Category Archives: Functional foods

March 22, 2016

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

Jobs

Lecturership in Human Microbiome Studies – University of Reading, UK

Pregnancy and birth

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

Infection, immunology, and transplantion microbiology

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

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

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

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

Human oral microbiome

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

Human eye and skin microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

Animal models

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

Cave microbiome

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

Built environment microbiology

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

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

Food microbiology

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

Bioinformatics, techniques, and metagenomics

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

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

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

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

Metagenomics and viruses

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

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

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

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

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

More microbiology

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

Microbes in the news

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

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

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

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

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

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

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

Space gives bacteria room to grow – Dan Satherley – NewsHub

Uncovering bacterial role in platinum formation – University of Adelaide

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

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

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

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

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

Blog posts by me:

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

Extreme environments at home – Elisabeth Bik – MicroBEnet

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March 19, 2016

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General microbiome

Prospect: Know your neighbor: Microbiota and host epithelial cells interact locally to control intestinal function and physiology – Felix Sommer – BioEssays

Review: Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance – Andrés Moya – Trends in Microbiology

Human oral microbiome

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus – Andrew T. Ozga – American Journal of Physical Anthropology

Oral microbiota species in acute apical endodontic abscesses – Noelle George – Journal of Oral Microbiology

Human gut microbiome

Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment – Bumjo Oh – Helicobacter

Gut microbiota produce alcohol and contribute to NAFLD – Lixin Zhu – Gut

Probiotics

Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili – Hanne L. P. Tytgat – PLOS ONE

Animal microbiome

Metagenomic Survey of Viral Diversity Obtained from Feces of Subantarctic and South American Fur Seals – Mariana Kluge – PLOS ONE

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla) – Klára Vlčková – Microbial Ecology

Induction of trap formation in nematode-trapping fungi by bacteria-released ammonia – H.N. Su – Letters in Applied Microbiology

Plant, root, and soil microbiome

The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots – Larry M. York – Journal of Experimental Botany

Impact of an invasive N2-fixing tree on arbuscular mycorrhizal fungi and development of native species – Alejandra, Guisande-Collazo – AoB Plants

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado? – Renata Carolini Souza – BMC Microbiology

Water microbiome

High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling – Tomàs Llorens-Marès – Microbial Ecology

Food and medicine microbiology

Characterization of malolactic bacteria isolated from Aosta Valley wines and evidence of psychrotrophy in some strains – I. Vigentini – Journal of Applied Microbiology

A review of melanized (black) fungal contamination in pharmaceutical products—incidence, drug recall and control measures – R. Vijayakumar – Journal of Applied Microbiology

Microbes in the news

Researchers Extract and Sequence Ancient DNA From Biofilm Coating Teeth – Genome Web

New green toothpaste reveals biofilm – Maria Perno Goldie – Dentistry IQ

Video: Pink Lake Mystery Solved: Lake Hillier Bacteria – SciShow – YouTube

SlideShow: Experiments with my Microbiome – Richard Sprague – LinkedIn

Video: #GMFH2016 (5th Gut Microbiota for Health World Summit ) Interviews: Prof. Joël Doré – YouTube
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Somewhere between March 8 and March 9, 2016

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Human symbionts inject to persist, diet and exercise in mice, a 17-year long experiment, and using peanut butter as a vehicle to deliver probiotics in developing countries.

Human skin microbiome

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses – C. Cosseau – One Health

Human respiratory microbiome

Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia –  Etienne Ruppé – Future Microbiology

Human gut microbiome

Analysis of Gut Microbiota in Coronary Artery Disease Patients: a Possible Link between Gut Microbiota and Coronary Artery Disease – Takuo Emoto – Journal of Atherosclerosis and Thrombosis

PhD Thesis: Indigenous Australians have a distinctive gut microbial profile compared to Caucasian controls and patients with inflammatory bowel disease – Iyngkaran, Guruparan – Melbourne Medical School

Review: Changes in the Intestinal Microbiome and Alcoholic- and Non-alcoholic Liver Diseases—Causes or Effects? – Naga S. Betrapally – Gastroenterology

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

Review: Extensive Intestinal Resection Triggers Behavioral Adaptation, Intestinal Remodeling and Microbiota Transition in Short Bowel Syndrome – Camille Mayeur – MDPI Microorganisms

Microbiome models

Human symbionts inject and neutralize antibacterial toxins to persist in the gut – Aaron G. Wexler – PNAS

The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice – Sara C. Campbell – PLOS ONE

Chronic Psychological Stress Disrupted the Composition of the Murine Colonic Microbiota and Accelerated a Murine Model of Inflammatory Bowel Disease – Yohei Watanabe – PLOS ONE

Flavanol-Enriched Cocoa Powder Alters the Intestinal Microbiota, Tissue and Fluid Metabolite Profiles, and Intestinal Gene Expression in Pigs – Saebyeol Jang – The Journal of Nutrition

Deletion of the Toll-Like Receptor 5 Gene Per Se Does Not Determine the Gut Microbiome Profile That Induces Metabolic Syndrome: Environment Drumpfs Genotype
Wei Zhang – PLOS ONE

Animal microbiome

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance – Bettina Glasl – ISME Journal

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis – Filip Husnik – BioRxiv

No access for me, but I assume this is in birds: Microbial shifts associated with necrotic enteritis – Gunther Antonissen – Avian Pathology

Plant, root, and soil microbiome
Orchids: Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica – Hans Jacquemyn – Annals of Botany

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment – Ben Bond-Lamberty – PLOS ONE

Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples – Y. Degefu – EPPO Bulletin

Shifts in symbiotic associations in plants capable of forming multiple root symbioses across a long-term soil chronosequence – Felipe E. Albornoz – Ecology and Evolution

Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China – Bingchang Zhang – Journal of Basic Microbiology

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica – Marc W. Van Goethem – FEMS Microbiology Ecology

Bacterial indicator taxa in soils under different long-term agricultural management – N.G. Jiménez-Bueno – Journal of Applied Microbiology

Water and extremophile microbiome

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge – Huiluo Cao – Scientific Reports

Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica – Tyler J. Kohler – FEMS Microbiology Ecology

Bioreactor microbiology

Gut microbiota-involved mechanisms in enhancing systemic exposure of ginsenosides by coexisting polysaccharides in ginseng decoction – Shan-Shan Zhou – Scientific Reports

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis
Gang Luo – Biotechnology for Biofuels

Waste and pollution microbiology

Temporal dynamics of biotic and abiotic drivers of litter decomposition – Pablo García-Palacios – Ecology Letters

Microbial Community Structures in Petroleum Contaminated Soils at an Oil Field, Hebei, China – Yizhi Sheng – CLEAN – Soil, Air, Water

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment – Sanghyun Jeong – Chemical Engineering Journal

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems – Journal of Environmental Sciences – A.O. Babatunde

Functional foods and food microbiology

For applications in developing countries: Influence of probiotics, included in peanut butter, on the fate of selected Salmonella and Listeria strains under simulated gastrointestinal conditions – Y.A.K. Klu – Journal of Applied Microbiology

Bioinformatics and metagenomics

Read networks and k-laminar graphs – Finn Volkel – ArXiv

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment – Jeongsu Oh – PLOS ONE

Protocol: Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments – Luke K. Ursell – Springer Protocols Handbooks

Regression Analysis for Microbiome Compositional Data – Pixu Shi – ArXiv

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences – Chen Shi-Yi – Journal of Computational Biology

Techniques

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies – James L. O’Donnell – PLOS ONE

More microbiology

Alice’s living croquet theory – Didier Raoult – International Journal of Antimicrobial Agents

Genomic approaches for understanding dengue: insights from the virus, vector, and host – Shuzhen Sim – Genome Biology

Microbes and infection

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using a high-density resequencing pathogen microarray platform – Moussa Kourout – Transfusion

Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages – Rachelle Mariano – mSystems

Microbes in the news

Cutting Board Companions – Katherine Dahlhausen – MicroBEnet @PhDKD

Standard practice of giving premature babies antibiotics needs to be rethought, argues new study – Jessica Firger – Newsweek

Bacterial brawls mark life in the gut’s microbiome – Bill Hathaway – Phys.org

How your microbiome can put you at the scene of the crime – Kai Kupferschmidt – Science

Soy protein may diversify gut microbiota more than dairy protein: Study – Stephen Daniells – Nutraingredients
Sleep Deprivation Caused By Jet Lag And Shift Work Could Be Treated Through Your Gut Microbiome – Cayla Dengate – Huffington Post

U-M Students Analyze Their Own Biological Samples to Study How Microbes Affect Human Health – Infection Control Today

#1 is outdated but rest ok: 10 things you need to know about your gut – Naomi Mead – Netdoctor

The Dannon Company Announces Fourth-Annual Winner of Yogurt and Probiotics Fellowship Grant: Micah Eimerbrink – BusinessWire

Science, publishing, and career

Insights into the PeerJ Preprint: “Gender bias in open source” – PeerJ Blog

Bik’s Picks

I Speak Whale: Vast assembly of vocal marine mammals from diverse species on fish spawning ground – Delin Wang – 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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December 26, 2015

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Gut microbiota of patients with and without abdominal bloating, probiotics to help with academic stress, and a copper gradient near a Canadian mine.

Pregnancy and birth

Review: The microbiome and childhood diseases: Focus on brain-gut axis –
Siobhain M. O’ Mahony – Birth Defects Research Part C: Embryo Today: Reviews

Human respiratory tract microbiome

Microbiological and Molecular Identification of Bacterial Species Isolated from Nasal and Oropharyngeal mucosa of Fuel Workers in Riyadh, Saudi Arabia – Suaad S. AlWakeel – Saudi Journal of Biological Sciences

Human gut microbiome

Molecular Characterization of the Intestinal Microbiota in Patients With and Without Abdominal Bloating – Tamar Ringel-Kulka – American Journal of Physiology

Microbiome models

Choline Diet and Its Gut Microbe–Derived Metabolite, Trimethylamine N-Oxide, Exacerbate Pressure Overload–Induced Heart Failure – Chelsea L. Organ – Circulation: Heart Failure

Bidirectional interactions between indomethacin and the murine intestinal microbiota
Xue Liang

A simple coculture system shows mutualism between anaerobic faecalibacteria and epithelial Caco-2 cells – Mehdi Sadaghian Sadabad – Scientific Reports

Animal microbiome

Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows – Dipti W. Pitta – Anaerobe

Age-Related Shifts in Bacterial Diversity in a Reef Coral – Alex D. Williams – PLOS ONE

Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches – Yislem Beltrán – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity – Martina Köberl – FEMS Microbiology Ecology

Locally adapted arbuscular mycorrhizal fungi improve vigor and resistance to herbivory of native prairie plant species – Elizabeth L. Middleton – Ecosphere

Root Exudation by Aphid Leaf Infestation Recruits Root-associated Paenibacillus spp. to Lead Plant Insect Susceptibility – Bora Kim – Journal of Microbiology and Biotechnology

Effects of the allelochemical coumarin on plants and soil microbial community – E. Niro – Soil Biology and Biochemistry

Water and waste microbiome

Microbiome analysis across a natural copper gradient at a proposed Northern Canadian mine site – Thea Van Rossum – Frontiers in Environmental Science

Evaluation of Community-Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds – Gerald L. Kurten – North American Journal of Aquaculture

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages – David H. Case – mBio

Microbial colonisation and litter decomposition in a Cerrado stream are limited by low dissolved nutrient concentrations – Adriana O. Medeiros – Limnetica

Diversity, community structure, and bioremediation potential of mercury-resistant marine bacteria of estuarine and coastal environments of Odisha, India – Hirak R. Dash – Environmental Science and Pollution Research

Review: Microbial Surface Colonization and Biofilm Development in Marine Environments – Hongyue Dang – Microbiology and Molecular Biology Reviews

Bioinformatics and metagenomics

Effect of k-tuple length on sample-comparison with high-throughput sequencing data – Ying Wang – Biochemical and Biophysical Research Communications

Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses – Hervé Seligmann – Current Opinion in Microbiology

Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data – Rohita Sinha – BMC Genomics

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis – Phelim Bradley – Nature Communications

Proteomics

Review: The challenge of metaproteomic analysis in human samples – Jonathan M Blackburn – Expert Review of Proteomics

Functional foods

Fermented milk containing Lactobacillus casei strain Shirota prevents the onset of physical symptoms in medical students under academic examination stress – A. Kato-Kataoka – Beneficial Microbes

Microbes in the news

Topical Mupirocin Changes Sinus Microbiome – Interview with Tara F. Carr – Medical Research

Is This Snowy Wonderland Or The World Inside A Petri Dish? – Meredith Rizzo – NPR

End of the year lists

From Blood Rain to Green Poo: 10 Weirdest Science Stories of 2015 – Elizabeth Palermo – Live Science

The Altmetric Top 100 Research Papers 2015 – Altmetric
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December 9, 2015

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Student activity about the microbiome that uses pasta, nutritional supplementation in Malawian infants, fungi and drywall, and microbial aerosols from soiled hospital linens.

General microbiome

Cool student activity: Modeling the Dynamic Digestive System Microbiome – Anne M. Estes – Journal of Microbiology & Biology Education

Pregnancy and birth

Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery – Elizabeth A. Baldwin – PeerJ

No effect of supplementation: Gut microbiota in Malawian infants in a nutritional supplementation trial – Yin Bun Cheung – Tropical Medicine & International Health

Human vaginal microbiome

Bacterial vaginosis and inflammatory response showed association with severity of cervical neoplasia in HPV-positive women – Juçara Maria de Castro-Sobrinho – Diagnostic Cytopathology

Human gut microbiome

Review: Gut Microbiota Modulation and Mucosal Immunity: Focus on Rifaximin – Loris R. Lopetuso – Mini-Reviews in Medicinal Chemistry

Animal microbiome

The effects of omeprazole therapy on bacterial colonization of the pharynx in healthy dogs – Lauren A. Sullivan – Journal of Veterinary Emergency and Critical Care

Water microbiome

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

 

Built environment microbiome

Moisture parameters and fungal communities associated with gypsum drywall in buildings – Sandra Dedesko – Microbiome

A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses – Thomas Weinmaier – Microbiome

Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting – Alina Handorean – Microbiome

Phages and viruses

Better together: bacteriophage combinations significantly reduce Clostridium difficile growth in vitro and proliferation in vivo – Janet Y. Nale – Antimicrobial Agents and Chemotherapy

Infection and transplantation

A genetic modifier of the gut microbiome influences the risk of GVHD and bacteremia following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation

World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis – Martyn D. Kirk – PLOS Medicine

Functional foods

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods – Remco Kort – Microbial Cell Factories

Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences – Tong Zhang – PLOS ONE

Bioinformatics and metagenomics

Small Sample Kernel Association Tests for Human Genetic and Microbiome Association Studies – Jun Chen – Genetic Epidemiology

Microbes in the news

Questions About the Science Of Beer – Matt Shipman – NC State University News

Guest Post – Stadium Seat Bacteria – PeerJ – David Coil

How microbes in your gut today hold clues to tomorrow’s medicines: For the second episode of “Science Happens,” we hung out with Pamela Silver, a scientist who wants to hack the microbiome – Carl Zimmer – STAT news

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December 1, 2015

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African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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November 10, 2015

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Oral and gut microbiomes respond differently to antibiotics, looking two gifted horses in the mouth, BMIs and Bifidos, Drosophila mating, gut microbes and tumorigenesis, microbial food webs in clay rocks, and don’t forget that Bonferroni correction.

Pregnancy and birth (Probiotics too!)

Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit – J. M. Franasiak – Journal of Assisted Reproduction and Genetics

Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study – Ulla Uusitalo – JAMA Pediatrics

Human oral microbiome

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces – Egija Zaura – mBio

Crossover clinical trial of different methods of removing a denture adhesive and the influence on the oral microbiota – Élen Massaro Nunes – The Journal of Prosthetic Dentistry

Human gut microbiome

Correlation between body mass index and fecal microbiota from children – A. Ignacio – Clinical Microbiology and Infection

Review: Clostridium difficile infection and intestinal microbiota interactions – C. Rodriguez – Microbial Pathogenesis

Animal and bioreactor models

A Statistical Error in: “Analysis of Caecal Microbiota in Rats Fed with Genetically Modified Rice by Real-Time Quantitative PCR” – Alexander Panchin – Journal of Food Science

In mice: Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis -Joseph P. Zackular – mSphere

The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster – Devin Arbuthnott – Journal of Evolutionary Biology

Chemostat culture systems support diverse bacteriophage communities from human feces – Tasha M. Santiago-Rodriguez – Microbiome

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans – Nicholas A. Pudlo – mBio

Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass – Sharon A. Huws – FEMS Microbiology Ecology

Animal microbiome

In-depth snapshot of the equine subgingival microbiome – Wenling Gao – Microbial Pathogenesis

Occurrence and distribution of Malassezia species on skin and external ear canal of horses – Hojjatollah Shokr – Mycoses

Review: The functionality of the gastrointestinal microbiome in non-human animals – Irene Hanning – Microbiome

Plant, root, and soil microbiome

The effect of altitudinal gradient on soil microbial community activity and structure in moso bamboo plantations – Ed-Haun Chang – Applied Soil Ecology

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea – A Metagenomic Approach – Marta Filipa Simões – Genomics, Proteomics & Bioinformatics

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches – Pranitha S. Pandit – Environmental Microbiology

Effects of Sulfamethazine and Zinc on the Functional Diversity of Microbial Communities during Composting – Manli Duan – Environmental Microbiology

Evidence for duplication in title words: Prokaryotes in subsoil – evidence for spatial separation of oligotrophs and copiotrophs by co-occurrence networks – Michael Schloter – Frontiers in Microbiology

A minimalistic microbial food web in an excavated deep subsurface clay rock -Alexandre Bagnoud – FEMS Microbial Ecology

Water microbiome

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms – Sara Kleindienst – PNAS

Extremophile microbiome

Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter – Evgeniya Matyugina – Chinese Journal of Oceanology and Limnology

Built environment microbiome

Differences in intertidal microbial assemblages on urban structures and natural rocky reef – Elisa L. Tan – Frontiers in Microbiology

Waste microbiology

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments – Lilian M. Guibert – Environmental Microbiology

Cultivating Microbial Dark Matter in Benzene-Degrading Methanogenic Consortia –
Fei Luo – Environmental Microbiology

Metagenomics and bioinformatics

DESM: portal for microbial knowledge exploration systems – Adil Salhi – Nucleic Acids Research

Techniques

Coupling dye-integrated polymeric membranes with smartphone detection to classify bacteria – Lígia Bueno – RSC Advances

Microbes in the news

9 Fascinating Facts About The Microbiome, The Trillions Of Microbes Hidden Inside Us — Jessica Leber – Fast Co.Exist

NTU scientists use dead bacteria to kill colorectal cancer – EurekAlert

Science, publishing, and career

(A)Historical Science: why scientists should care more about the history of science – Arturo Casadevall and Ferric C. Fang – Infection and Immunity

November 2, 2015

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Overview of key players of the human microbiome in different sites, foals are born with a rich gut microbiome, biogeography of salmon microbiome, bacteria on Chinese glaciers, and the effect of X-rays on the mango microbiome.

General human microbiome

Diversity of key players in the microbial ecosystems of the human body – Ferenc Jordán – Scientific Reports

Pregnancy and birth

Intestinal microbiota in neonates requiring urgent surgery: assessing the role of probiotics using fecal DNA sequencing – Hiroshi Murakami – Pediatric Surgery International

Review: Bacterial munch for infants: potential pediatric therapeutic interventions of probiotics – Mohsin Khurshid – Future Microbiology

Review: Introduction : Microbiome in human reproduction – Jason M. Franasiak – Fertility and Sterility

Correspondence: Vaginal microbiota during pregnancy: Pathways of risk of preterm delivery in the absence of intrauterine infection? – Jeffrey A Keelan – PNAS

Reply to Keelan and Payne: Microbiota-related pathways for preterm birth – Daniel B DiGiulio – PNAS

Human oral microbiome

Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation – Brenda P.F.A. Gomes – Journal of Endodontics

Oral microbiota in patients with atherosclerosis – Frida Fåk – Atherosclerosis

Review: Intermicrobial interactions as a driver for community composition and stratification of oral biofilms – Nicholas S. Jakubovics – Journal of Molecular Biology

Review: The Fungal Biome of the Oral Cavity – Jyotsna Chandra – Candida Species

Human respiratory microbiome

Are bronchoalveolar lavages a good source for microbial profiling? Differences between throat and bronchoalveolar lavage microbiomes – Alexandra Zimmermann – Journal of Medical Microbiology

Human gut microbiome

Donor species richness determines fecal microbiota transplantation success in inflammatory bowel disease – Severine Vermeire – Journal of Crohn’s and Colitis

Gut mucosal microbiome across stages of colorectal carcinogenesis – Geicho Nakatsu – Nature Communications

Review: Gut mycobiota and adenomas – Chunguang Luan – Gut Microbes

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Animal microbiome

Development of the faecal microbiota in foals – M. C. Costa – Equine Veterinary Journal

Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment – Saria Otani – Microbial Ecology

The biogeography of the atlantic salmon (Salmo salar) gut microbiome – Martin S Llewellyn – The ISME Journal

Exposure to West Nile Virus Increases Bacterial Diversity and Immune Gene Expression in Culex pipiens – Steven D. Zink – Viruses

Plant, root, and soil microbiome

Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture – Linkun Wu – Scientific Reports

Drivers of bacterial beta diversity in two temperate forests –  Wang – Ecological Research

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing – Chris Munday – Aerobiologia

Review: Influence of soil microbiota in nurse plant systems – Susana Rodríguez-Echeverría – Functional Ecology

Review: The Role of Plant–Microbe Interactions and Their Exploitation for Phytoremediation of Air Pollutants – Nele Weyens – International Journal of Molecular Sciences

Water and extremophile microbiome

Metagenomic analysis of the bacterial community of the Sea of Azov – D. G. Matishov – Marine Biology

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India – Jhasketan Badhai – Frontiers in Microbiology

High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing – Qing Liu – Systematic and Applied Microbiology

Review: Databases of the marine metagenomics – Katsuhiko Mineta – Gene

Waste microbiology

Changes in Microbial Composition of Wastewater During Treatment in a Full-Scale Plant – Marija Kaevska – Current Microbiology

Wastewater treatment and microbial communities in an integrated photo-bioelectrochemical system affected by different wastewater algal inocula – Li Xiao – Algal Research

Review: Microbial diversity in support of anaerobic biomass valorization – M. Jobard – Critical Reviews in Biotechnology

Food microbiology

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

Metagenomics and bioinformatics

Poster: Alignment-free methods for metagenomic profiling – Shanshan Gao – BMC Bioinformatics

Infection microbiology

Microbial diversity on intravascular catheters from paediatric patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Phages and viruses

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile – Pierre Boudry – mBio

Microbial Ecology

Do modern theories of biodiversity fail to predict commonness and rarity among microbes? – William R. Shoemaker – PeerJ

Strongly Deterministic Population Dynamics in Closed Microbial Communities – Zak Frentz – Physical Review

Microbes in the news

Scientists debate mega-microbiome initiatives: Research standards will advance the field, proponents say, but critics counter that they will stifle creativity – Rachel Becker – Nature

Foals born with rich microbial community in their gut – study – Horsetalk

Halloween: Monster Microbiology, 101: If werewolves and other ghouls existed, they’d surely have microbiomes – Rob Dunn – Science Friday

Bacteria in space – ‘You cannot just open the window’ – Interview with Ralf Möller about microbes found on the ISS – DW

New technique could prevent biofilms on catheters and medical implants – EurekAlert

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October 29, 2015

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Library prep technology, skin communities in urban and rural populations, rarity in aquatic microbes, and the microbiome of solar panels.

Pregnancy and birth

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons – Anuradha Ravi – Scientific Reports

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life – Tanya L Alderete – The American Journal of Clinical Nutrition

Human skin microbiome

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations – Shi Ying – PLOS ONE

Human respiratory microbiome

Review: A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS) – Mahboobeh Mahdavinia – Clinical & Experimental Allergy

Human gut microbiome

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

DGGE: The duodenal microbiota composition in children with active coeliac disease is influenced for the degree of enteropathy – F. Girón Fernández-Crehuet – Anales de Pediatría (English Edition)

Review: The microbiome and its pharmacological targets: therapeutic avenues in cardiometabolic diseases – Ana Luisa Neves – Current Opinion in Pharmacology

Review: Microbiome impact on metabolism and function of sex, thyroid,
growth and parathyroid hormones – Michał Kunc – Acta Biochimica Polonica

Review: Intestinal Microbiota: From Inflammatory Bowel Disease to Bone Marrow Transplantation – Ernst Holler – Blood

Review: Dysbiotic gut microbiome: A key element of Crohn’s disease – Styrk Furnes Øyri – Comparative Immunology, Microbiology and Infectious Diseases

Infection microbiology

Serum bacterial DNA detection in patients with cholangitis after Kasai procedure – Qianfu Luo – Pediatrics International

Deceiving title (not about microbiome but infection): Breast Implant–Associated Infections: The Role of the National Surgical Quality Improvement Program and the Local Microbiome – Cohen, Justin B. – Plastic and Reconstructive Surgery

Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration – Dagmar Chudobova – The Brazilian Journal of Infectious Diseases

Animal and bioreactor models

The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia – Tim J Schuijt – Gut

In mice: The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation – Mario M. Zaiss – Cell

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization – Malin E.V. Johansson – Cell Host & Microbe

Microbiota-Dependent Hepatic Lipogenesis Mediated by Stearoyl CoA Desaturase 1 (SCD1) Promotes Metabolic Syndrome in TLR5-Deficient Mice – Vishal Singh – Cell Metabolism

Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing – Yongchao Xie – Chemosphere

The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals – A. Schoster – Equine Veterinary Journal

A longitudinal assessment of changes in bacterial community composition associated with the development of periodontal disease in dogs – Corrin Wallis – Veterinary Microbiology

Assessment of prebiotic potential of Akpan-yoghurt-like product and effects on the human intestinal microbiota – Beatriz Gullón – Journal of Functional Foods

Relationship between inflammation, the gut microbiota, and metabolic osteoarthritis development: studies in a rat model – K.H. Collins – Osteoarthritis and Cartilage

Plant, root, and soil microbiome

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem – Claudia M. Boot – Soil Biology and Biochemistry

Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil? – Erik Verbruggen – Journal of Ecology

Editorial: Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Water microbiome

Review: Rarity in aquatic microbes: placing protists on the map – Ramiro Logares – Research in Microbiology

Waste microbiology

Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion – Eoin Gunnigle – FEMS Microbiology Ecology

An ‘omics’ approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge – D.J. Beale – Water Research

Extremophile microbiome

Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community – Alexander Crits-Christoph – BioRxiv

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city – Pedro Dorado-Morales – BioRxiv

Food microbiology

Microbial community dynamics in thermophilic undefined milk starter cultures – Eugenio Parente – International Journal of Food Microbiology

Metagenomics and bioinformatics

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition – David Koslicki – PLOS ONE

Linear-time superbubble identification algorithm for genome assembly – Ljiljana Brankovic – Theoretical Computer Science

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut – Christian Milani – Scientific Reports

Power law analysis of the human microbiome – Zhanshan (Sam) Ma – Molecular Ecology

More microbiology

Bioactive natural products from novel microbial sources – Victoria L. Challinor – Annals of the New York Academy of Sciences

Conference report: Bacterial Networks in Cells and Communities – Victor Sourjik – Journal of Molecular Biology

Self-establishing communities enable cooperative metabolite exchange in a eukaryote – Kate Campbell – eLife

Techniques

Library preparation methodology can influence genomic and functional predictions in human microbiome research – Marcus B. Jones – PNAS

Microbes in the news

Scientists Urge National Initiative on Microbiomes – Carl Zimmer – New York Times

Fecal transplant pills: Large-scale production begins: Nonprofit stool bank launched by MIT researchers completes first dose-finding study – GlobeNewsWire
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