Category Archives: Water microbiome

August 1, 2015

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So many new papers, so here is another Saturday installment of The Digest. Several papers on microbiome during pregnancy or the first months of life, ear infections, having older siblings, rhizosphere on volcanic islands, and aquatic fungal communities.

General human microbiome

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota – David J. Roach – PLOS Genetics

Opinion: The human–microbe metaorganism, evolution and extraterrestrial colonization – Leonard A Mermel – Future Microbiology

Frailty and the Microbiome – Meehan C.J. – Frailty in Aging

Pregnancy and birth microbiome

Secretor Status Is Strongly Associated with Microbial Alterations Observed during Pregnancy – Himanshu Kumar – PLOS ONE

Longitudinal Survey of Microbiota in Hospitalized Preterm Very Low Birth Weight Infants – Patel, Aloka L. – Journal of Pediatric Gastroenterology & Nutrition

Lactation and Intestinal Microbiota: How Early Diet Shapes the Infant Gut
Felicia Goldsmith – Journal of Mammary Gland Biology and Neoplasia

DGGE: Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Early Gut Colonization with Lactobacilli and Staphylococcus in Infants: the Hygiene Hypothesis Extended – Salminen, Seppo – Journal of Pediatric Gastroenterology & Nutrition

Association between positive urine cultures and necrotizing enterocolitis in a large cohort of hospitalized infants – Leslie C. Pineda – Early Human Development

Human oral microbiome

Strains of Enterococcus faecalis differ in their ability to coexist in biofilms with other root canal bacteria – L. E. Chávez de Paz – International Endodontic Journal

Human respiratory microbiome

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation – Elise S. Cowley – mBio

Human skin and ear microbiome

The microbiome of otitis media with effusion in Indigenous Australian children – Jake Jervis-Bardy – International Journal of Pediatric Otorhinolaryngology

Review: Probiotics in personal care products – Mei-Chiung Jo Huang – Microbiology Discovery

Human gut microbiome

Having older siblings is associated with gut microbiota development during early childhood – Martin Frederik Laursen – BMC Microbiology

Serum Trimethylamine-N-Oxide is Elevated in CKD and Correlates with Coronary Atherosclerosis Burden – Jason R. Stubbs – Journal of the American Society of Nephrology

Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer – Zhiguang Gao – Molecular Medicine Reports

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

Review: Gut microorganisms as promising targets for the management of type 2 diabetes – Nathalie M. Delzenne – Diabetologia

Microbiome models

Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection – Andrew Leber – PLOS ONE

Evaluation of mucositis induced by irinotecan after microbial colonization in germ-free mice – Silvia H S P Pedroso – Microbiology

Animal microbiome

Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow trout Oncorhynchus mykiss (Walbaum) using next generation sequencing (NGS) – Philip P. Lyons – Aquaculture Research

Plant, root, and soil microbiome

Rhizosphere on volcanic islands: Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands – Yoon-Jong Nam – The Journal of General and Applied Microbiology

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants – Rashi Gupta – PLOS ONE

Vulnerability of Soil and Its Associated Organic Matter to Degradation in a Subtropical Region: A Study From São Paulo State, Brazil – Alexandre Marco da Silva – Environment Quality Management

Effects of historical logging on soil microbial communities in a subtropical forest in southern China – Piao Song – Plant and Soil

Effects of rotifers, copepods and chironomid larvae on microbial communities in peatlands – Tomasz Mieczan – European Journal of Protistology

Methanogenic microbial community of the Eastern Paris Basin: Potential for energy production from organic-rich shales – Margaux Meslé – International Journal of Coal Geology

All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Phylogenetic structure of arbuscular mycorrhizal community shifts in response to increasing soil fertility – Yongjun Liu – Soil Biology and Biochemistry

Water and extremophile microbiome

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge – Erin M. Bertrand – PNAS

Effects of hydrostatic pressure on yeasts isolated from deep-sea hydrothermal vents – Gaëtan Burgaud- Research in Microbiology

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data – Katrin Panzer – PLOS ONE

Metaproteomics of aquatic microbial communities in a deep and stratified estuary – David Colatriano – Proteomics

Waste treatment microbiology

Review: Meta-omics approaches to understand and improve wastewater treatment systems – Elisa Rodríguez – Reviews in Environmental Science and Bio/Technology

Metagenomics and bioinformatics

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples – Tal Korem – Science

Spaced seeds improve k-mer-based metagenomic classification – Karel Břinda – Bioinformatics

Microbial Ecology

Resource pulses can alleviate the biodiversity–invasion relationship in soil microbial communities – Cyrus A. Mallon – Ecology

Not sure if I like this term: Tritagonist as a new term for uncharacterised microorganisms in environmental systems – Florian M Freimoser – ISME Journal

Microbes in the news

Bacteria on chicken, turkey, pork linked to bladder infections – Lynne Terry – Oregon Live

Byproduct of intestinal bacteria may jeopardize heart health in kidney disease patients – Medical Xpress

Oregon architecture researchers to study indoor air quality in 72 homes – EurekAlert

Research spotlights a previously unknown microbial ‘drama’ playing in the Southern Ocean – Science Daily

Government of Canada Invests in New Western Canadian Microbiome Centre – Sys-Con Media

A Video of the destruction can be seen here: Wood-Decay Fungus Identified as Culprit Consuming Pomona Family’s Home – LA Testing

Microbes and Art

Don’t Be Grossed Out, The Bacteria On These Petri Dish Plates Is Art – Andrew Liszewski – Gizmodo

Call for Entries! ASM’s 2015 Agar Art Contest: Submit your work by September 3th – MicrobeWorld

Bik’s Picks: drought edition

Puget Sound sweltering from the drought and Blob – Department of Ecology – Courier Herald

Extreme Droughts Weaken Trees’ Ability to Soak Up Carbon – William R L Anderegg – Gizmodo

It’s Raining Spiders! Weirdest Effects of California Drought – Tia Ghose – Live Science

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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 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 18, 2015

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Microbes lighting up the clouds, bacterial degradation of human bone, and probiotics after colonoscopy.

Microbiome of death

An Investigation Into the Relationship Between Funerary Treatment and Bacterial Bioerosion in European Archaeological Human Bone – T. J. Booth – Archaeometry

Human oral microbiome

Cytokine expression in peri-implant crevicular fluid in relation to bacterial presence
– Stefan Renvert – Journal of Clinical Periodontology

High-quality draft genome sequences of five anaerobic oral bacteria and description of
Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae – Maria V. Sizova – Standards in Genomic Sciences

The metabonomic studies of tongue coating in H.pylori positive chronic gastritis patients – Xuan Liu – Evidence Based Complimentary and Alternative Medicine

Human gut microbiome

Randomized controlled trial of probiotics after colonoscopy – Basil D’Souza – ANZ Journal of Surgery

Animal models of microbiome

Chlorinated Water Modulates the Development of Colorectal Tumors with Chromosomal Instability and Gut Microbiota in Apc-Deficient Mice – Tatsunari Sasada – PLOS ONE

A novel “humanized mouse” model for autoimmune hepatitis and the association of gut microbiota with liver inflammation – Muhammed Yuksel – Hepatology

Modulation of gut microbiota in rats fed high-fat diets by processing whole-grain barley to barley malt – Yadong Zhong – Molecular Nutrition & Food Research

Effects of microcystin-LR on gut microflora in different gut regions of mice – Jing Chen – The Journal of Toxicological Sciences

Animal microbiome

Review: Advancements in Bovine Rumen Microbial Ecology: A Review – Nidhi R. Parmar – Int.J.Curr.Microbiol.App.Sci

Bacteria detected in the honeybee parasitic mite Varroa destructor collected from beehive winter debris – Jan Hubert – Journal of Applied Microbiology

A comparative study on microbiota from the intestine of Prussian carp (Carassius gibelio) and their aquatic environmental compartments, using different molecular methods – Elena N. Kashinskaya – Journal of Applied Microbiology

Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons – Sara Mishamandan – Environmental Microbiology

Host-Specific and pH-Dependent Microbiomes of Copepods in an Extensive Rearing System – Alf Skovgaard – PLOS ONE

Microenvironment and Phylogenetic Diversity of Prochloron Inhabiting the Surface of Crustose Didemnid Ascidians – Daniel A. Nielsen – Environmental Microbiology

Plant, root, and soil microbiome

Editorial: Environmental phytoremediation: plants and microorganisms at work – Antonella Furini – Frontiers in Plant Science

Diversity and distribution of endophytic bacterial community in the Noni (Morinda citrifolia L.) plant – Yang Liu – African Journal of Microbiology Research

Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests – Hui Li – Scientific Reports

Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity – Johan Habig – Environments

Resilience and receptivity worked in tandem to sustain a geothermal mat community amidst erratic environmental conditions – Wriddhiman Ghosh – Scientific Reports

Determinants of bacterial communities in Canadian agroforestry systems – Samiran Banerjee – Environmental Microbiology

Indigenous arsenic(V)-reducing microbial communities in redox-fluctuating near-surface sediments of the Mekong Delta – S. C. Ying – Geobiology

Impact of soil salinity on arbuscular mycorrhizal fungi biodiversity and microflora biomass associated with Tamarix articulataVahll rhizosphere in arid and semi-arid Algerian areas – Karima Bencherif – Science of The Total Environment

Water microbiome

Natural aerosols explain seasonal and spatial patterns of Southern Ocean cloud albedo – Daniel T. McCoy – Science Advances

Diversity of bacterioplankton in the surface seawaters of Drake Passage near the Chinese Antarctic station – Mengxin Xing – FEMS Microbiology Letters

Seasonality in molecular and cytometric diversity of marine bacterioplankton: the reshuffling of bacterial taxa by vertical mixing – Francisca C. García – Environmental Microbiology

Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool – Weipeng Zhang – Environmental Microbiology

Waste treatment microbiology

Changes in bacterial and archaeal communities in anaerobic digesters treating different organic wastes – Young Mo Kim – Chemosphere

The role of starvation in biomass harvesting and lipid accumulation: Co-culture of microalgae–bacteria in synthetic wastewater – Yanjia Xu – Environmental Progress & Sustainable Energy

A high-throughput sequencing study of bacterial communities in an autohydrogenotrophic denitrifying bio-ceramsite reactor– Dan Chen – Process Biochemistry

Food microbiology

Packaging gas selects lactic acid bacterial communities on raw pork – Timo T Nieminen – Journal of Applied Microbiology

Metabolic networks

Enteric Pathogens Exploit the Microbiota-generated Nutritional Environment of the Gut – Alline R. Pacheco – Microbiology Spectrum

Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH – Martin Kaltenpoth – The ISME Journal

Techniques

Phospholipid fatty acid profiling of microbial communities – a review of interpretations and recent applications – C Willers – Journal of Applied Microbiology

Microbes in the news

Tiny Ocean Microbes are Brightening Up the Sky – Maddie Stone – Gizmodo

Baby’s Microbiome: Why Birth to Age Three Is So Critical For Your Child’s Health – Toni Harman – Huffington Post

These caffeine-addicted beetles are using bacteria to ruin all of our coffee – Elahe Izadi – Washington Post

Unearthing Cornerstones in Root Microbiomes. Defining core members of a microbial community for normal plant growth – Joint Genome Institute

You Need Way More Nutrients for Good Gut Health – Rachael Schultz – Shape

Targeting gut microbiome boosted metformin tolerance – Jennie Smith – Clinical Endocrinology News

Scientist develops model for robots with bacteria-controlled brains – Phys.org

Bik’s Picks

Watch what happens when a spinning basketball gets thrown off a dam – Chris Matyszczyk – CNET

Restaurant Food May Be Unhealthier Than Fast Food – Mandy Oaklander – Time

U.S. Adults Are Not Eating Enough Vegetables, Fruit – Says New Study – Matthew Rideout – The Times Gazette

Sea turtle released off Florida Keys tracked by satellite – Daily Commercial

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July 17, 2015

Posted on by

Laser Capture Microdissection of tissue from infants with NEC, skin microbiome from Chinese subjects, paromomycin treatment effects on human gut microbiome.

General human microbiome

Prenatal exposure to systemic antibacterials and overweight and obesity in danish schoolchildren: A prevalence study – A Mor – International Journal of Obesity

Review: Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior – Peter Kramer – Perspectives on Psychological Science

Pregnancy and birth microbiome

Application of Laser Capture Microdissection and 16S rRNA Gene PCR in the Analysis of Bacteria Colonizing the Intestinal Tissue of Neonates with Necrotizing Enterocolitis – Jingli Yang – The Pediatric Infectious Disease Journal

Human oral microbiome

Checkerboard Assay: Advanced Caries Microbiota in Teeth with Irreversible Pulpitis –
Isabela N. Rôças – Journal of Endodontics

Human skin microbiome

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups – Marcus H. Y. Leung – Scientific Reports

Human gut microbiome

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin – Femke-Anouska Heinsen – Gut Microbes

Short-term High Fat Diet Increases Postprandial Trimethylamine-N-Oxide in Humans – Nabil E. Boutagy – Nutrition Research

In Brief/ Editorial: Modifying the gut to treat liver diseases – Cláudio Nunes-Alves – Nature Reviews Microbiology

Review: Talking microbes: when gut bacteria interact with diet and host organs – Patrice D. Cani – Molecular Nutrition & Food Research

Review: Metagenomic Surveys of Gut Microbiota – Rahul Shubhra Mandal – Genomics, Proteomics & Bioinformatics

Review: The bilateral responsiveness between intestinal microbes and IgA – Andrew J. Macpherson – Trends in Immunology

Animal and other models

How free of germs is germ-free? Detection of bacterial contamination in a germ free mouse unit – Clinton A Fontaine – Gut Microbes

Microbes & Neurodevelopment – Absence of Microbiota during Early Life Increases Activity-Related Transcriptional Pathways in the Amygdala – Roman M. Stilling – Brain, Behavior, and Immunity

Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut – Aaron Conrad Ericsson – Physiological Genomics

Polyphenols-rich fruit in maternal diet modulates inflammatory markers and the gut microbiota and improves colonic expression of ZO-1 in offspring – Carina Almeida Morais – Food Research International

Defined Nutrient Diets Alter Susceptibility to Clostridium difficile Associated Disease in a Murine Model – John H. Moore – PLOS ONE

Soluble Dextrin Fibers Alter Intestinal Microbiota and Reduce Proinflammatory Cytokine Secretion in Male IL-10–Deficient Mice – Rosica Valcheva – The Journal of Nutrition

Kiwifruit fermentation drives positive gut microbial and metabolic changes irrespective of initial microbiota composition – Paul Blatchford – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

The potential roles of bacterial communities in coral defence: A case study at Talang-talang reef – Felicity W. I. Kuek – Ocean Science Journal

Soil

Land-use system shapes soil bacterial communities in Southeastern Amazon region – Lucas William Mendes – Applied Soil Ecology

Water microbiome

Seasonal progression of microbial communities on the Faroe shelf – Anni Djurhuus – Marine Biology Research

Waste treatment microbiology

Understanding the linkage between elevation and activated sludge bacterial community along a 3600 m elevational gradient in China – Lihua Niu – Applied and Environmental Microbiology

Techniques

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities – Mads Albertsen – PLOS ONE

Microbial ecology

Interaction networks for identifying coupled molecular processes in microbial communities – Magnus Bosse – BioData Mining

Microbes in the news

10 Ways to Cultivate Good Gut Bacteria and Reduce Depression – Therese Borchard – Everyday Health

Science, publishing, and career

Hundreds sign letter criticizing Science for reinforcing “damaging stereotypes” – Shannon Palus – Retraction Watch

Bik’s Picks

International report confirms: 2014 was Earth’s warmest year on record – NOAA

A second FDA approval frees Theranos to do a blood test outside lab – Roger Parloff – Fortune

Mosquitoes first sniff then attack their host – Dispatch Times

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