Author Archives: eliesbik

November 30, 2015

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Red algae growing in sea otter fur, noroviruses in a Thai river, virus dispersal by hand drying, and the dark side of salad.

Jobs and events

Postdoctoral Position, Evolutionary Genomics, University of California, Davis – Gregory Lanzaro – Phylogenomics

“The Dark Side of Salad: Internalization & Movement of Human Pathogenic Bacteria in Plants,” Guest Speaker: Dr. Amanda Deering – December 2, 2015, Purdue University

General microbiome

Review: Functions of innate immune cells and commensal bacteria in gut homeostasis – Hisako Kayama – Journal of Biochemistry

Human stomach microbiome

Identification of low abundance microbiome in clinical samples using whole genome sequencing – Chao Zhang – Genome Biology

Human gut microbiome

Review: The antimicrobial effects of rifaximin on the gut microbiota – H. L. DuPont – Part of a special issue: “Understanding mechanisms of the actions of rifaximin in selected gastrointestinal diseases “- Alimentary Pharmacology & Therapeutics

Animal models

Influence of Flaxseed Oil on Fecal Microbiota, Egg Quality and Fatty Acid Composition of Egg Yolks in Laying Hens – Jun-Yeong Lee – Current Microbiology

Duodenojejunal Bypass Leads to Altered Gut Microbiota and Strengthened Epithelial Barriers in Rats – Po-Jen Yang – Obesity Surgery

Animal microbiome

Characterization of the putatively introduced red alga Acrochaetium secundatum (Acrochaetiales, Rhodophyta) growing epizoically on the pelage of southern sea otters (Enhydra lutris nereis) – Gena B. Bentall – Marine Mammal Science

The mechanism for microsporidian parasite suppression of the hindgut bacteria of the migratory locust Locusta migratoria manilensis – Shu-qian Tan – Scientific Reports

Comparative Analysis of Microbial Diversity in Termite Gut and Termite Nest Using Ion Sequencing – Arumugam Manjula – Current Microbiology

Plant, root, and soil microbiology

Seasonal dynamics of the soil microbial community: assimilation of old and young carbon sources in a long-term field experiment as revealed by natural 13C abundance – G. Börjesson – European Journal of Soil Science

Aboveground litter quality is a better predictor than belowground microbial communities when estimating carbon mineralization along a land-use gradient – Nicolas Fanin – Soil Biology and Biochemistry

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands – Jie Chen – Journal of Soils and Sediments

Water and extremophile microbiome

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Environmental switching during biofilm development in a cold seep system and functional determinants of species sorting – Weipeng Zhang – Molecular Ecology

Molecular detection and characterization of noroviruses in river water near Thailand – K. Inoue – Letters in Applied Microbiology

Biogeochemistry and microbial diversity in the marine cavity beneath the McMurdo Ice Shelf, Antarctica – Trista J. Vick-Majors – Limnology and Oceanography

Waste microbiology

New insights into the genetic and metabolic diversity of thiocyanate-degrading microbial consortia – Mathew P. Watts – Applied Microbiology and Biotechnology

Diversity and Distribution of Arsenic-Related Genes Along a Pollution Gradient in a River Affected by Acid Mine Drainage – Angélique Desoeuvre – Microbial Ecology

Seasonal variations of microbial community in a full scale oil field produced water treatment plant – Q. Xie – Global Journal of Environmental Science and Management

Built environment microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon processing plants – Solveig Langsrud – Journal of Applied Microbiology

Evaluation of the potential for virus dispersal during hand drying: a comparison of three methods – Patrick T. Kimmitt – Journal of Applied Microbiology

Metabolomics

Review: Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Bioinformatics and metagenomics

Assessing the Unseen Bacterial Diversity in Microbial Communities – Alejandro Caro-Quintero – Genome Biology Evolution

Finding New Order in Biological Functions from the Network Structure of Gene Annotations – Kimberly Glass – PLOS Computational Biology

Microbes in the news

Bacteria on the Brain: A brilliant surgeon offered an untested treatment to dying patients. Was it innovation or overreach? – Emily Eakin – The New Yorker

Legionnaires’ Disease Bacteria Found In Minneapolis Hospital Water Samples – Angela Laguipo – Tech Times

The four bugs that protect us from asthma – Elizabeth Finkel – Cosmos Magazine
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November 28, 2015

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Events

2nd Microbiome R&D and Business Collaboration Congress – Early registration ends Monday – February/March 2016, Kuala Lumpur, Malaysia

Human oral microbiome

Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project – Zongxin Ling – Scientific Reports

Human gut microbiome

Altered Fecal Microbiota in Paediatric Inflammatory Bowel Disease – Johanna Maukonen – Journal of Crohn’s and Colitis

Microbiome models

Perspective: Could microbial therapy boost cancer immunotherapy? – Alexandra Snyder – Science

Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function – Spenser Reed – Nutrients

Microbiota is an essential element for mice to initiate a protective immunity against Vaccinia virus – Maurício T. Lima – FEMS Microbiology Ecology

Impacts of Extended Laboratory Rearing on Female Fitness in Florida Colonies of the Parasitoid Spalangia cameroni (Hymenoptera: Pteromalidae) With an Analysis of Wolbachia Strains – E.T. Machtinger – Annals of the Entomological Society of America

Animal microbiome

Fish: Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures – Laetitia G. E. Wilkins – Scientific Reports

Termites: Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites – Karen Rossmassler – Microbiome

Ticks: Emerging horizons for tick-borne pathogens: from the ‘one pathogen–one disease’ vision to the pathobiome paradigm – Muriel Vayssier-Taussat – Future Microbiology

Beetles: Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex – Audrey-Anne Durand – Scientific Reports

Coral: Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Plant, root, and soil microbiome

Illumina High-Throughput Sequencing and Comparative Analysis of Bacterial Communities in Cherry Orchard Soil – Lingzhi Liu – Toxicological & Environmental Chemistry

Water microbiome

Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon – Suchismita Srichandan – Marine Pollution Bulletin

New insights into relationships between active and dormant organisms, phylogenetic diversity and ecosystem productivity – Jacob A. Cram – Molecular Ecology

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS – Rafael R. C. Cuadrat – International Journal of Molecular Sciences

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality – K. Jordaan – Environmental Science and Pollution Research

Extremophile microbiome

The impact of temperature on microbial diversity and AOA activity in the Tengchong Geothermal Field, China – Haizhou Li – Scientific Reports

Built environment microbiome

Characterizing the Bacterial Communities in Retail Stores in the United States – A Hoisington – Indoor Air

Viruses and phages

A New Zamilon-like Virophage Partial Genome Assembled from a Bioreactor Metagenome – Meriem Bekliz – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – ArXiv

Microbial Ecology

Resource limitation drives spatial organization in microbial groups – Sara Mitri – The ISME Journal

Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Biofilms / Infection microbiology

Microbial biofilms associated with intravascular catheter-related bloodstream infections in adult intensive care patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Review: The limitations of in vitro experimentation in understanding biofilms and chronic infection – Aled E L Roberts – BioRxiv

Review: The Application of Metagenomic Approaches in the Management of Infectious
Diseases – Jinhua Wu – Tropical Medicine & Surgery

Food microbiology

Sourdough microbial community dynamics: An analysis during French organic bread-making processes – Emilie Lhomme – Food Microbiology

Bacteria in the news

Woolly rhino bacteria cleans up oil spills – Energy Global

A personal touch to wine microbiology – Kyanah Lawson – Food Magazine

Arizona inspectors find Theranos lab issues – AZ Central

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November 26, 2015

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Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!

General microbiome

Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science

Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:

Pregnancy and birth

Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports

The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters

Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases

Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy

Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews

Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility

Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility

Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility

Human skin microbiome

Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics

Human respiratory microbiome

The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society

Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society

Human oral microbiome

Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials

Human gut microbiome

Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function

The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function

The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology

Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology

Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology

The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease

Animal models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE

Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B

Animal microbiome

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia

Plant, root, and soil microbiome

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports

Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology

Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology

Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE

Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research

Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis

Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology

Built environment microbiology

ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Food microbiology

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science

Microbial Ecology

Complete nitrification by Nitrospira bacteria – Holger Daims – Nature

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

Metagenomics and bioinformatics

Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv

Techniques

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg

New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire

Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist

Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard

Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American

Science, publishing, and career

China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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November 25, 2015 – another digest

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Two digests today, to catch up with all literature that came out earlier this week. Gut microbiota of patients with stroke or TIAs, symbiosis within symbiosis, the coffee-machine microbiome, and chocolate making with yeasts.

Human gut microbiome

Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic Attack – Jia Yin – Journal of the American Heart Association

Siri, What Should I Eat? – Reiner Jumpertz von Schwartzenberg, Peter J. Turnbaugh – Cell

Human skin microbiome

Microbiologic Safety of the Transareolar Approach in Breast Augmentation – Dana Mihaela Jianu – Aesthetic Surgery Journal

Microbiome models

Microbiota’s No Wasting Policy – Miguel P. Soares – Cell

Animal microbiome

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis
Mateus Laguardia-Nascimento – PLOS ONE

Review: The natural occurrence of secondary bacterial symbionts in aphids – Sharon E. Zytynska – Ecological Entomology

Plant, root, and soil microbiome

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts
Philippe Remigi – Trends in Microbiology

Soil microbial response to tetracycline in two different soils amended with cow manure – Luigi Chessa – Environmental Science and Pollution Research

Reviews: Friends or foes? Emerging insights from fungal interactions with plants – Susanne Zeilinger – FEMS Microbiology Reviews

Review: Extinction risk of soil biota – worrying paucity of existing information – Stavros D. Veresoglou – Nature Communications

Extremophile microbiome

Integrated ‘Omics’, Targeted Metabolite and Single-cell Analyses of Arctic Snow Algae Functionality and Adaptability – Stefanie Lutz – Frontiers in Microbiology

Water microbiome

Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Built environment microbiome

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach – Cristina Vilanova – Scientific Reports

Food microbiology

Tuning chocolate flavor through development of thermotolerant Saccharomyces cerevisiae starter cultures with increased acetate ester production – Esther Meersman – Applied and Environmental Microbiology

Microbial genomes and ecology

Migration and horizontal gene transfer divide microbial genomes into multiple niches –
Rene Niehus – Nature Communications

The Good, the Bad, and the Tiny: A Simple, Mechanistic-Probabilistic Model of Virus-Nutrient Colimitation in Microbes – B. B. Cael – PLOS ONE

Microbes are trophic analogs of animals – Shawn A. Steffan – PNAS

Animal–microbe interactions and the evolution of nervous systems – Heather L. Eisthen – Philosophical Transactions B

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi – Martin Ryberg – Molecular Ecology

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – Bioinformatics

Techniques

Comparative Evaluation of DNA Extraction Methods from Feces of Multiple Host Species for Downstream Next-Generation Sequencing – Marcia L. Hart – PLOS ONE

Bacteria in the news

Your gut bacteria are controlling your appetite, study finds – Bec Crew – ScienceAlert

Beastly bacteria on extinct ancient carcasses offers ‘cure’ for modern oil pollution – Vera Salnitskaya – The Siberian Times

This ‘Plant Lamp’ uses bacteria to generate electricity – Sean Buckley – EnGadget
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November 25, 2015

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My apologies for 2 missed posts (due to overseas family circumstances). Gut microbiota of infants with botulism, gut microbial diversity in US Midwest population, decomposing pig carcasses, oil-degrading microbes and sunlight.

Events

5th Annual Microbiology of the Built Environment Conference – June 1-3 2016, Boulder, CO

Jobs

Our lab at Stanford University is hiring a Clinical Study Coordinator to be based out of UCSF School of Dentistry. Great position for someone who eventually wants to go to medical or dental school.

Pregnancy and birth

The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Epigenomics

Human oral microbiome

The impact of different DNA extraction methods on the analysis of microbial diversity of oral saliva from healthy youths by polymerase chain reaction-denaturing gradient gel electrophoresis – Ming Chen – Journal of Dental Sciences

Human gut microbiome

Characterizing the fecal microbiota of infants with botulism – T. Brian Shirey – Microbiome

Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults – Sushmita G. Yallapragada – Pediatric Annals

Impact of demographics on human gut microbial diversity in a US Midwest population – Jun Chen – PeerJ Preprint

Review: Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development – Manu S. Goyal – PNAS

Review: Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome – Maayan Levy – Genome Medicine

Review: The relationship between early-life environment, the epigenome and the microbiota – Amber V Majnik – Future Medicine

Microbiome models

Gut Commensal E. coli Proteins Activate Host Satiety Pathways following Nutrient-Induced Bacterial Growth – Jonathan Breton – Cell Metabolism

Plant, root, and soil microbiome

From Rare to Dominant: A Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation – Sebastián Fuentes – Applied and Environmental Microbiology

Metabarcoding analysis of Phytophthora diversity using genus specific primers and 454 pyrosequencing – Maria I Prigigallo – Phytopathology

Structures of microbial communities in alpine soils: seasonal and elevational effects – Anna Lazzaro – Frontiers in Microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

The community structures of prokaryotes and fungi in mountain pasture soils are highly correlated and primarily influenced by pH – Anders Lanzen – Frontiers in Microbiology

Water microbiome

Application of Microfluidic QPCR (MFQPCR) Technique to Monitor Bacterial Pathogens in Beach Water and Complex Environmental Matrices – Muruleedhara Byappanahalli – Environmental Science & Technology Letters

Natural sunlight shapes crude oil-degrading bacterial communities in northern Gulf of Mexico surface waters – Hernando P. Bacosa – Frontiers in MIcrobiology

Bacterioplankton community resilience to ocean acidification: evidence from microbial network analysis – Yu Wang – ICES Journal of Marine Sciences

Microbial Diversity and Bioactive Substances in Disease Suppressive Composts from India – C. M. Mehta – Compost Science & Utilization

Extremophile microbiome

Microbial metagenomics of oil sands tailings ponds: small bugs, big data – Julia M. Foght – Genome

Built environment microbiome

Changes in Microbes of the Built Environment in Early Stages of Urbanization – Maria Gloria Dominguez-Bello

Microbiome of death

The impact of carrion decomposition on the fatty acid methyl ester (FAME) profiles of soil microbial communities in southern Canada – Heloise Breton – Canadian Society of Forensic Science Journal

Metagenomics and bioinformatics

Assembly: a resource for assembled genomes at NCBI – Nucleic Acid Research

Web Resources for Metagenomics Studies – Pravin Dudhagara – Genomics, Proteomics & Bioinformatics

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data – Martial Marbouty – Trends in Genetics

EBI metagenomics in 2016 – an expanding and evolving resource for the analysis and archiving of metagenomic data – Alex Mitchell – Nucleic Acids Research

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 – Daniel Greuter – Nucleic Acids Research

Microbial ecology / more microbiology

Review: Microbial Invasions: The Process, Patterns, and Mechanisms – Cyrus Alexander Mallon – Trends in Microbiology

Review: Microbial diversity — exploration of natural ecosystems and microbiomes –
Sean M Gibbons – Current Opinion in Genetics & Development

Microbes As Friends, Not Foes: Shifting the Focus from Pathogenesis to Symbiosis – Sheila A. Homburger – The American Biology Teacher

Microbes in the news

Leading Antibiotic Doomsayer Mellows on Infection Armageddon – Michael Byrne – Motherboard
and
I believed we would face an antibiotics apocalypse – until now – Richard James – The Guardian

Tardigrades: Inside the Bizarre Genome of the World’s Toughest Animal – Ed Yong – The Atlantic

C&EN Talks With Microbiome Surveyor Stefanie Kandels-Lewis: The laboratory technician turned fixer kept the Tara Oceans project, an expedition to map the oceans’ microbial populations, afloat for four years – Sarah Everts – C&EN

Kiwi scientists invent stomach ulcer cure – Olivia Wannan – Stuff NZ

A Doctor Wrestles With Whether To Keep Wearing His White Coat – John Henning Schumann – NPR

When will the world wake up to the potential of poo power? – John Vidal – The Guardian

At TEDMED 2015: How microbiome studies could improve the future of humanity – ScopeBlog

Two Types of Diet May Protect Against Type 2 Through Regulation of Gut Microbiota – Diabetes in Control

Symberix lands two SBIRs for GI drug that targets the microbiome – Meghana Keshavan – MedCity News

Diet study overturns all we know about healthy eating – Israel21c

Liberia monitors over 150 Ebola contacts as virus re-emerges – James Harding Giahyue – Reuters

Now We Can Use Microbes to Make Designer Chocolate Flavors – Esther Inglis-Arkell – Gizmodo

Fossils show sign of ancient vampire microbes – Punctures in fossils suggest predation drove the evolution of self-defense systems – Thomas Sumner – Student Science

Science, publishing and career

Stepping Away from the Lab:Emilie, Can I Ask You? Why I made the decision to leave academic research and become an editor.- Cell

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November 21, 2015

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Human respiratory microbiome

Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation – Sang Hu Kim – PLOS Pathogens

Human gut microbiome

Review: Immune Interactions with Pathogenic and Commensal Fungi: A Two-Way Street – David M. Underhill – Immunity

Animal and other models

A Wave of Regulatory T Cells into Neonatal Skin Mediates Tolerance to Commensal Microbes – Tiffany C. Scharschmidt – Immunity

Animal microbiome

Spatial Variation of the Gut Microbiota in Broiler Chickens as Affected by Dietary Available Phosphorus and Assessed by T-RFLP Analysis and 454 Pyrosequencing – Maren Witzig – PLOS ONE

Variation in species diversity and functional traits of sponge communities near human populations in Bocas del Toro, Panama – Cole G. Easson – PeerJ

Water microbiome

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea – Meng Li – Nature Communications

Built environment microbiology

Fungal compositions and diversities on indoor surfaces with visible mold growths in residential buildings in the Seoul Capital Area of South Korea – C. An – Indoor Air

Characterization of Microbial Communities in Household Washing Machines – Ilka D. Nix – Tenside Surfactants Detergents

Metagenomics and Bioinformatics
DUDE-Seq: Fast Universal Denoising of Nucleotide Sequences – Byunghan Lee – ArXiv

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads – Xiao Zhu – BMC Bioinformatics

Viruses and phages

Inferring the Clonal Structure of Viral Populations from Time Series Sequencing – Donatien F. Chedom – PLOS Computational Biology

Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity – Magdalena Calusinska – Environmental Microbiology

Microbes in the news

Entering the Natural Antibiotic Arms Race – Anne Estes – Mostly Microbes

This Synthetic Bio Company Is Hacking Microbes to Build the Smells of the Future – Britt Wray – Motherboard

U of T researchers discover mysterious fungus that defends against neighbouring bacteria – News Medical

The Secret is Out! Review of “The Secret World Inside You” at the American Museum of Natural History in New York. – Anne Estes – Mostly Microbes

Innovative microbiome technology may help fight certain infections – News Medical

Science, publication, and career

America’s science legacy – Neil deGrasse Tyson – Science

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November 20, 2015

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Dog licking and microbe sharing, glycemic response and gut microbiome, fungi in the Amazon, and separating the bacteria from the poop. And an image I could not resist creating:

 

Screen Shot 2015-11-20 at 10.13AM, Nov 20

 

Human gut microbiome

Personalized Nutrition by Prediction of Glycemic Responses – David Zeevi – Cell

DNA fingerprinting approaches to trace E. coli sharing between dogs and owners – Zahra Naziri – Journal of Applied Microbiology

Metabolomic fingerprint of severe obesity is dynamically affected by bariatric surgery in a procedure-dependent manner – Ewa Gralka – American Journal of Clinical Nutrition

Review: T Lymphocyte Dynamics in Inflammatory Bowel Diseases: Role of the Microbiome – C. B. Larmonier – BioMed Research International

Animal models

Calcium supplementation modulates gut microbiota in a prebiotic manner in dietary obese mice – Alice Chaplin – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

Fungal Community Assembly in the Amazonian Dark Earth – Adriano Reis Lucheta – Microbial Ecology

Molecular diversity and distribution of marine fungi across 130 European environmental samples – Thomas A. Richards – Proceedings of the Royal Society B

Extremophile microbiome

Analysis of cbbL, nifH, and pufLM in Soils from the Sør Rondane Mountains, Antarctica, Reveals a Large Diversity of Autotrophic and Phototrophic Bacteria – Guillaume Tahon – Microbial Ecology

Infection microbiology

The role of biofilms as environmental reservoirs of antibiotic resistance – José L. Balcázar – Frontiers in Microbiology

Elucidating Host–Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches – Vaishnavi Ravikumar – Frontiers in Microbiology

Techniques

Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof – Arancha Hevia – Scientific Reports

Microbes in the news

Different parasitic worms can raise or lower female fertility – Sam Wong – New Scientist

The Secret World of Museums: How Hidden Science Becomes Public Exhibit – Katharine Trendacosta – IO9
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November 19, 2015

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Fungal dysbiosis in Crohn’s disease, a vagina monologue, stool sample storage, giraffe poop, Yellowstone lake, and extraction of bacteriophages.

Pregnancy and birth

Helminth infection, fecundity, and age of first pregnancy in women – Aaron D. Blackwell – Science

A Vagina Monologue: Mom’s Stress, Bugs, and Baby’s Brain – William A. Banks – Endocrinology

Human respiratory microbiome

The sinonasal bacterial microbiome in health and disease – Vijay R. Ramakrishnan – Current Opinion in Otolaryngology & Head & Neck Surgery

Human vaginal microbiome

Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity – A. Mitra – Scientific Reports

Human urinary tract microbiome

Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Human gut microbiome

Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients –
Giuseppina Liguori – Journal of Crohn’s and Colitis

Celiac Disease Genomic, Environmental, Microbiome, and Metabolomic (CDGEMM) Study Design: Approach to the Future of Personalized Prevention of Celiac Disease – Maureen M. Leonard – Nutrients

Sample storage conditions significantly influence faecal microbiome profiles – Jocelyn M Choo – Scientific Reports

Analysis of the Bacterial Diversity in Liver Abscess: Differences between
Pyogenic and Amoebic Abscesses – Miriam E. Reyna-Fabian – Am J Trop Med Hyg

Review: Gut microbiota regulates key modulators of social behavior – Arun Parashar – European Neuropsychopharmacology

Review: Metabolomic insights into the intricate gut microbial–host interaction in the development of obesity and type 2 diabetes – Magali Palau-Rodriguez – Frontiers in Microbiology

Animal models

The effect of microbial colonization on the host proteome varies by gastrointestinal location – Joshua S Lichtman – The ISME Journal

Animal microbiome

Analysis of the distal gut bacterial community by 454-pyrosequencing in captive giraffes (Giraffa camelopardalis) – Ousama AlZahal – Zoo Biology

Panamanian frog species host unique skin bacterial communities – Lisa K. Belden – Frontiers in Microbiology

Climate change stressors destabilize the microbiome of the Caribbean barrel sponge, Xestospongia muta – Michael P. Lesser – Journal of Experimental Marine Biology and Ecology

Plant, root, and soil microbiome

Bacteria in a wood fungal disease: characterization of bacterial communities in wood tissues of esca-foliar symptomatic and asymptomatic grapevines – Emilie Bruez – Frontiers in Microbiology

Water and extremophile microbiome

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China – Qiufang Zhang – Frontiers in Microbiology

Distribution of cold adaptation proteins in microbial mats in Lake Joyce, Antarctica: Analysis of metagenomic data by using two bioinformatics tools – Hyunmin Koo – Journal of Microbiological Methods

Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function – William P. Inskeep – Frontiers in Microbiology

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica – Tom O. Delmont – Frontiers in Microbiology

Book Chapter: Microbiological Monitoring of Lake Baikal – Valentina V. Parfenova – Novel Methods for Monitoring and Managing Land and Water Resources in Siberia

Waste microbiology

Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils – Silvena Boteva – Environmental Science and Pollution Research

Seasonal Changes in Bacterial Communities Cause Foaming in a Wastewater Treatment Plant – Ping Wang – Microbial Ecology

Temporal–spatial variation of bacterial diversity in estuary sediments in the south of Zhejiang Province, China – Xiao-Ming Lu – Applied Microbiology and Biotechnology

Viruses, metagenomics and bioinformatics

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut – Josué L. Castro-Mejía – Microbiome

Comparison of Illumina de novo assembled and Sanger sequenced viral genomes: A case study for RNA viruses recovered from the plant pathogenic fungus Sclerotinia sclerotiorum – Mahmoud E. Khalifa – Virus Research

ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens – David Bonsall – F1000 Research

More microbiology

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study – Yi-Yun Liu – The Lancet Infectious Diseases

Microbes in the news

Seafloor communities create electricity. In the digital age, we’re all connected by electricity — and some microbes are too – Meghan Bartels – ScienceLine

Microbe cheerleader: interview with Richard Roberts – Gijsbert Werner – Nature
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November 18, 2015

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My sincere apologies: the website was down most of today. I am not sure what it was – the problem was on the host server site. But I’m back, with tea rhizobacteria, bacteria reporting explosives in the soil, fungi in a glacier, and a bacterial protein preventing ice cream drip.

Animal models

Editorial: Worming Their Way into the Picture: Microbiota Help Helminths Modulate Host Immunity – Lisa A. Reynolds, B. Brett Finlay – Immunity

Plant, root, and soil microbiome

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes – Ximei Zhang – Global Change Biology

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains – Remo Freimann – Frontiers in Microbiology

Resistance of Undisturbed Soil Microbiomes to Ceftriaxone Indicates Extended Spectrum β-Lactamase Activity – Joao Gatica – Frontiers in Microbiology

Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars – Jintu Dutta – Frontiers in Microbiology

Water / extremophile microbiome

Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea – Meng Li – Nature Communications

Fungal biodiversity in the periglacial soil of Dosdè Glacier (Valtellina, Northern Italy) – Marinella Rodolfi – Journal of Basic Microbiology

Winter severity determines functional trait composition of phytoplankton in seasonally ice-covered lakes – Deniz Özkundakci – Global Change Biology

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria – Katrin Zwirglmaier – Frontiers in Microbiology

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities – Kemal Sanli – Frontiers in Microbiology

Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin – Ying He – Frontiers in Microbiology

Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing – Neng Fei Wang – Frontiers in Microbiology

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust – Everett C. Salas – Frontiers in Microbiology

Waste and built environment microbiology

Review: Genetically engineered microorganisms for the detection of explosives’ residues – Benjamin Shemer – Frontiers in Microbiology

Self-healing of early age cracks in cement-based materials by mineralization of carbonic anhydrase microorganism – Chunxiang Qian – Frontiers in Microbiology

Infection microbiology

Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness – Matthew J. Binnicker – Journal of Clinical Microbiology

FilmArray Respiratory Panel Assay: Comparison of Nasopharyngeal Swabs and Bronchoalveolar Lavage Samples – Natalya Azadeh – Journal of Clinical Microbiology

Editorial: Variability in Antibiotic Prescribing: An Inconvenient Truth – Lauri A. Hicks and Martin J Blaser – Journal of the Pediatric Infectious Diseases Society

Variation in Antibiotic Prescribing Across a Pediatric Primary Care Network – Jeffrey S. Gerber – Journal of the Pediatric Infectious Diseases Society

Innate Immune Signaling Activated by MDR Bacteria in the Airway – Dane Parker – Physiological Reviews

Tropheryma whipplei, a Potential Commensal Detected in Individuals Undergoing Routine Colonoscopy – M. E. Grasman -Journal of Clinical Microbiology

Bioinformatics and metagenomics

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes – Samuel C. Forster – Nucleic Acids Research

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics – Matthias Willmann – Antimicrobial Agents and Chemotherapy

Current and future resources for functional metagenomics – Kathy N. Lam – Frontiers in Microbiology

Microbial Ecology

Slow and Fast Evolving Endosymbiont Lineages: Positive Correlation between the Rates of Synonymous and Non-Synonymous Substitution – Francisco J. Silva – Frontiers in Microbiology

Microbes in the news

How the Western Diet Has Derailed Our Evolution: Burgers and fries have nearly killed our ancestral microbiome – Moises Velasquez-Manoff – Nautilus

Bacterial biofilm protein prevents ice cream drip – Elisabeth Bik – NPJ Biofilms Community
and
Ice cream designed to drip slowly – Lydia Chain – Popular Science

Bacteria Hysteria

You Don’t Know Where That’s Been: Part 2 – KGNS TV

Science, publishing, and career

Racial bias continues to haunt NIH grants – Minorities still less likely to win biomedical funding – Erika Check Hayden – Nature

Ask Me Anything on Reddit with Carl Zimmer, science journalist at The New York Times, National Geographic and STAT.

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November 17, 2015

Posted on by

Detecting bacteriophage DNA in mummies, microbiome depletion reduces obesity (in mice), viruses in city rats, microbes in alkaline hotsprings and in glaciers.

Events

European Microbiome Congress 2015: 18-19 November 2015, London.

Human respiratory tract microbiome

Viral aetiology of common colds of outpatient children at primary care level and the use of antibiotics – Janete Kamikawa – Mem. Inst. Oswaldo Cruz

Human reproductive tract microbiome

A DNA tool for early detection of vaginal dysbiosis in African women – Vicky Jespers – Research in Microbiology

Human gut microbiome

Natural mummification of the human gut preserves bacteriophage DNA – Tasha M. Santiago-Rodriguez – FEMS Microbiology Letters

Review: Inhibition of methanogenic archaea by statinsas a targeted management strategy for constipation andrelated disorders – K. Gottlieb

Review: Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target – Ali Ramezani – American Journal of Kidney Diseases

Opinion: The Microbiome and Cancer: Is the ‘Oncobiome’ Mirage Real? – Ryan M. Thomas – Trends in Cancer

Review: The effect of gut microbiota on drug metabolism – Mi Jeong Kang – Expert Opinion on Drug Metabolism & Toxicology

Animal and bioreactor models

Microbiota depletion promotes browning of white adipose tissue and reduces obesity –
Nicolas Suárez-Zamorano – Nature Medicine

Variable responses of human and non-human primate gut microbiomes to a Western diet –
Katherine R. Amato – Microbiome

Research Highlight: Commensal bacterium prevents wasting – Cláudio Nunes-Alves – Nature Reviews Microbiology

Impact of a probiotic, inulin, or their combination on the piglets’ microbiota at different intestinal locations – V.A. Sattler – Beneficial Microbes

Iron Modulates Butyrate Production by a Child Gut Microbiota In Vitro – Alexandra Dostal – mBio

Research Hightlight: Scaling up spatial imaging of the gut microbiota – Naomi Attar – Nature Reviews Microbiology

Metagenomic analysis of anammox communities in three different microbial aggregates – Jianhua Guo – Environmental Microbiology

Microbial community analysis of a full-scale DEMON bioreactor – Alejandro Gonzalez-Martinez – Bioprocess and Biosystems Engineering

Re-appraisal of the phylogeny and fluorescence in situ hybridization probes for the analysis of the Competibacteraceae in wastewater treatment systems – Simon J. McIlroy – Environmental Microbiology Reports

Animal microbiome

New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics – Thomas Arn Hansen – PLOS ONE

Bleaching of Baikalian sponge affects the taxonomic composition of symbiotic microorganisms – O. V. Kaluzhnaya – Russian Journal of Genetics

Experimental Infection of Snakes with Ophidiomyces ophiodiicola Causes Pathological Changes That Typify Snake Fungal Disease – Jeffrey M. Lorch – mBio

Plant, root, and soil microbiome

Glyphosate effects on soil rhizosphere-associated bacterial communities – Molli M. Newman – Science of the Total Environment

Soil microarthropods support ecosystem productivity and soil C accrual: Evidence from a litter decomposition study in the tallgrass prairie – Jennifer L. Soong – Soil Biology and Biochemistry

Microbial communities and organic matter composition in surface and subsurface sediments of the Helgoland mud area, North Sea – Oluwatobi E. Oni – Frontiers in Microbiology

Shifts in the composition and potential functions of soil microbial communities responding to a no-tillage practice and bagasse mulching on a sugarcane plantation – Toshiko Miura – Biology and Fertility of Soils

Local climatic conditions constrain soil yeast diversity patterns in Mediterranean forests, woodlands, and scrub biome – Andrey M. Yurkov – FEMS Yeast Research

Coal mining practices reduce the microbial biomass, richness and diversity of soil –
Patricia Dorr de Quadros – Applied Soil Ecology

Water microbiome

The Fate of Marine Bacterial Exopolysaccharide in Natural Marine Microbial Communities – Zilian Zhang – PLOS ONE

Comparative study on composition and abundance of major planktons and physico-chemical characteristics among two ponds and Lake Tana, Ethiopia – Wondie Zelalem Amanu – Journal of Coastal Life Medicine

Extremophile microbiome

Metagenomics of an alkaline hot spring in Galicia (Spain): microbial diversity analysis and screening for novel lipolytic enzymes – Olalla López-López – Frontiers in Microbiology

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic – Purnima Singh – Journal of Basic Microbiology

Built environment microbiology

Microbiota formed on attached stainless steel coupons correlate with the natural biofilm of the sink surface in domestic kitchens – Birgitte Moen – Canadian Journal of Microbiology

Towards an antimicrobial ‘microglove’ – Ewoud Reilman – Scientific Reports

Infection microbiology

Research Highlight: The Origin of a Killer Revealed by Bronze Age Yersinia Genomes – Shijulal Nelson-Sathi – Cell Host & Microbe

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago – Simon Rasmussen – Cell

Review: The Black Death: Its origin and routes of dissemination – Kristina Lenz – Scandinavian Journal of History

Review: Emerging methodologies for pathogen identification in positive blood culture testing – Grégory Dubourg – Expert Review of Molecular Diagnostics

Microbial ecology

Integrating ecological and engineering concepts of resilience in microbial communities – Hyun-Seob Song – Frontiers in Microbiology

Perspective: Rethinking “mutualism” in diverse host-symbiont communities – Alexandra A. Mushegian – BioEssays

Techniques

Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community – Yang Lu – PLOS ONE

Bioinformatics, viruses, and metagenomics

The State of Software in Evolutionary Biology: code quality of 15 highly cited tools – Diego Darriba – bioRxiv

Kaiju: Fast and sensitive taxonomic classification for metagenomics – Peter Menzel – bioRxiv

A novel group of diverse Polinton-like viruses discovered by metagenome analysis – Natalya Yutin – BMC Biology

Microbes in the news

Taking Antibiotics Can Change the Gut Microbiome for Up to a Year. A new study illuminates the problems antibiotic overuse could cause for individual patients – Julie Beck – The Atlantic

Health Experts Are Explaining Drug-Resistant Bacteria Poorly: Their confusing jargon is pushing people toward bad decisions – Ed Yong – The Atlantic

5 Common Myths About Antibiotic-Resistant Bacteria – Alexandra Sifferlin – Time

There’s Life in Rocks Deep Below the Sea Floor. Seriously. – Heather Goldstone – Cape and Islands

More armadillos that carry leprosy bacteria found in Southern US – Amanda Lane – Midday Daily

Blood-Gut Barrier. Scientists identify a barrier in mice between the intestine and its blood supply, and suggest how Salmonella sneaks through it – Ruth Williams – The Scientist

Microbes Play Role in Anti-Tumor Response
Gut microbiome composition can influence the effectiveness of cancer immunotherapy in mice – Anna Azvolinsky – The Scientist

How depleting the gut microbiota protects from obesity – MedicalXpress

A Complex Disorder. Factors that likely contribute to obesity include disruptions to intercellular signaling, increased inflammation, and changes to the gut microbiome – Stephen D. Hursting – The Scientist

 

Effect of feed on microbiota balance in piglets – All About Feed

Skin Must Develop Tolerance to ‘Good’ Bacteria Early In Life, Says New Study: Research Probes How Skin’s Resident Communities of Microbes Are Established – Pete Farley – University of California San Francisco

How You’re Born May Affect Your Brain Development – Stephanie Pappas – Brain Decoder

Bacteria Hysteria

Doctors say to watch out for bacteria in your makeup bag – NBC News

Proper Use Of Wipes Kills Germs, Improper Use Could Spread Them – Maria Simbra – CBS Local

Microbiology and Art

What Lives on the Subway Pole? – Jen Kirby – New York Magazine

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