Category Archives: General Microbiome

January 27, 2016 – second edition

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

Events

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

General human microbiome

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

Pregnancy and birth

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

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

Human vaginal microbiome

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

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

Human skin microbiome

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

Human urinary tract microbiome

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

Human gut microbiome

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

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

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

Animal models

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

Water and waste microbiome

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

Extremophile microbiome

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

Bioinformatics and metagenomics

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

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

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

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

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

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

Science, publishing, and career

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

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January 27, 2016

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Catching up after 2 busy days:

Effects of antibiotic use in Finnish children, skin microbiota of salmon transitioning from freshwater to seawater, and California coastal phages.

General human microbiome

Review: The microbial environment and its influence on asthma prevention in early life – Erika von Mutius – Journal of Allergy and Clinical Immunology

Human respiratory tract microbiome

COPD and the microbiome – Manoj J. Mammen – Respirology

Human urinary tract microbiome

Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction – Suzanne L. Groah – The Journal of Urology

Human gut microbiome

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children – Katri Korpela – Nature Communications

Animal models

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves – Richard Van Vleck Pereira – PLOS ONE

Editorial: Host response: Microbiota prime antiviral response – Julie K. Pfeiffer – Nature Microbiology

Animal microbiome

Comparison of Intestinal Microbiota in Intestinal Tracts of the Wild and Cultured Seahorses, Hippocampus trimaculatus (Leach) – Kai Wang – Journal of the World Aquaculture Society

Social wasps are a Saccharomyces mating nest – Irene Stefanini – PNAS

Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon – Jep Lokesh – Scientific Reports

The role of tissue-specific microbiota in initial establishment success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, soil, and root microbiome

Kisameet Clay Exhibits Potent Antibacterial Activity against the ESKAPE Pathogens – mBio

Plant-microbe communication enhances auxin biosynthesis by a root-associated bacterium Bacillus amyloliquefaciens SQR9 – Yunpeng Liu – Molecular Plant-Microbe Interactions

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces – Minsu Kim – PLOS ONE

Analysis of bacterial communities associated with potting media – A. M. Al‑Sadi – Springer Plus

Water microbiome

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California – Subbarao V. Ravva – PLOS ONE

Built environment and waste microbiome

Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors – Igor Shuryak – PLOS ONE

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology – Łukasz Jałowiecki – PLOS ONE

Microbial Ecology

The Effect of Immigration on the Adaptation of Microbial Communities to Warming – Diane Lawrence – The American Naturalist

Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process – Sabine Koch – Biotechnology for Biofuels

Microbes in the news

Early-Life Antibiotic Use Affects Gut Microbiome Composition, New Study Says – Genome Web

Classroom research project: detecting phages – MT Standard

 

Uncovering hidden microbial lineages from hot springs – EurekAlert

Your Food’s Bacteria is a Big Data Gold Mine. IBM and Mars are tracking food’s microbiome to improve safety and productivity – David Z. Morris – Fortune

What Causes Cavities? The Balance Of Bacteria In Your Mouth Can Lead To Tooth Decay – Samantha Olson – Medical Daily

First Nations’ ancient medicinal clay shows promise against today’s worst bacterial infections – University of British Columbia

Ferring, Karolinska Institutet Launch Human Microbiome Collaboration – GenEngNews

WTF?: Fat Summit conference: Deepak Chopra Says Bacteria Listen To Our Thoughts – “we are the awakening of bacterial consciousness” – Kavin Senapathy – Forbes
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January 23, 2016

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

General human microbiome

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

Pregnancy and birth

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

Human oral microbiome

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

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

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

Human gut microbiome

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

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

Models of microbiome research

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

Water and extremophile microbiome

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

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

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

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

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

Food microbiology

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

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

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

Bioinformatics, metagenomics, and protocols

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

Microbes in the news

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

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

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

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

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

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

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

Science, publishing, and career

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

Bik’s Picks

Secular trends in family dinner frequency among adolescents – Kathryn Walton – BMC Research Notes
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January 16, 2016

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Gut microbiota in acute malnutrition, social behavior and the chimpanzee pan-microbiome, arctic marine fungi, and learning ecological networks.

General microbiome

Immune-Microbiota Interactions: Dysbiosis as a Global Health Issue – Alan C. Logan – Current Allergy and Asthma Reports

Human oral microbiome

Long-term prospective cohort study on dental implants: clinical and microbiological parameters – Henri Tenenbaum – Clinical Oral Implants Research

Human reproductive tract microbiome

Alterations in the Genital Microbiota in Women With Spinal Cord Injury – Pires, Cristhiane V.G. – Obstetrics & Gynecology

Human gut microbiome

Gut Microbiota in Children Hospitalized with Oedematous and Non-Oedematous Severe Acute Malnutrition in Uganda – Kia Hee Schultz Kristensen – PLOS Neglected Tropical Diseases

Editorial: Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes – Adil Mardinoglu – Cell Metabolism

Review: Impact of high fat diets, prebiotics and probiotics on gut microbiota and immune function, with relevance to elderly populations – Yue Liu – Nutrition and Aging

Review: Transkingdom control of viral infection and immunity in the mammalian intestine – Julie K. Pfeiffer – Science

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Animal models

In rats: Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet – Nadeem O. Kaakoush – Molecular Nutrition & Food Research

In mice: Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model – Mark Bazett – Scientific Reports

Animal microbiome

Social behavior shapes the chimpanzee pan-microbiome – Andrew H. Moeller – Science Advances

Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient – Kathleen M. Morrow – Environmental Microbiology

Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster – Susanna López-Legentil – Frontiers in Zoology

Plant, root, and soil microbiome

Uncultivated margins are source of soil microbial diversity in an agricultural landscape –
Luciana D’Acunto – Agriculture, Ecosystems & Environment

Editorial: Deep influence of soil microbes – Karl Gruber – Nature Plants

Review: Soil microbes and community coalescence – Matthias C. Rillig – Pedobiologia

Water and extremophile microbiome

Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavor Segment, Juan de Fuca Ridge – T. J. Lin – Geochemistry, Geophysiscs, Geosystems

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock – Dhiraj Paul – Frontiers in Microbiology

Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond – Shimin Lu – Frontiers in Microbiology

Chytrids Dominate Arctic Marine Fungal Communities – B.T. Hassett – Environmental Microbiology

Built environment microbiome

Bacterial Monitoring in the International Space Station-“Kibo” Based on rRNA Gene Sequence – Nobuyasu Yamaguchi – Transactions of the Japan Society for Aeronautical and Space Sciences

Metagenomics and bioinformatics

Safe and complete contig assembly via omnitigs – Alexandru I. Tomescu – ArXiv

More microbiology and ecology

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv

Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes – Edgardo Galán-Vásquez – PLOS ONE

Learning Ecological Networks from Next-Generation Sequencing Data – Corinne Vacher – Advances in Ecological Research

Microbes in the news

Chimps Share Microbes When Socializing – Kate Yandell – The Scientist

How Your Social Life Changes Your Microbiome – Ed Yong – The Atlantic

Social Contact Helps Beneficial Gut Bacteria Spread – Brian Handwerk – Smithsonian

Prevent severe diarrhea by controlling levels of specific gut bacteria – Bel Marra Health

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January 15, 2016

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Distinct microbiotas in 2 West Nile Virus-carrying mosquitoes, co-occurrence networks in Chinese soil, microbial communities associated with retreating glaciers.

Events

Open for international proposals: 2016 Mo Bio Microbiome Awards – Deadline May 31

Human oral microbiome

In Vitro Cultivation of ‘Unculturable’ Oral Bacteria, Facilitated by Community Culture and Media Supplementation with Siderophores – Sonia R. Vartoukian – PLOS ONE

Human gut microbiome

Synbiotics Easing Renal Failure by Improving Gut Microbiology (SYNERGY): A Randomized Trial – Megan Rossi – Clinical Journal of the American Society of Nephrology

Perspective: Effect of Synbiotic Therapy on Gut–Derived Uremic Toxins and the Intestinal Microbiome in Patients with CKD – Nosratola D. Vaziri – Clinical Journal of the American Society of Nephrology

Animal models

Editorial: Microbiome: Fibre for the future – Eric C. Martens – Nature

Animal microbiome

Culex pipiens and Culex restuans mosquitoes harbor distinct microbiota dominated by few bacterial taxa – Ephantus J. Muturi – Parasites & Vectors

Plant, root, and soil microbiome

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China – Bin Ma – The ISME Journal

Evidence of the Generation of Isosaccharinic Acids and Their Subsequent Degradation by Local Microbial Consortia within Hyper-Alkaline Contaminated Soils, with Relevance to Intermediate Level Radioactive Waste Disposal – Simon P. Rout – PLOS ONE

Biodiversity and succession of mycobiota associated to agricultural lignocellulosic waste-based composting – Juan Antonio López-González – Bioresource Technology

Water/soil/glacier microbiome

Shifts in diversity and function of lake bacterial communities upon glacier retreat –  Hannes Peter – The ISME Journal

Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier – Thomas Rime – The ISME Journal

Other microbiology

Automated broad range molecular detection of bacteria in clinical samples – Andries E. Budding – Journal of Clinical Microbiology

Natural environments, nature relatedness and the ecological theater: connecting satellites and sequencing to shinrin-yoku – Jeffrey M. Craig – Journal of Physiological Anthropology

Biodegradation of antibiotic ciprofloxacin: pathways, influential factors, and bacterial community structure – Xiaobin Liao – Environmental Science and Pollution Research

Techniques

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling – Rosalinda D’Amore – BMC Genomics

Microbes in the news

Gut Microbes Need Fiber, Too – Karen Zusi – The Scientist

Would You Take Poop Pills If They Made You Thin? – Susan Rinkunas – New York Magazine

Weird headline above article about Sonnenburg Nature paper: Pet owners urged NOT to wash hands after handling animals to keep friendly bacteria – Laura Mowat – Express

Another puzzling project: ‘Child scientist’ Mustafa develops technique to protect crops from bacteria – Siasat

Stinging Report On Pandemics Makes Louis Pasteur Look Like A Prophet – Jason Beaubien – NPR

After Ebola, 2 Other Tropical Diseases Pose New Threats – Kate Kelland – Scientific American

Science, publishing, and career

Opinion: The Postdoc Crisis. A lack of jobs leaves postdocs without a future in academia in the United States. Meanwhile, other challenges threaten the postdoc community abroad – Muhammed Z. Ahmed – The Scientist

Is sexual harassment less common in biology than in astronomy? – Lenny Teytelman – The Spectroscope

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January 14, 2016

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Sorry for a late post today – I had a lot of meetings. Here is what I found:

Gut microbiota shaped via fecal microRNA, the microgenderome, dysbiosis in Vitiligo skin lesions, metatranscriptomics, and an 18th century Yersinia pestis.

General microbiome

Perspective: Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease – Niv Zmora – Cell Host & Microbe

The Human Microbiome: Opportunities for Dynamics, Systems, and Control
(based on the IFAC blog post Translate or Die) – Travis E. Gibson – Submitted to ACC 2016

Human skin microbiome

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects – Parul Ganju – Scientific Reports

Human oral microbiome

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing – Soo Eon Lee – Acta Odontologica Scandinavica

Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity – C Reilly – Oral Diseases

Commentary: A new association for the oral metagenome – Nicholas S Jakubovics – Oral Diseases

Human vaginal microbiome

Review: Vaginal microbiota and microbiome:- Role in health and disease – Dr Amit A. Rangari – Indian Journal of Basic and Applied Medical Research;

Human gut microbiome

Support for the Microgenderome: Associations in a Human Clinical Population – Amy Wallis – Scientific Reports

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota – Annett Klinder – Food & Function

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile – Ranjit Kumar – BMC Microbiology

Review: The microbiome and its implications in intestinal transplantation – Kroemer, Alexander – Current Opinion in Organ Transplantation

Animal models

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease – Karishma Kamdar – Cell Host & Microbe

The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell Host & Microbe

Animal microbiome

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica – Ngare Wilkinson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Culturable endophytic bacterial communities associated with field grown soybean – Karla Bianca de Almeida Lopes – Journal of Applied Microbiology

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture – Colin Averill – Global Change Biology

Water and waste microbiome

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water – Marta Gómez-Doñate – Microbiology Open

Bacterial diversity in oil-polluted marine coastal sediments – Alejandro Acosta-González – Current Opinion in Biotechnology

Spatial and temporal variability of bacterial communities in high alpine water spring sediments – Alfonso Esposito – Research in Microbiology

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation – Angelo Rubino – PLOS ONE

Metagenomics, metatranscriptomics, and bioinformatics

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – BioRxiv

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality – Yue Jiang – BMC Microbiome Journal

Viral metagenomics and blood safety – V. Sauvage – Transfusion Clinique et Biologique

Microbes in the news

Does our Microbiome Control Us or Do We Control It? – Dina Fine Maron – Scientific American

Your gut’s trick for controlling the bacteria that live in it – New Scientist

Mammals shape their microbiome to prevent disease – Science Codex

Low-Fiber Diets Cause Waves of Extinction in the Gut – Ed Yong – The Atlantic

Bad diets today can alter our great-great-grandkids’ biology – Katherine Ellen Foley – Quartz

Thoughtful and balanced comparison: mothur and QIIME – Pat Schloss – Mothur blog

Modifying the structure of wood alters plant microbiome – Science Daily

Gut Microbiome Similar in Formula- and Combination-Fed Babies – Troy Brown – MedScape

Eglin medical group first to find bacteria unseen in humans: Borrelia turicatae – Ilka Cole – US Air Force

Protecting the infant microbiome – Kathryn Kos – Examiner

Microbiology and art

Sunshine and microbiology inspire Reading artist’s work – Francesca Perryman – Get Reading

Science, publishing, and career

Re: Your Recent Email to Your Professor: Students who use emojis in their emails and write “heeeeelp!” in the subject line don’t necessarily know better.  – Paul T. Corrigan and Cameron Hunt McNabb – Inside Higher Education

ORCID: Publishers embrace scheme to end name confusion – John Bohannon – Science

Give teachers a physics test from a woman and they’ll give her worse grades – John Timmer – Ars Technica

Astronomy’s snowballing sexual harassment scandal picks up even more cases – Rachel Feltman – Washington Post

Bik’s Picks

Inside the Eye: Nature’s Most Exquisite Creation – Ed Yong – National Geographic
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January 12, 2016

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The ecology of microbiome research (in the new journal Nature Microbiology), gut microbiome of infants, dentition status and teeth microbes, human impact on corals, metagenomics, CRISPRs, rainforest and desert soils, and tropical oceans.

General microbiome

An assessment of US microbiome research – Elizabeth Stulberg – Nature Microbiology

Microbiome: Ecology of stable gut communities – Luke McNally – Nature Microbiology

Pregnancy and birth microbiome

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants – Juliette C. Madan – JAMA Pediatrics

Human oral microbiome

Supragingival Microbial Profiles of Permanent and Deciduous Teeth in Children with Mixed Dentition – Weihua Shi – PLOS ONE

Human gut microbiome

Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity – Jiffin K. Paulose – PLOS ONE

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites – Nathalie M. L. Côté – PLOS ONE

Intestinal Microbiota in Patients with Spinal Cord Injury – Bilgi Gungor – PLOS ONE

Editorial: A Potential Role for Host- Microbe Dysbiosis in Enteropathy Associated with HIV Infection – Michael D. George – Primary & Acquired Immunodeficiency Research

Review: The obese gut microbiome across the epidemiologic transition – Lara R. Dugas – Emerging Themes in Epidemiology

Animal microbiome

Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations – Takahiro Hosokawa – Nature Microbiology

The Microbiome of Ehrlichia-Infected and Uninfected Lone Star Ticks (Amblyomma americanum) – R. T. Trout Fryxell – PLOS ONE

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea – Maren Ziegler – Marine Pollution Bulletin

Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces – Da Sun – Environmental Science and Pollution Research

Review: Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics – what is the evidence? – Silke Schmitz – Veterinary Medicine and Science

Plant, root, and soil microbiome

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest – Julia Elidia Lima-Perim – PLOS ONE

Corky root severity, root knot nematode galling and microbial communities in soil, rhizosphere and rhizoplane in organic and conventional greenhouse compartments –
Ariena H.C. van Bruggen – Applied Soil Ecology

Metacommunity analysis of amoeboid protists in grassland soils – Anna Maria Fiore-Donno – Scientific Reports

Microbial communities of buried soils of the Tsaritsyn Defense Line (1718–1720) – T. S. Demkina – Soil Biology

Perspective: Exploring rhizospheric interactions for agricultural sustainability: The need of integrative research on multi-trophic interactions – Rama Kant Dubey – Journal of Cleaner Production

Water microbiome

Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations – Irina N. Shilova – PLOS ONE

Low diversity of planktonic bacteria in the tropical ocean – Mathias Milici – Scientific Reports

Out of thin air: Microbial utilization of atmospheric gaseous organics in the surface ocean – Jesus M. Arrieta – Frontiers in Microbiology

Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms – Jasmin C. Lawes – Biofouling

Waste microbiology

Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats – Nidaa Ali – Microbial Biotechnology

Sequential Changes of Microbial Community Composition During Biological Wastewater Treatment in Single Unit Waste Stabilization System – Subhasis Sarkar – Waste and Biomass Valorization

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch – Yu Xia – Scientific Reports

Food microbiology

Investigation of chocolate produced from four different Brazilian varieties of cocoa (Theobroma cacao L.) inoculated with Saccharomyces cerevisiae – Aline Galvão Tavares Menezesa – Food Research International

Microbial diversity and metabolite composition of Belgian red-brown acidic ales – Isabel Snauwaert – International Journal of Food Microbiology

Metagenomics, CRISPRs, viruses, and bioinformatics

Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls – Tatiana C. Mangericao – BMC Systems Biology

Identification of physical interactions between genomic regions by enChIP-Seq – Toshitsugu Fujita – BioRxiv

Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses – Evelien M. Adriaenssens – MDPI Viruses

A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads – Vinh Van Le – BMC Bioinformatics

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations – Matthew L Bendall – The ISME Journal

Techniques in microbiology

The 6th International Conference on Analysis of Microbial Cells at the Single Cell Level, Retz, Austria, 19-22 July, 2015 – Nina Bydlinski – New Biotechnology

Microbes in the news

Microbe Cells Don’t Outnumber Your Own – Marissa Fessenden – Smithsonian

Getting to know the vagina: Microbiomes and our health – Daniel Vosberg – McGillDaily

Acidification affects the ability of bacteria to clean our oceans – Phys.org

Science, publishing, and career

Do prestigious science journals attract bad science? – Julia Belluz – Vox

Female professors are woefully outnumbered at med schools nationwide – Melissa Bailey – STAT News
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January 9, 2016

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Microbiomes of musk deer, Tasmanian Devils, Panamanian frogs, roots of truffle-associated Douglas firs, and the Great Barrier Reef lagoon.

General human microbiome

Editorial: Getting fat from an inflamed relationship? The revenge of the holobiont
Andrew Moore – BioEssays

Perspective: Has provoking microbiota aggression driven the obesity epidemic? – Benoit Chassaing – BioEssays

Pregnancy and birth

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data – Erica Plummer- OMICS Proteomics & Bioinformatics

Review: Infection and preterm birth – Hugh C.G. Nadeau – Seminars in Fetal and Neonatal Medicine

Human gut microbiome

Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects – Radilla-Vázquez R.B. – Obesity Facts

Animal models

The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice – Jinyu Xu – Scientific Reports

Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation – Allison Agus – Scientific Reports

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior – Mark Lyte – PLOS ONE

Effects of BmCPV Infection on Silkworm Bombyx mori Intestinal Bacteria – Zhenli Sun – PLOS ONE

Antibiotic-treated versus germ-free rodents for microbiota transplantation studies – Randi Lundberg – Gut Microbes

Animal microbiome

The musk chemical composition and microbiota of Chinese forest musk deer males
Diyan Li – Scientific Reports

Pasteurellaceae bacteria from the oral cavity of Tasmanian Devils (Sarcophilus Harrisii) show high MIC values towards aminoglycosides and clindamycin – Nicole Gutman – Letters in Applied Microbiology

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis – Eria A Rebollar – The ISME Journal

Plant, root, and soil microbiome

Prokaryotic diversity in biodeteriorated wood coming from the Bükkábrány fossil forest – Katerina Nikolouli – International Biodeterioration & Biodegradation

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia – Alyssa Cornall – Environmental Toxicology and Chemistry

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum) – Gian Maria Niccolò Benucci – Mycorrhiza

Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils – Patrick L. Tomco – Environmental Toxicology and Chemistry

Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months – Daquan Sun – Applied Soil Ecology

Water and extremophile microbiome

Deep Microbial Life in High-Quality Granitic Groundwater from Geochemically and Geographically Distinct Underground Boreholes – Kohei Ino – Environmental Microbiology Reports

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication – Jesse Colangelo-Lillis – Environmental Microbiology Reports

Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community – Richard A. White III – Frontiers in Microbiology

Partitioning of fungal assemblages across different marine habitats – T.C. Jeffries – Environmental Microbiology Reports

Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities – Stéphane Jomini – Environmental Pollution

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions – Hon Lun Wong – MDPI Microorganisms

Microbial genetic diversity in soils along salinealkaline gradients at the coast of Laizhou Bay – Feng Zhao – Protistology

Influence of Zinc on Bacterial Populations and their Proteolytic Enzyme Activities in Freshwater Environments: A Cross-Site Comparison – Lauren Rasmussen – Canadian Journal of Microbiology

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events – Florent E. Angly – Peer J

Food microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Infection microbiology

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh – Shafiqul Alam Sarker – EBioMedicine

Book Chapter: Reducing pathobiomes could slow arms race between man and microbes
S. Romano-Bertrand – Microbiology 5

Bioinformatics and metagenomics

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery – Eric Marinier – BioRxiv

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities – Lisa Oberding – MDPI Microorganisms

Conference abstracts from the 2015 IEEE International Conference onBioinformatics and Biomedicine (BIBM):
Leveraging the k-Nearest Neighbors classification algorithm for Microbial Source Tracking using a bacterial DNA fingerprint library – Jeffrey D McGovern
A computational framework for integrative analysis of large microbial genomics data – Erliang Zeng
Computational challenges in microbiome research – Mihai Pop

Microbes in the news

New Year’s Resolutions for your Microbiome – Anne Estes – Mostly Microbes

West Hartford Children Museum Starts Scientific Discussion Series – Kristin Stoller – Hartford Courant

Balbriggan pair named Young Scientists of the Year: Maria Louise Fufezan and Diana Bura claim first place for research into soil fertility and nematodes – Dick Ahlstrom – The Irish Times

Body’s bacteria don’t outnumber human cells so much after all – Tina Hesman Saey – Science News

Are we really made up of more bacteria than human cells? – Lindsey Kratochwill – Popular Science

P&G granted patent for prebiotic agent-containing composition targeting skin microbiome – Andrew McDougall – Cosmetic Design-Europe.com

Science, publishing, and career

Nobel winner pulls out of Melb conference run by controversial Indian company (OMICS, EB) – Andrew Masterson – The Age

Cheer up, my academic colleagues! We’re so lucky to do this job – Anonymous Academic – The Guardian

Publishers to require ORCID identifiers for authors – EurekAlert

Bik’s Picks

Healthy Diet Helps 183-Year-Old Tortoise Feel Young Again – Jason Bittel – National Geographic

 

January 7, 2016

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A new estimate of the ratio microbial:human cells in our bodies, a 5300-year old Helicobacter genome, antibiotics alter bile metabolism, microbiota from 59 bird species, and fecal contamination of Kathmandu drinking water.

Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, which will take place in London, on the 11th and 12th of April, 2016. Early registration closes Jan 15th.

Mysterious Microbes Webinar Series 1 of 3: Microbes and the miracle of compost tea, with Noah Fierer and Ryan Heiland, on Jan 14. Learn how and why microbes are the natural secret to green lawns, lush flowers, and abundant produce

General human microbiome

Revised estimates for the number of human and bacteria cells in the body – Ron Sender – bioRxiv

Review: The human microbiota: the role of microbial communities in health and disease – Luz Elena Botero – Acta Biologica Columbiana

Pregnancy and birth microbiome

A comparative study of bifidobacteria in human babies and adults – Shadi Khonsari – Bioscience of Microbiota, Food and Health

Human oral microbiome

Salivary Antimicrobial Peptides in Early Detection of Periodontitis – Güliz N. Güncü – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

The 5300-year-old Helicobacter pylori genome of the Iceman – Frank Maixner – Science

Microbiome animal and other models

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine – Casey M. Theriot – mSphere

The Gut Microbiota Reduces Colonization of the Mesenteric Lymph Nodes and IL-12-Independent IFN-γ Production During Salmonella Infection – María Fernández-Santoscoy – Frontiers in Cellular and Infection Microbiology

Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health – Lonneke Onrust – Frontiers in Veterinary Science

Animal microbiome

Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology

Plant, root, and soil microbiome

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast –
Melike Balk – Frontiers in Microbiology

Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa – Hanan R. Shehata – Journal of Applied Microbiology

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants – Gerald Otti – Journal of Applied Microbiology

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria  – Max-Bernhard Ballhausen – Frontiers in Microbiology

Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150 – Lihua Li – MDPI Agriculture

Water and waste microbiome

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals – Galina Radeva – Canadian Journal of Microbiology

Master thesis: Evaluation of Two Culture-Independent Methods for Quantification of the Fraction of K-and r-Strategists within Water Microbial Communities – Brandsegg, Hege – Norges teknisk-naturvitenskapelige universitet

Built environment microbiome

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water – Abhilasha Karkey – PLOS Neglected Tropical Diseases

Application of the Environmental Relative Moldiness Index in Finland – Martin Täubel – Applied and Environmental Microbiology

Food microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology

Metagenomics and bioinformatics

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics – Alejandra Escobar-Zepeda – Frontiers in Genetics

Science, publishing, and career

Peer review: tips from field experts for junior reviewers – Sabina Alam – BMC Medicine

Microbes in the news

Gut bacteria from Otzi the Iceman reveals our intimate ties to one microbe – Rachel Feltman – Washington Post

Scientists unearth bacteria from stomach of 5,300-year-old iceman – Carl Zimmer – StatNews

The Famous Ancient “Iceman” Had Ulcer Bacteria In His Gut – Dan Vergano – BuzzFeed

High Stress Environments May Lead To Unhealthy Gut Microbiomes: How To Protect Yourself From The Consequences – Lecia Bushak – Medical Daily

Antibiotics Pave Way for C. Diff Infections – North Carolina State University

Jackson Laboratory Hosted Microbiome Symposium Related to Cancer and Immunology – Lexology

The Bacteria That May Be Causing Your Nasty Cold. “The most common one of them in Mycoplasma Pneumoniae Infection,” Martin explained. – Fox29

Bik’s Picks

A “Pedi” Cures All: Toenail Trimming and the Treatment of Ulcerative Dermatitis in Mice – Sean C. Adams – PLOS ONE
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December 24, 2015

Posted on by

Merry Christmas! The stream of microbiome research papers never appears to take a break, so I will keep on posting during the holidays. Today I found two nice review papers on the oral microbiome and cystic fibrosis microbiome, an upcoming hands-on workshop on mothur (Microbial Ecology software), the acne microbiome, and bacterial exchange in your washing machine.

Events

Throughout the year, Pat offers 4-5 workshops on mothur and programming in R for microbial ecologists. February mothur workshop by Patrick Schloss, February 8-10, Detroit

General microbiome

Review: Tools for the Microbiome: Nano and Beyond – Julie S. Biteen – ACS Nano

Human skin microbiome

Microorganisms inhabiting follicular contents of facial acne are not only Propionibacterium but also Malassezia spp. – Narifumi Akaza – The Journal of Dermatology

Human oral microbiome

Review: Beyond the oral microbiome – Howard F. Jenkinson – Environmental Microbiology

Prevalence of Candida albicans and Candida dubliniensis in caries-free and caries-active children in relation to the oral microbiota—a clinical study – A. Al-Ahmad – Clinical Oral Investigations

Human respiratory microbiome

Looking beyond respiratory cultures: Microbiome-cytokine signatures of bacterial pneumonia and tracheobronchitis in lung transplant recipients – Jyoti Shankar – American Journal of Transplantation

The Lung Immune Response to Bacteria in Chronic Obstructive Pulmonary Disease – Paul T. King – American Journal of Respiratory and Critical Care Medicine

Review: The Microbiome in Cystic Fibrosis – Yvonne J. Huang – Clinics in Chest Medicine

Human gut microbiome

Not a very novel insight: Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing – Ravi Ranjan – Biochemical and Biophysical Research Communications

Review: The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – Alcohol Research Current Reviews

Review: The First Line of Defense: The Effects of Alcohol on Post-Burn Intestinal Barrier, Immune Cells, and Microbiome – Adam M. Hammer

Microbiome models

Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis – David Berry – Frontiers in Microbiology

The Anti-Oxidant Drug Tempol Promotes Functional Metabolic Changes in the Gut Microbiota – Jingwei Cai – Journal of Proteome Research

Effects of the dietary protein level on the microbial composition and metabolomic profile in the hindgut of the pig – Liping Zhou – Anaerobe

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis – Zhengyu Du – Gut Pathogens

Animal microbiome

The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs – Evelyne Mann – Frontiers in Microbiology

Microbial community of Pacific abalone (Haliotis discus hannai) juveniles during a disease outbreak in South China – Liu-yang Shi – Aquaculture Research

The Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, root, and soil microbiomes

Impact of forest management practices on soil bacterial diversity and consequences for soil processes – Federica Colombo – Soil Biology and Biochemistry

Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology – Mushafau Adewale Akinsanya – Genomics Data

Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA – Shijin Wu – Applied Microbiology and Biotechnology

Copper pollution decreases the resistance of soil microbial community to subsequent dry–rewetting disturbance – Jing Li – Journal of Environmental Sciences

Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA – Chao Liang – Soil Biology and Biochemistry

Water and waste microbiome

Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers – Lorenzo Proia – Environmental Pollution

Biogeochemical importance of the bacterial community in uranium waste deposited at Key Lake, Northern Saskatchewan – VF Bondici – Geomicrobiology Journal

Built environment microbiome

Bacterial Exchange in Household Washing Machines – Chris Callewaert- Frontiers in Microbiology

Survival of Antarctic Cryptoendolithic Fungi in Simulated Martian Conditions On Board the International Space Station – Onofri Silvano – Astrobiology

Darkening on lead-based pigments: Microbiological contribution – Tânia Rosado – Color Research & Application

Microbes in the news

Giant Balls of Bacteria Pile Up on Arctic Lake Beds, Ooze Toxin – Emily Benson – EOS

This Squid Could Help Humans Repel Dangerous Flesh-Eating Bacteria – Esther Inglis-Arkell – Gizmodo

Lackner Investigates Whether Brain Changes Affect Gut Microbiome – University of Buffalo

Science, publishing, and career

2015 London Naturejobs Career Expo: Science communication videos – Julie Gould – Nature Blogs
How to deal with the media
How to get a job
How to deal with articles that misrepresent science
Do you need a PhD?

Korean prosecutors seek jail time for professors in massive plagiarism scheme – Mark Zastrow – Retraction Watch

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