper: Backbones of evolutionary history test biodiversity theory for microbes – James O. Dwyer – The Tree of Life

New open source uBiome github repository for data analysis tools – Alexandra Carmichael – uBiome

Bik’s Picks

The picture almost made me cry. Early signs that drug ‘may delay Alzheimer’s decline’ – James Gallagher – BBC News

Earth’s Most Famous Climate Scientist Issues Bombshell Sea Level Warning – Eric Holthaus – Slate

Space travel thins your skin: Spending a significant amount of time in space has several negative effects on the body. The latest discovery: thinner skin – Michelle Starr – CNET

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July 21, 2015

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Microbiome of a dead pig in the snow, two papers on oral microbiome in HIV infection, sweetener consumption and microbiome, proteomics of preterm infant colonization, sequencing platform and primer choices, and including microbial ecology in Pre-med programs.

Microbiology of death

Using Bacterial and Necrophagous Insect Dynamics for Post-Mortem Interval Estimation during Cold Season: Novel Case Study in Romania – Lavinia Iancu – Forensic Science International

Pregnancy and birth / Proteomics

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant – Brandon Brooks

Human oral microbiome

The Oral Microbiome in HIV-positive Individuals – James O. Kistler – Journal of Medical Microbiology

Exploring salivary microbiota in AIDS patients with different periodontal statuses using 454 GS-FLX Titanium pyrosequencing – Fang Zhang – Frontiers in Cellular and Infection Microbiology

Review: Bacteria and Archaea Paleomicrobiology of the Dental Calculus: a Review – Hong T.T. Huynh – Molecular Oral Microbiology

Human urinary tract microbiome

Review: Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Human gut microbiome

High-intensity sweetener consumption and gut microbiome content and predicted gene function in a cross-sectional study of adults in the United States – Cara L. Frankenfeld – Annals of Epidemiology

Pomegranate extract induces ellagitannin metabolite formation and changes stool microbiota in healthy volunteers – Zhaoping Li – Food & Function

Models of microbiome

Neutrophil gelatinase-associated lipocalin regulates gut microbiota of mice – Katsuya Mori – Journal of Gastroenterology and Hepatology

Effect of Dietary Protein Levels on Composition of Odorous Compounds and Bacterial Ecology in Pig Manure – Sungback Cho – Asian Australas. J. Anim. Sci

Animal microbiome

Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis – Martin Zinicola – PLOS ONE

Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Isolation, characterization, and antibiotic resistance of Vibrio spp. in sea turtles from Northwestern Mexico – Alan A. Zavala-Norzagaray – Frontiers in Microbiology

Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese – Cristina M. Hansen – Applied and Environmental Microbiology

An insight into the functional role of thioredoxin reductase, a selenoprotein, in maintaining normal native microbiota in the Gulf Coast tick (Amblyomma maculatum) – K. Budachetri – Insect Molecular Biology

Chemotaxis by natural populations of coral reef bacteria – Jessica Tout – The ISME Journal

Review: Exploring the avian gut microbiota: current trends and future directions – David W. Waite – Frontiers in Microbiology

Plant, root, and soil microbiome

Lactic acid bacteria are endophytic components of durum wheat plant following the whole life cycle from plant to flour – Fabio Minervini – Applied and Environmental Microbiology

Application of mesotrione at different doses in an amended soil: Dissipation and effect on the soil microbial biomass and activity – Eva Pose-Juan – Science of The Total Environment

Plant species richness does not attenuate responses of soil microbial and nematode communities to a flood event – Daniela Wagner – Soil Biology and Biochemistry

Declined soil suppressiveness to Fusarium oxysporum by rhizosphere microflora of cotton in soil sickness – Xiaogang Li – Biology and Fertility of Soils

Water / extremophile microbiome

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea – Yue Guan – Research in Microbiology

Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions – Christopher M. Bellas – Frontiers in Microbiology

A Paleoarchean coastal hydrothermal field inhabited by diverse microbial communities: the Strelley Pool Formation, Pilbara Craton, Western Australia – K. Sugitani – Geobiology

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents – Daniel C Reed – The ISME Journal

Waste and bioreactor microbiology

GeoChip-based analysis of microbial community of a combined nitritation-anammox reactor treating anaerobic digestion supernatant – Jian Zhao – Water Research

Arsenic toxicity effects on microbial communities and nutrient cycling in indoor experimental channels mimicking a fluvial system – Baigal-Amar Tuulaikhuu – Aquatic Toxicology

Microbial ecology

Review: Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis – Florent Lassalle – Research in Microbiology

Microbiology and Ecology Are Vitally Important to Premedical Curricula – Val H. Smith – Evolution, Medicine, and Public Health

Bioinformatics and metagenomics
MCaVoH: A toolkit for Mining, Classification and Visualization of Human Microbiota –
Maryum Nisar – Journal of Microbiological Methods

An intriguing new bacterial phylum – Naomi Attar – Nature Reviews Microbiology

Metabolic networks

A biosynthetic pathway for a prominent class of microbiota-derived bile acids – A Sloan Devlin – Nature Chemical Biology

Methanogenic food web in the gut contents of methane-emitting earthworm Eudrilus eugeniae from Brazil – Kristin Schulz – The ISME Journal

Auxotrophy and intra-population complementary in the ‘interactome’ of a cultivated freshwater model community – Sarahi L Garcia – Molecular Ecology

Techniques

Primer and platform effects on 16S rRNA tag sequencing – Julien Tremblay – Frontiers in Microbiology

Microbes in the news

Programming Bacteria to Kill Cancer Cells – Lecia Bushak – Newsweek

Scientists keep finding more evidence that bacteria in your stomach are connected to your mood – Kevin Loria – Business Insider

#BacteriaHysteria: The even grosser cause behind gross smelling feet – Stephanie Bell-Flynt

Bik’s Picks
One Migration from Siberia Peopled the Americas: Study – Discovery

Study: Women With Mild Memory Problem Worsen Faster Than Men – Lauran Neergaard – ABC News

Marijuana helps broken bones heal, says Israeli scientific team – Ruth Schuster – Haaretz

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