Category Archives: Techniques

February 10, 2016

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Socioeconomic status and microbiota diversity, metagenome of a carnivorous plant, microbiota of homes of CF patients, and high-resolution phylogenetic microbial community profiling.

Events

ASM Microbe 2016, June 16-20, Boston MA. With opening keynote lecture by Bill Gates

SC2: Microbiome: Sorting out the hype from the hope – March 6-11 2016, San Francisco

Probiotics and Prebiotics – June 21-23, Budapest

Pregnancy and birth

Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome – Abdulkadir B. – Neonatology

Human oral microbiome

Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication – Sadia Ambreen Niazi – Clinical Oral Investigations

Human gut microbiome

Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach – Francesca Turroni – The ISME Journal

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults – Gregory E. Miller – PLOS ONE

The features of mucosa-associated microbiota in primary sclerosing cholangitis –
J. Torres – Alimentary Pharmacology & Therapeutics

Review: Physiological Role of Gut Microbiota for Maintaining Human Health – Andoh A. – Digestion

Editorial: You Are What You Feed Your Gut Microbiome – Joseph E. Scherger – Health Affairs

Review: Gastroenvironmental distress: metaphorical antecedents of the gut microbiome – Nitin K Ahuja – Medical Humanities

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Models of microbiome research

Drosophila: Preventing Age-Related Decline of Gut Compartmentalization Limits Microbiota Dysbiosis and Extends Lifespan – Hongjie Li – Cell Host & Microbe

Editorial: Microbes without Borders: Decompartmentalization of the Aging Gut – Erin S. Keebaugh – Cell Host & Microbe

Mice (and humans): Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation – Lirui Wang – Cell Host & Microbe

Editorial: Alcohol Lowers Your (Intestinal) Inhibitions – Namrata Iyer – Cell Host & Microbe

Mice: Daikenchuto (TU-100) shapes gut microbiota architecture and increases the production of ginsenoside metabolite compound K – Takumu Hasebe – Pharmacology Research & Perspectives

Editorial: Microbiota Control of Malaria Transmission – Miguel P. Soares – Trends in Parasitology

Animal microbiome

Beetles: Trophic and Non-Trophic Interactions in a Biodiversity Experiment Assessed by Next-Generation Sequencing – Julia Tiede – PLOS ONE

Plant, root, and soil microbiome

The Metagenome of Utricularia gibba’s Traps: Into the Microbial Input to a Carnivorous Plant – Luis David Alcaraz – PLOS ONE

Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria – Sai Shiva Krishna Prasad Vurukonda – Microbiological Research

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity –
Fatemeh Mohammadipanah – Frontiers in Microbiology

Organic Fertilization in Traditional Mediterranean Grapevine Orchards Mediates Changes in Soil Microbial Community Structure and Enhances Soil Fertility – Fuensanta García-Orenes – Land Degradation & Development

Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland – Dima Chen – Journal of Ecology

Water microbiome

Plankton networks driving carbon export in the oligotrophic ocean – Lionel Guidi – Nature

Built environment microbiome

Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections – Alya Heirali – PLOS ONE

Metabolomics

Microbial metabolomics in open microscale platforms – Layla J. Barkal – Nature Communications

More microbiology

Open for discussion: Bacterial sequences detected in 99 out of 99 serum samples from Ebola patients – Marina Manrique – bioRxiv

Ethanol Production by Selected Intestinal Microorganisms and Lactic Acid Bacteria Growing under Different Nutritional Conditions – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Rapid radiation in bacteria leads to a division of labour – Wook Kim – Nature Communications

Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli – Akira Nakagawa – Nature Communications

Bioinformatics and metagenomics

PhyloTags: High-resolution phylogenetic microbial community profiling – Esther Singer – The ISME Journal

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum – Karthik Anantharaman – PeerJ

Microbes in the news

The Good, the Bad and the Microbiome – Rachel Reisig – University of Minnesota

Unraveling the Mysterious Function of the Microbiome – by Mike Orcutt – MIT Technology Review

Wound-healing intestinal bacteria: Like shrubs after a forest fire
Akkermansia + other anaerobic bacteria temporarily bloom – EurekAlert

San Diego Scientists Find Data Brewing In Local Fermentation Culture – David Wagner – KPBS

Bacteria Have Ability to ‘See,’ Eye-Opening Study Finds – Maggie Fox – NBC News

A gut feeling about bacteria: Men are from Mars, women are from Venus – and their gut bacteria is just as different. – The Senior

How Your Gut Affects Your Bones. The surprising new science of how intestinal bacteria control bone strength – Rana Samadfam – Scientific American

Scientists Discover New Bacteria Responsible For Lyme Disease – David Beasly – Huffington Post

Overhyped: Sci-Q: The Science Of Love: The role of the microbiome in romantic attraction

Science, publishing, and career

Improving the peer-review process and editorial quality: key errors escaping the review and editorial process in top scientific journals – Antoni Margalida – PeerJ

Does it take too long to publish research? – Kendall Powell – Nature

The history of publishing delays – Daniel Himmelstein

The sexual misconduct case that has rocked anthropology – Michael Balter – Science
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February 9, 2016

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Human skin metagenome, gout patients, malaria and gut microbes, the secrets of the rhizosphere, and single-stranded DNA phages.

Events

2nd Annual Translational Microbiome Conference – April 20-21 2016, Boston MA

Pregnancy and birth

Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks – Michael J. McGeachie – Scientific Reports

Review: Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates – Nadim Cassir – Future Microbiology

Human skin microbiome

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing – Yu-Chih Tsai – mBio

Human urinary tract microbiome

Male non-gonococcal urethritis: From microbiological etiologies to demographic and clinical features – Shin Ito – International Journal of Urology

Research highlight: Altered gut microbiota in CKD – Jessica K. Edwards – Nature Reviews Nephrology

Human respiratory microbiome

Review: Microbiome, biofilms, and pneumonia in the ICU – Massimiliano Pirrone – Current Opinion in Infectious Diseases

Human gut microbiome

Intestinal Microbiota Distinguish Gout Patients from Healthy Humans – Zhuang Guo – Scientific Reports

Effect of Proton Pump Inhibitors and Antibiotics on the Gut Microbiome of Hospitalised Older Persons – Caoilfhionn O’Donoghue – Journal of Infection

Editorial: A metabolic bridge between microbiota and humans – Kiyoshi Takeda – Nature Reviews Immunology

Review: The Gut Microbiome: Potential Innovations for the Understanding and Treatment of Psychopathology – Matilda E. Nowakowski – Canadian Psychology/Psychologie canadienne

Review: Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

Review: The influence of commensal bacteria on infection with enteric viruses – Stephanie M. Karst – Nature Reviews Microbiology

Review: One more role for the gut: microbiota and blood brain barrier – Laure Michel – Annals of Translational Medicine

Review: Expanding role of gut microbiota in lipid metabolism – Anatole Ghazalpour – Current Opinion in Lipidology

Models of microbiome research

Mice: Composition of the gut microbiota modulates the severity of malaria – Nicolas F. Villarino – PNAS

Mice: Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection – Paul J. Planet – mBio

Dogs: Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Goats: The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome – Robert W. Li – Scientific Reports

More goats: Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats – Huimin Ye – Scientific Reports

Rats: The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet – Chunlong Mu – The Journal of Nutrition

Rats: Resistant Starch Alters Gut Microbiome and Metabolomics Profiles Concurrent with Amelioration of Chronic Kidney Disease in Rats – Dorothy A. Kieffer – American Journal of Physiology – Renal Physiology
http://ajprenal.physiology.org/content/early/2016/02/01/ajprenal.00513.2015.abstract

Drosophila: From pathogens to microbiota: how Drosophila intestinal stem cells react to gut microbes – Alessandro Bonfini – Developmental & Comparative Immunology

Animal microbiome

Host plant determines the population size of an obligate symbiont Buchnera aphidicola in aphids – Yuan-Chen Zhang – Applied and Environmental Microbiology

Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis – Fangyuan Zhou – Scientific Reports

Plant, root, and soil microbiome

Soil amendments yield persisting effects on the microbial communities—a 7-year study – Catherine L. Reardon – Applied Soil Ecology

Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland – Elise Morrison – Geoderma

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke – Hui Yan – Scientific Reports

Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi – Yuh Tzean – Microbial Biotechnology

Dilution reveals how viral lysis and grazing shape microbial communities – Jacob A. Cram – Limnology and Oceanography

Response of Soil Bacterial Community Structure to Land-use Conversion of Natural Forests in Maoershan National Forest Park, China – Fanjuan Meng – Molecular Soil Biology

Editorial: Unlocking the Secrets of the Rhizosphere – Susanne C. Brink – Trends in Plant Science

Spotlight: The soil-borne supremacy – Corné M.J. Pieterse – Trends in Plant Science

Water and pollution microbiome

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay – Yan Zhang – Journal of Environmental Sciences

Built environment microbiome

Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite – Dongshan An – Frontiers in Microbiology

Viruses and phages

Viral metagenomics: are we missing the giants? – S Halary – Current Opinion in Microbiology

Single-Stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology – Anna J. Székely – FEMS Microbiology Letters

Sequencing techniques

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms – Nagaraju Indugu – PeerJ

Bioinformatics and metagenomics

Improved environmental genomes via integration of metagenomic and single-cell assemblies – Daniel R. Mende – Frontiers in Microbiology

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes – Ivan Gregor- PeerJ

Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu – PeerJ

Metabolomics

Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

More microbiology

Cyanobacteria use micro-optics to sense light direction – Nils Schuergers – eLIFE

Ultrasensitive Detection of Bacteria by Targeting Abundant Transcripts – Xinhui Wang – Scientific Reports

Microbes in the news

Pill measures gut gas – Swallowable tool may eventually help reveal digestive problems – Sarah Schwartz – Science News

Gut environment could reduce severity of malaria – EurekAlert

Great stockphoto: Hibernation Helpers: Gut microbes may help regulate the metabolic changes a bear experiences before and during hibernation, scientists show – Catherine Offord – The Scientist

The complex marketing of “probiotic” cosmetics – Éva Lagarde – Premium Beauty News

Plants trick bacteria into attacking too soon – Chris Samoray – Science News

Obstructive sleep apnea-induced hypertension linked to gut microbiome – Baylor College of Medicine

Includes Rob Knight. HT: Tomer Altman. Deepak Chopra Convenes 30+ of the World’s Preeminent Thought Leaders, Philosophers, Scientists, Musicians and Artists to Explore Consciousness at a 3-Day Symposium This Fall – PR Newswire

Researchers identify most dangerous strains of often-deadly bacteria – University of Maryland – EurekAlert

Science, publishing, and career

Harvard Medical School students decry lack of diversity – Melissa Baily – STATnews

I make an appearance here: Getting credit for peer review – Sandeep Ravindran – Science

Change the system to halt harassment – Joan Schmelz – Nature

Bik’s Picks

The peptidergic control circuit for sighing – Peng Li – Nature

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February 8, 2016

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Plasmid-mediated salt tolerance in the gut microbiota, Tuft cells and immunity, microbes of the Cerrado, impact of sequencing technique on microbiota analysis, and a new microbiome tool on the cloud.

Events

Introducing Nephele, NIAID’s new cloud-based microbiome analysis tool. Webinar on March 7. See also under Bioinformatics below.

Human oral microbiome

Research highlight: FISHing in the oral microbiota – Naomi Attar – Nature Reviews Microbiology

Human gut microbiome

Intestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Evidence for plasmid mediated salt tolerance in the human gut microbiome and potential mechanisms – Eileen Broaders – FEMS Microbiology Ecology

Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD – Thomas Lee – Gut

Review: Novel Strategies for Applied Metagenomics – Moore-Connors, Jessica M. – Inflammatory Bowel Diseases

Research highlight: ntestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Models of microbiome research

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut – Michael R. Howitt – Science

Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance – H. Yan – Journal of Animal Physiology and Animal Nutrition

Beneficial Effects of Fecal Microbiota Transplantation on Ulcerative Colitis in Mice – Zhihui Tian – Digestive Diseases and Sciences

Plant, root, and soil microbiome

Soil bacterial communities associated with natural and commercial Cyclopia spp. – Anneke Postma – FEMS Microbiology Ecology

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere – Siddarthan Venkatachalam – Plant Biology

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils – Alinne Pereira de Castro – PLOS ONE

Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost – M. García-Jaramillo – Science of The Total Environment

Opinion: Plant microbiota affects seed transmission of phytopathogenic micro-organisms – Matthieu Barret – Molecular Plant Pathology

Built environment microbiome

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children – Karen C. Dannemiller – The Journal of Allergy and Clinical Immunology

Antibiotics in drinking water in Shanghai and its contribution to antibiotic exposure of school children – Hexing Wang – Environmental Science & Technology

Pollution and waste microbiology

Characterisation of biofilm and planktonic bacterial and fungal communities transforming high molecular weight polycyclic aromatic hydrocarbons – Benjamin D Folwell – Applied and Environmental Microbiology

Shift in antibiotic resistance gene profiles associated with nanosilver during wastewater treatment – Yanjun Ma – FEMS Microbiology Ecology

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water – Mathew L. Frankel- PLOS ONE

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Impacts of pristine and transformed Ag and Cu engineered nanomaterials on surficial sediment microbial communities appear short-lived – Joe D Moore – Environmental Science & Technology

Food microbiology

Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters – Ene Viiard – PLOS ONE

Techniques

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis – Adam G. Clooney – PLOS ONE

Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array – Shawn P. Brown – Molecular Ecology Resources

Probiotics

Probiotic and Functional Characterization of Bifidobacteria of Indian Human Origin – Nancy Awasti – Journal of Applied Microbiology

Bioinformatics

Nephele, microbiome analysis without boundaries. NIAID’s new tool offering cloud-based storage, file transfer, and analysis.

Note: 16S is not the same as metagenomics: Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets – Sunil Nagpal – PLOS ONE

Microbes in the news

Smart Science: Wolbachia Bacteria Might Stop Zika and Dengue Viruses – Judy Stone – Forbes

The science of treating depression during pregnancy – Josie Glausiusz – Quartz

GIANTmicrobes – When Teachers Throw Things – Anne Estes

Gut bacteria may influence alcoholics’ liver damage – Kathryn Doyle – Reuters
Scientists Seek Answers on Zika in Other Viruses – Carl Zimmer – New York Times

Bears’ Hibernation Linked To Unusual Changes In Their Gut Microbes – Samantha Mathewson – Nature World News

Bears hibernate ‘with bacterial help’ – Jonathan Webb – BBC News

The Tardigrade story a.k.a. Open Science Wins – Surya Saha – Storify

This Bacteria-Powered Microrobot Navigates via Electric Fields – Michael Byrne – Motherboard

Sainsbury’s Recall Camembert Cheese Products Over Food Poisoning Concerns – Natasha Hinde – The Huffington Post UK

EFSA update: Fully defining microbiota cause-and-effect: Yolanda Sanz provides update –
Will Chu – Nutraingredients

Satire: Trump Proposes Ban On All Microbiome Researchers “Until We Know What They Are Up To” “When I become president, we are going to make American poo great once again.” – The Allium

Bacteria Hysteria

What’s hiding in your handbag? Contact 6 tests purses for bacteria – Katrina Cravy – Fox

Bik’s Picks

Natural History Museums Are Teeming With Undiscovered Species – Ed Yong – The Atlantic

New species of tarantula found near Folsom Prison named for Johnny Cash – Rachel Feltman – Washington Post

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February 4, 2016

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A late digest today – Meetings and lab work kept me busy all day! Review about gut microbiota and malnutrition, Helicobacter infection affects local microbiome, salinity tolerance in corals, rhizosphere reviews, microbial mats in Shark Bay, and missing CRISPR regions in major bacterial lineages.

Jobs

Assistant, Associate or Senior Editor (Microbiology and Infectious Disease), Nature Communications, London, New York or Shanghai

Bioinformatics Scientist, Microbiome – Synthetic Genomics, Inc. – La Jolla CA

Pregnancy and birth
Routine Amoxicillin for Uncomplicated Severe Acute Malnutrition in Children – Sheila Isanaka – New England Journal of Medicine

Review: The case in favour of probiotics before, during and after pregnancy: insights from the first 1,500 days – G. Reid – Beneficial Microbes

Review: Development of the Neonatal Intestinal Microbiome and Its Association With Necrotizing Enterocolitis – Timothy G. Elgin – Clinical Therapeutics

Human oral microbiome

Interesting choice of  journal: Periodontitis induced by Porphyromonas gingivalis drives periodontal microbiota dysbiosis and insulin resistance via an impaired adaptive immune response – Vincent Blasco-Baque

Non-oral gram-negative facultative rods in chronic periodontitis microbiota – Arie J. van Winkelhoff – Microbial Pathogenesis

Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis – S. Bizzarro – Scientific Reports

Human respiratory microbiome

Effect of Advanced HIV Infection on the Respiratory Microbiome – Homer L Twigg III – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The emerging view of Firmicutes as key fibre degraders in the human gut – David Berry – Environmental Microbiology

Review: Gut Microbiota and Malnutrition – Matthieu Million – Microbial Pathogenesis

Review: Diet, Microbiota, And Dysbiosis: A ‘Recipe’ For Colorectal Cancer – Kishore Vipperla – Food & Function

Review: Microbiota, Immunity and the Liver – T. Vaikunthanathan – Immunology Letters

Animal and other models of microbiome research

Alterations of the Ileal and Colonic Mucosal Microbiota in Canine Chronic Enteropathies – Eric Cassmann – PLOS ONE

In a Neonatal Piglet Model of Intestinal Failure, Administration of Antibiotics and Lack of Enteral Nutrition Have a Greater Impact on Intestinal Microflora Than Surgical Resection Alone – Crystal L. Levesque – Journal of Parenteral & Enteral Nutrition

Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity – Anne L. Ballou – Frontiers in Veterinary Science

Gastric Helicobacter pylori Infection Affects Local and Distant Microbial Populations and Host Responses – Sabine Kienesberger – Cell Reports

Salmonella enterica Serovar Typhimurium Exploits Inflammation to Modify Swine Intestinal Microbiota – Rosanna Drumo – Frontiers in Cellular and Infection Microbiology

Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection – Qiuhong Niu – Scientific Reports

Chitosan lowers body weight through intestinal microbiota and reduces IL-17 expression via mTOR signalling – Dingfu Xiao – Journal of Functional Foods

The effect of agave fructan products on the activity and composition of the microbiota determined in a dynamic in vitro model of the human proximal large intestine – Marjorie E. Koenen – Journal of Functional Foods

Animal microbiome

Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome – Till Röthig – Molecular Ecology

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet – Wen Wang – Microbiology Open

Plant, root, and soil microbiome

Spatial Distribution of Fungal Communities in an Arable Soil – Julia Moll – PLOS ONE

Soil Nitrogen Status Modifies Rice Root Response to Nematode-Bacteria Interactions in the Rhizosphere – Yanhong Cheng – PLOS ONE

Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria – Paul C. A. Wintermans – Plant Molecular Biology

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition – Cheng Wang – Biotechnology for Biofuels

Microbial Profiling of a Suppressiveness-Induced Agricultural Soil Amended with Composted Almond Shells – Carmen Vida – Frontiers in Microbiology

Editorial: How does the tree root microbiome assemble? Influence of ectomycorrhizal species on Pinus sylvestris root bacterial communities – Aurélie Deveau – Environmental Microbiology

Lots of reviews on the plant rhizosphere in Trends in Plant Science: 

Review: Impact of Bacterial–Fungal Interactions on the Colonization of the Endosphere – Leonard S. van Overbeek – Trends in Plant Science

Review: Signaling in the Rhizosphere – Vittorio Venturi – Trends in Plant Science

Review: Root–Root Interactions: Towards A Rhizosphere Framework – Liesje Mommer – Trends in Plant Science

Review: Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication – Nicole M. van Dam – Trends in Plant Science

Opinion: Mannitol in Plants, Fungi, and Plant–Fungal Interactions
Takshay K. Patel – Trends in Plant Science

Water and extremophile microbiome

Evolution of Chemical Characteristics of Technosols in an Afforested Coal Mine Dump over a 20-year Period – Ivana M. Rivas-Pérez – Land Degradation and Development

Microbial mats: New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia – E. P. Suosaari – Scientific Reports

Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China – Peike Gao – Scientific Reports

Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea) – Christina Pavloudi – Marine Genomics

Microbial diversity in European alpine permafrost and active layers – Beat Frey – FEMS Microbiology Ecology

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Food microbiology

Unraveling the Enzymatic Basis of Wine “Flavorome”: A Phylo-Functional Study of Wine Related Yeast Species – Ignacio Belda – Frontiers in Microbiology

Developmental Peculiarities and Seed-Borne Endophytes in Quinoa: Omnipresent, Robust Bacilli Contribute to Plant Fitness – Andrea Pitzschke – Frontiers in Microbiology

Viruses, phages, and CRISPRs

Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems – David Burstein – Nature Communications

High-Throughput Isolation of Giant Viruses in Liquid Medium Using Automated Flow Cytometry and Fluorescence Staining – Jacques Y. B. Khalil – Frontiers in Microbiology

Review: Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems – Mart Krupovic – Current Opinion in Microbiology

Techniques

Assessing the impact of long term frozen storage of faecal samples on protein concentration and protease activity – Laura S. Morris – Journal of Microbiological Methods

More microbiology

Elie Metchnikoff, the Man and the Myth – Gordon S. – Journal of Innate Immunology

Microbes in the news

What Your Low-Fiber Diet Does to Your Health – Mandy Oaklander – Time

Your beard doesn’t contain poop, but it could help develop new antibiotics – Sarah Kaplan – The Washington Post

Modern microbial ecosystems provide window to early life on Earth. UM Rosenstiel School-led team reveals new details on modern-day stromatolites – Science Daily

Two Santa Clara University Students Confirmed with Meningitis – ABC7

USDA Imposes Stricter Limit On Salmonella Bacteria In Poultry Products – NPR Morning Edition

Young scientists present intriguing and surprising research – Kristen Browning-Blas – Colorado State University

Meet the CEO of Europe’s Leading Microbiome Biotech, Pierre Belichard of Enterome – Labiotech

Podcast: As Arctic Permafrost Thaws, Microbes Kick Into Action – with Janet Jansson – Science Friday

Podcast: Bear Gut Microbes Help Prep Hibernation – Karen Hopkin – Scientific American

Podcast: The Good Side of Viruses – Medical Discovery News
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February 2, 2016, second edition

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Updated status of the microbial census, bacteria in the nasopharynx, deodorant and armpit microbiome, lichen microbiome, fungi on decomposing forest materials, and metagenomics cover the amplicon gaps. So many papers I had to do a second installment today!

Events and jobs

Microbiology and bioinformatics positions at Whole Biome in San Francisco. Wearing hoodies encouraged.

General microbiome

The status of the microbial census: an update – Patrick D Schloss – BioRxiv

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R Theis – BioRxiv

Human oral microbiome

Interactions between Streptococcus oralis, Actinomyces oris, and Candida albicans in the development of multispecies oral microbial biofilms on salivary pellicle – Indira M.G. Cavalcanti – Molecular Oral Microbiology

Human respiratory microbiome

Unraveling the Molecular Mechanisms Underlying the Nasopharyngeal Bacterial Community Structure – Wouter A. A. de Steenhuijsen Piters – mBio 

Human skin microbiome

The effect of habitual and experimental antiperspirant and deodorant product use on the armpit microbiome – Julie Urban – PeerJ

Skin microbiome surveys are strongly influenced by experimental design – Jacquelyn S. Meisel – Journal of Investigative Dermatology

Unique features of a global human ectoparasite identified through sequencing of the bed bug genome – Joshua B. Benoit – Nature Communications

Human vaginal microbiome

Hormonal Contraceptive Effects on the Vaginal Milieu: Microbiota and Immunity – Jessica Tarleton – Current Obstetrics and Gynecology Reports

Human gut microbiome

Sex differences in the gut microbiome–brain axis across the lifespan – Eldin Jašarević – Philosophical Transactions of the Royal Society B

Very poor English and presentation, does not look peer reviewed: Preliminary analysis showed country-specific gut resistome based on 1267 feces samples – Zhenyu Yang – Gene

Confusing study design and interpretations: Gut Microbiota Linked to Sexual Preference and HIV Infection – Marc Noguera-Julian – EBioMedicine

Sequence-based methods for detecting and evaluating the human gut mycobiome – M.J. Suhr – Letters in Applied Microbiology

Review: Microbiota and arthritis: correlations or cause? – Bravo-Blas, Alberto – Current Opinion in Rheumatology

Perspective: Gut microbiota in 2015: Prevotella in the gut: choose carefully – Ruth E. Ley – Nature Reviews Gastroenterology & Hepatology

Editorial: PPIs alter gut microbiota composition – Nature Reviews Gastroenterology & Hepatology

Review: Samples and techniques highlighting the links between obesity and microbiota –
Emmanouil Angelakis – Microbial Pathogenesis

Animal models of microbiome

Bidirectional interactions between indomethacin and the murine intestinal microbiota – Xue Liang – eLife

 

Mixed feelings about this study that killed turtles to look at effect of probiotics on their shells: Dietary Probiotics Affect Gastrointestinal Microbiota, Histological Structure and Shell Mineralization in Turtles – Mateusz Rawski – PLOS ONE

Animal microbiome

The Role of the Microbial Environment in Drosophila Post-Embryonic Development –
Maura Strigini – Developmental & Comparative Immunology

Plant, root, and soil microbiome

Review about lichen bacterial microbiome: Understanding microbial multi-species symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology

Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community – Vendula Brabcová – New Phytologist

Litter decomposition, residue chemistry and microbial community structure under two subtropical forest plantations: A reciprocal litter transplant study –
Zongming He – Applied Soil Ecology

Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers – Michael Ackermann – Nematology

Using native trees and cacti to improve soil potential nitrogen fixation during long-term restoration of arid lands – Nguyen E. Lopez-Lozano – Plant and Soil

Warming and nitrogen deposition are interactive in shaping surface soil microbial communities near the alpine timberline zone on the eastern Qinghai–Tibet Plateau, southwestern China – Qinli Xiong – Applied Soil Ecology

Short-term effects of mechanical drainage on fungal and bacterial community structure in a managed grassland soil – B.J. Fay – Applied Soil Ecology

Water and extremophile microbiome

Microbial Communities in Methane- and Short Chain Alkane-Rich Hydrothermal Sediments of Guaymas Basin – Frederick Dowell – Frontiers in Microbiology

Bioreactor and crude oil microbiology

Illumina MiSeq sequencing reveals the key microorganisms involved in partial nitritation followed by simultaneous sludge fermentation, denitrification and anammox process – Bo Wang – Bioresource Technology

Microbial communities of light crude from Nigeria and potential for in situ biodegradation, souring, and corrosion – Okoro Chuma Conlette – Petroleum Science and Technology

Built environment microbiome

Rhinitis, Ocular, Throat and Dermal Symptoms, Headache and Tiredness among Students in Schools from Johor Bahru, Malaysia: Associations with Fungal DNA and Mycotoxins in Classroom Dust – Dan Norbäck – PLOS ONE

Bioinformatics and metagenomics

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity – Emiley A. Eloe-Fadrosh – Nature Microbiology

Development of an Analysis Pipeline Characterizing Multiple Hypervariable Regions of 16S rRNA Using Mock Samples – Jennifer J. Barb – PLOS ONE

Optimization of alignment-based methods for taxonomic binning of metagenomics reads – Magali Jaillard – Bioinformatics

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes – John A Lees – BioRxiv

Proteomics

Review: Recent development of mass spectrometry and proteomics applications in identification and typing of bacteria – Keding Cheng – Proteomics – Clinical Applications

Microbes in the news

Study shows maternal diet alters the breast milk microbiome and microbial gene content – EurekAlert

Deodorant And Antiperspirant Alter The Skin Microbiome, But Researchers Can’t Be Sure Of Long-Term Effects – Stephanie Castillo – Medical Daily

Beard bacteria could lead to new antibiotics – Matthew Stock – Reuters

Science, publishing, and career

“Those who can, publish. Those who can’t, blog.” Jingmai O’Connor – Current Biology

Chill out about Jingmai O’Connor’s criticism of bloggers – Jeremy Fox – Dynamic Ecology

Paul Knoepfler: Stem cell scientist finds his ‘niche’ in blogging – Karen Weintraub – STAT News

How to (not) write a microbiome grant, part I

How to (not) write a microbiome grant, part II. A deeper dive on preliminary data – David Baltrus – My Chrobial Romance

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January 27, 2016 – second edition

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A call from the White House, synergy between Mycoplasma and Gardnerella, urinary microbiome, sarcoidosis, and a hiking guide to microbes on the seafloor.

Events

The White House wants feedback from “All Microbiome-Science Champions” – give it – give it now – Jonathan Eisen – MicroBEnet
and
Calling All Microbiome-Science Champions! – Jo Handelsman and Elizabeth Stulberg – The White House

General human microbiome

Review: Exploring and Understanding the Biochemical Diversity of the Human Microbiota – Nitzan Koppel – Cell Chemical Biology

Pregnancy and birth

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content – Zachery T. Lewis – PeerJ

The common vaginal commensal bacterium Ureaplasma parvum is associated with chorioamnionitis in extreme preterm labour – Ciara Cox – The Journal of Maternal-Fetal & Neonatal Medicine

Human vaginal microbiome

Mycoplasma hominis and Gardnerella vaginalis display a significant synergistic relationship in bacterial vaginosis – C. Cox – European Journal of Clinical Microbiology & Infectious Diseases
Human oral microbiome

The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology – Mohsen Sohrabi – Journal of Microbiological Methods

Human skin microbiome

Note: 1 person per study group: Skin microbiota of first cousins affected by psoriasis and atopic dermatitis – Lorenzo Drago – Clinical and Molecular Allergy

Human urinary tract microbiome

Review: The human urinary microbiome and how it relates to urogynecology – Jenifer Schneeweiss – International Urogynecology Journal

Human gut microbiome

Metabolomics connects aberrant bioenergetic, transmethylation, and gut microbiota in sarcoidosis – Andreea Geamanu – Metabolomics

Review: Role of antibiotics for treatment of inflammatory bowel disease – Orna Nitzan – World Journal of Gastroenterology

Review: Gut microbiota imbalance and colorectal cancer – Johan Gagnière – World Journal of Gastroenterology

Animal models

In mice: A detrimental role of immunosuppressive drug, dexamethasone, during Clostridium difficile infection in association with a gastrointestinal microbial shift – Hyeun Bum Kim – Journal of Microbiology and Biotechnology

Animal microbiome

Diversity of the gastric microbiota in Thoroughbred racehorses having gastric ulcer – Hee-Jin Dong – Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest – Ju-pei Shen – Scientific Reports

Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies – Wiebke Sickel – Microbial Ecology

Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia – Yuji Jiang – Soil Biology and Biochemistry

Emergence in mapping microbial diversity in tea (Camellia sinensis (L.) O. Kuntze) soil of Assam, North-East India: A novel approach – PN Bhattacharyya – European Journal of Biotechnology and Bioscience

High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea – Shuai Zhao – Current Microbiology

Water and waste microbiome

Use of matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant – Laura Sala-Comorera – International Journal of Hygiene and Environmental Health

Extremophile microbiome

The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation – Andreas Teske – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities – Boyu Ren – ArXiv

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets – Jai Ram Rideout – PeerJ Preprint

Characterization of sequence-specific errors in various next-generation sequencing systems – Sunguk Shin – Molecular Biosystems

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data – Claudia Sala – BMC Bioinformatics

Protocol: “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities – Lejla Pašić – Microbial Environmental Genomics (MEG)

Protocol: Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler – Microbial Environmental Genomics (MEG)

Science, publishing, and career

Funding: What stops women getting more grants? – David McAllister – Nature

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January 25, 2016

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Today’s digest features biogeography of the human mouth, MALDI-TOF-MS, and microbes from ancient halite. OK, it is technically already Tuesday, but I was busy life tweeting from the Microbiome Symposium today at Stanford. The symposium featured many of the microbiome stars of our University – see my combined life tweets during the conference at Storify

Events

Gut microbiota in health and disease – from concept to evidence – March 17, 2016, Stockholm, Sweden. The symposium will be webcasted live at kva.se and will later be available as video-on-demand at kvatv.se.

Human oral microbiome

Biogeography of a human oral microbiome at the micron scale – Jessica L. Mark Welch – PNAS

Animal models of microbiome research

Experimental modulation of external microbiome affects nestmate recognition in harvester ants (Pogonomyrmex barbatus) – Andy Dosmann – PeerJ

Review: Incorporating the gut microbiota into models of human and non-human primate ecology and evolution – Katherine R. Amato – American Journal of Physical Anthropology

Animal microbiome

Faecal contamination of echinoderms: first report of heavy Escherichia coli loading of sea urchins from a natural growing area – M. Bouchoucha – Letters in Applied Microbiology

Extremophile microbiome

Review: Buried Alive: Microbes from Ancient Halite – Salla T. Jaakkola – Trends in Microbiology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – B.S.M. Mahmoud – Letters in Applied Microbiology

Techniques

Advantage of MALDI-TOF-MS over biochemical-based phenotyping for microbial identification illustrated on industrial applications – S.K. Urwyler – Letters in Applied Microbiology

More microbiology

Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training – André Antunes – Trends in Microbiology

Microbes in the news

Do probiotics cure asthma? Don’t believe the hype: Jonathan Eisen awards “prizes” to those who “oversell the microbiome” – Emma Bryce – Wired

The Forest In Your Mouth – Ed Yong – Phenomena National Geographic

Take your kids to the bugs on a Sunday afternoon – Micropia, the world’s only microbe zoo in Amsterdam – Mathias Grote – ASM Blog

IS-diagnostics Publishes Validation of PCR-Based Clinical Metagenomic MDx –  Madeleine Johnson – Genome Web

Bacteria Hysteria

Bacteria won’t wash, with the Brushield toothbrush cover – GizMag

Science, publishing, and career

#ResearchParasites and #ScienceColonialism – featuring Tweets from @DNLee5 & some discussion – Jonathan Eisen – Storify

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January 24, 2016

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Antibiotic therapy in preterm labor, shrimp microbial dynamics, volcanic desert on Mount Fuji, coffee processing, and Antarctic permafrost limits microbial life.

Pregnancy and birth

Antibiotic Therapy Increases the Risk of Preterm Birth in Preterm Labor without Intra-Amniotic Microbes, but may Prolong the Gestation Period in Preterm Labor with Microbes, Evaluated by Rapid and High-Sensitive PCR System – Satoshi Yoneda – American Journal of Reproductive Immunology

Human gut microbiome

Does the Intestinal Microbiota Explain Differences in the Epidemiology of Liver Disease between East and West – Nakamoto N. – Inflammatory Intestinal Diseases

Commentary: Microbiome-based companion diagnostics: no longer science fiction?
Jeroen Raes – Gut

Animal microbiome

Diary of a shrimpy kid: Dynamic changes of microbial communities in Litopenaeus vannamei cultures and the effects of environmental factors – Hao Zhang – Aquaculture

Plant, root, and soil microbiome
Substrate limitation to soil microbial communities in a subalpine volcanic desert on Mount Fuji, Japan – S. Yoshitake – European Journal of Soil Biology

Bottom-up control of fertilization on soil nematode communities differs between crop management regimes – Ting Liu – Soil Biology and Biochemistry

Interactive effects of precipitation and nitrogen spatial pattern on carbon use and functional diversity in soil microbial communities – Nianxun Xi – Applied Soil Ecology

Water and extremophile microbiome

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica – Jacqueline Goordial – The ISME Journal

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments – Petter Thureborn – PeerJ

 

Waste treatment microbiology

Metagenomic and quantitative insights into microbial communities and functional genes of nitrogen and iron cycling in twelve wastewater treatment systems – Duntao Shu – Chemical Engineering Journal

Food microbiology

High throughput sequencing identifies novel viruses in nectarine: Insights to the etiology of stem pitting disease – Dan Edward Veloso Villamor – Phytopathology

DGGE: Discrimination of post-harvest coffee processing methods by microbial ecology analyses – Yasmine Hamdouche – Food Control

Microbial Ecology

Integrating Theory and Experiment to Explain the Breakdown of Population Synchrony in a Complex Microbial Community – Emma J. Bowen – arXiv

Techniques

Poster abstract: Assembling Whole Genomes from Mixed Microbial Communities Using Hi-C – Ivan Liachko – Plant and Animal Genome Conference

Microbes in the news

Antarctic permafrost may not be habitable for microbes – so is Mars? Finding life on Mars might be harder than thought — or Martian microbes might be different – Emily Chung – CBC News

Microbes take their vitamins — for the good of science – EurekAlert

Bacteria that resist last-resort antibiotics were found in China two months ago, now they’re everywhere – Dominic Jackson – Shanghaiist

Newly Discovered Photosynthetic Bacteria Is Surprisingly Abundant – Science 2.0

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January 23, 2016

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Maturation of the mucin layer, periodontitis in Sjögren’s, Caenorhabditis elegans gut microbiota assembly, the rice-osphere, archaea in moonmilk, and microbial arsenic metabolism.

General human microbiome

The Human Microbiome and Public Health: Social and Ethical Considerations – Kieran C. O’Doherty – American Journal of Public Health

Pregnancy and birth

Review: Mucin–Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications – Sana Rokhsefat- Digestive Diseases and Sciences

Human oral microbiome

Periodontitis prevalence and serum antibody reactivity to periodontal bacteria in primary Sjögren’s syndrome: a pilot study – Bozo Lugonja – Journal of Periodontology

Temporal Stability of the Salivary Microbiota in Oral Health – Daniel Belstrøm – PLOS ONE

Review: Immune dysregulation mediated by the oral microbiome: potential link to chronic inflammation and atherosclerosis – C. Slocum – Journal of Internal Medicine

Human gut microbiome

Review: Microbiota manipulation for weight change – Tal Dror – Microbial Pathogenesis

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Models of microbiome research

Modulating the Gut Microbiota Improves Glucose Tolerance, Lipoprotein Profile and Atherosclerotic Plaque Development in ApoE-Deficient Mice – Ida Rune – PLOS ONE

Dysbiosis of the fecal microbiota in the TNBS-induced Crohn’s disease mouse model – Qing He – Applied Microbiology and Biotechnology

Animal microbiome

Note that the worms did not develop into adults without having veggies to eat: Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments – Maureen Berg – The ISME Journal

Plant, root, and soil microbiome

Rice-osphere? Rice Genotype Differences in Tolerance of Zinc-Deficient Soils: Evidence for the Importance of Root-Induced Changes in the Rhizosphere – Asako Mori – Frontiers in Plant Science

A perspective on inter-kingdom signaling in plant–beneficial microbe interactions – Amanda Rosier – Plant Molecular Biology

Chemotaxis signaling systems in model beneficial plant–bacteria associations – Birgit E. Scharf – Plant Molecular Biology

Water and extremophile microbiome

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system – Helena Osterholz – The ISME Journal

Unique pioneer microbial communities exposed to volcanic sulfur dioxide – Reiko Fujimura – Scientific Reports

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential – Christoph Reitschuler – Microbial Ecology

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria – Steven Smriga – PNAS

Review: The microbial genomics of arsenic – Jérémy Andres – FEMS Microbiology Reviews

Food microbiology

Kombucha tea fermentation: Microbial and biochemical dynamics – Somnath Chakravorty – International Journal of Food Microbiology

PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment – Obinna T. Ezeokoli – International Journal of Food Microbiology

Check your fridge for Thanksgiving leftovers: Direct Dynamic Kinetic Analysis and Computer Simulation of Growth of Clostridium perfringens in Cooked Turkey during Cooling – Lihan Huang – Journal of Food Science

Bioinformatics, metagenomics, and protocols

Protocol collection: Microbial Environmental Genomics (MEG)
MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function – Kevin P. Keegan
Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler
Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip – Joy D. Van Nostrand
Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning – Céline Ribière
Fungal Communities in Soils: Soil Organic Matter Degradation – Tomáš Větrovský
GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity – Samuel Dequiedt

Microbes in the news

Exploring the human gut microbiome. Scientific interest in this diverse world of bacteria has flipped from fear to fascination – Sabin Russell – Fred Hutch

Fungi Prevalent in Urine of Women With Chronic Pelvic Pain – Pam Harrison – MedPageToday

Microscopic subway passengers with a ticket to ride: Interview with Chris Mason – Labnews

To Fight Growing Threat From Germs, Scientists Try Old-Fashioned Killer – Gautam Naik – The Wall Street Journal

http://www.cnn.com/2016/01/22/health/flint-water-legionnaires-disease/Flint hospital reports finding Legionnaires’ bacteria in water – Ralph Ellis – CNN

Breast milk protein could be used in fight against antibiotic resistance – The Guardian

Listeria outbreak: Dole packaged salad linked to 12 bacteria infections and one death – John Houck – Inquisitr

Science, publishing, and career

By a 13 year old girl: Letter to BBC Wildlife Magazine on sexism in nature conservation – Mya-Rose Craig – BirdGirl

Bik’s Picks

Secular trends in family dinner frequency among adolescents – Kathryn Walton – BMC Research Notes
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January 22, 2016

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Viruses in desert soils, pneumonia etiology, and a concerning editorial in NEJM.

Human oral microbiome

Microbiological analysis after complete or partial removal of carious dentin using two different techniques in primary teeth: A randomized clinical trial – Deepak Kumar Singhal – Dental Research Journal

Human respiratory microbiome

The Modern Quest for the “Holy Grail” of Pneumonia Etiology – Seema Jain – Clinical Infectious Diseases

Plant, root, and soil microbiome

Review: Diversity and Ecology of Viruses in Hyperarid Desert Soils – Olivier Zablocki – Applied and Environmental Microbiology

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil – Matthew J. Meier – Applied and Environmental Microbiology

Techniques / phages and viruses

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches – Pingfeng Yu – Applied and Environmental Microbiology

More microbiology

Tuberculosis in Newborns: The Lessons of the “Lübeck Disaster” (1929–1933) – Gregory J. Fox – PLOS Pathogens

Microbes in the news

For children: Understanding Marine Microbes, the Driving Engines of the Ocean – Anna Kopf

15 min podcast: A Microbiome Is Born – Science Friday

Good Bacteria for Good Skin – Beauty brands say there is a beneficial effect when probiotics and fermented ingredients are applied topically – Fiorella Valdesolo – Wall Street Journal

Your DNA could make you resistant to certain bacteria – gene expression could help explain why some people are more immune to infection than others – Alexandra Ossola – Popular Science

Science, publishing, and career

An editorial in NEJM called Data Sharing, written by Dan L. Longo and Jeffrey M. Drazen, caused a lot of concern because it calls scientists who use other people’s published data “parasites”. Some reactions:

Data Scientists = Research Parasites? – David Shaywitz – Forbes

Research “parasitism” and authorship rights – Leonid Schneider – For Better Science

Attack of the Research Parasites – Derek Lowe – Science Magazine blogs

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