Category Archives: Science – Career – Publishing

October 26, 2016

Posted on by

Discount on San Diego Microbiome Congress, sleep deprivation, constipation, strange structures in blood are not bacteria, complexity in corals, grape microbiota, microbial corrosion.

Events

North American Microbiome Congress – San Diego, 24-25 January 2017. This is the conference that was criticized online by Jonathan Eisen (see here) and me about the initial lack of diversity in the speaker line-up. The organizers have taken this to heart, apologized, and will make an effort to do better in the future. After talking to the organizers, they are offering my readers a 15% discount code ‘DIGEST15’ on the conference fee. There are also reduced priced Early Bird tickets available until 31st October 2016.

Human respiratory microbiome

Re-emergence of Lower Airway Microbiota in Cystic Fibrosis Lung Transplant Patients – Saad A Syed – Annals of the American Thoracic Society

Human gut microbiome

Gut Microbiota and Glucometabolic Alterations in Response to Recurrent Partial Sleep Deprivation in Normal-weight Young Individuals – Christian Benedict – Molecular Metabolism

Press: Sleep loss tied to changes of the gut microbiota in humans – Science Daily
Sleep loss may be linked to changes in gut bacteria levels – Ryan Maass – UPI

Characterization of Microbiota in Children with Chronic Functional Constipation – Tim G. J. de Meij – PLOS ONE

Microbiome of nearly-sterile sites

Pleomorphic Structures in Human Blood Are Red Blood Cell-Derived Microparticles, Not Bacteria – Adam J. Mitchell – PLOS ONE

Animal models

Antibiotic effects on gut microbiota and metabolism are host dependent – Shiho Fujisaka – The Journal of Clinical Investigation

Diversity and resilience of the wood-feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations – Ying Wang – Ecology and Evolution

Animal microbiome

Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes – Amy Apprill – mSystems

Plant, root, and soil microbiome

Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data – José R. Valverde – PLOS ONE

Biochar-stimulated plant performance is strongly linked to microbial diversity and metabolic potential in the rhizosphere – Max Kolton – New Phytologist

Wine microbiology is driven by vineyard and winery anthropogenic factors – Cédric Grangeteau – Microbial Biotechnology

Effect of 40 and 80 Years of Conifer Regrowth on Soil Microbial Activities and Community Structure in Subtropical Low Mountain Forests – Ed-Haun Chang – Forests

Water microbiome

mdRNA-Seq analysis of marine microbial communities from the northern Red Sea – Shengwei Hou – Scientific Reports

Assessing Marine Microbial Induced Corrosion at Santa Catalina Island, California – Gustavo A. Ramírez – Frontiers in Microbiology

Bioreactor microbiology

Wow, this paper will cost you $63: Diversity of Microbial Communities in Biogas Reactors – Bernadett Pap – Current Biochemical Engineering

Viruses and phages

Viral Metagenomics on Blood-Feeding Arthropods as a Tool for Human Disease Surveillance – Annika Brinkmann – Int J Mol Sci

Techniques

An introduction to microbiome analysis for human biology applications – Katherine R. Amato – American Journal of Human Biology

Instrument for Real-Time Digital Nucleic Acid Amplification on Custom Microfluidic Devices – David A. Selck – PLOS ONE

Microbes in the news

Reef rehab could help threatened corals make a comeback. Solutions for threatened reefs vary by location and damage done – Amy McDermott – Science News

Bacteria get dangerously weird in space – Shayla Love – Washington Post

Cranberry extract disrupts communication between bacteria linked to pervasive infections – News Medical Net

LSU alumna Kaitlynn Fenley teaches microbiology cooking class – Allie Cobb – The Daily Reveille

NIH research project will upgrade ‘metagenomics’ system – Purdue

Science, publishing, and career

Beyond Traditional Scientific Training: The Importance of Community and Empowerment for Women in Ecology and Evolutionary Biology – M. Claire Horner-Devine – Frontiers in Ecology and Evolution

October 20, 2016

Posted on by

Events

2016-2017 Dannon Gut Microbiome, Yogurt and Probiotics Fellowship Grant Application Form
Also see: Leading Yogurt Company Challenges Students to Unearth New Data on the Gut Microbiome, Yogurt and Probiotics with $50K Grant Program. Dannon® will award two $25K grants to further scientific research – PR Newswire

Third Annual Microbiome Symposium – Penn Vet – October 26 and 27, 2016
Penn’s microbiome conference turns eye toward antibiotic use in livestock
Text by Katherine Unger Baillie – Penn Current

Q4 microbiome conferences roundup: Are you looking for a good scientific microbiome research symposium? Over the next three months, you have six exciting microbiome conferences from which to choose. – Megan M. MacBride – Taconic

Disappointing lack of diversity here: #YAMMM: 29 speakers, 4 women. Microbiome Drug Development Summit, 24-26 January 2017, Paris, France

General microbiome

An introduction to microbiome analysis for human biology applications – Katherine R. Amato – American Journal of Human Biology

Human oral microbiome

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Human respiratory microbiome

Role of microbiome in the pathophysiology and disease course of asthma – Singanayagam A – Curr Opin Pulm Med

Human skin microbiome

Review: Topographical and physiological differences of the skin mycobiome in health and disease – Jay-Hyun Jo – Virulence

Human vaginal microbiome

A fruitful alliance: the synergy between Atopobium vaginae and Gardnerella vaginalis in bacterial vaginosis-associated biofilm – Liselotte Hardy – Sexually Transmitted Infections

Human gut microbiome

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Similar Fecal Microbiota Signatures in Patients With Diarrhea-Predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

Review: Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches – R. Balfour Sartor – Gastroenterology

Review: The Microbiome and Human Disease Pathogenesis: How do you do what you do to me …? – Edward N. Janoff – Translational Research

Animal models

Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing – Geon Goo Hana – Veterinary Microbiology

Alterations of the Host Microbiome Affect Behavioral Responses to Cocaine – Drew D. Kiraly – Scientific Reports

Animal microbiome

Developmental and ecological benefits of the maternally transmitted microbiota in a dung beetle – Daniel B. Schwab – The American Naturalist

Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous sponge Chondrocladia grandis – Joost T.P. Verhoeven – FEMS Microbiology Ecology Letters

Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities – Jessica L. Ray – Molecular Ecology

Spatial Microbial Composition Along the Gastrointestinal Tract of Captive Attwater’s Prairie Chicken – Yan Zhang – Microbial Ecology

Plant, root, and soil microbiome

Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists – Ai Kawahara – PLOS ONE

Review: Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture – Yuan Qin – Biotechnology Advances

Water microbiome

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor – Katsunori Yanagawa – ISME J

More microbiology

Correspondence: Improving Microbiology Research: the Problems Are Less Statistical and More Biological – Dennis F. Lawler – mBio

What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015 – Erik Munson – Journal of Clinical Microbiology

Microbes in the news

Tasmanian devil milk fights superbugs – BBC News
Tasmanian devil milk kills several deadly superbugs that are resistant to existing drugs – Science Alert

There’s a breast microbiome, and it’s different in women with breast cancer – Erin Blakemore – Washington Post

Research Highlight: A protective protozoan in mucosal infection – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Outbreak of Biofilm-Forming Achromobacter xylosoxidans Due to Environmental Transmission – Infection Control Today

The Emergent Microbiome: A Revolution for the Life Sciences – Part VII, The Microbiome and Immunotherapy I – Dilworth IP – Lexology

New science museum exhibit explores ‘the secret world’ inside us: N.C. Museum of Natural Sciences in downtown Raleigh opens a new special exhibit this weekend – WRAL.com

Vedanta Biosciences Granted First European Patent Broadly Covering Pharmaceutical Compositions for Microbiome Therapeutics Based on Bacterial Consortia – Business Wire

Science, publishing, and career

Married to the(ir) job: living with an academic. Scholars and their significant others share the good, the bad and the ugly – Times Higher Education

Investigation Finds Pathologist Guilty of Systemic Misconduct – Bob Grant – The Scientist

Women need to be seen and heard at conferences. A neuroscience initiative is boosting the number of female invited speakers at meetings. Other disciplines should do the same – Nature

The Bearded Lady Project . Q&A: Lexi Jamieson Marsh and Ellen Currano: Face to face – Alexandra Witze – Nature

October 18, 2016

Posted on by

Vaginal probiotics, forensic analysis of skin bacteria on fabrics, Wolbachia in nematodes, ivy phyllosphere, microbial life in two polar extremes, how to improve the indoor environment, and mass spec analysis of human habitat molecules.

Pregnancy and early life

Vaginal Probiotic Administration in the Management of Preterm Premature Rupture of Membranes – Daskalakis G.J. – Fetal Diagnosis and Therapy

General human microbiome

Review: Health Disparities and the Microbiome – Keisha Findley – Trends in Microbiology

Human respiratory microbiome

Review: Host–Bacterial Crosstalk Determines Staphylococcus aureus Nasal Colonization – Michelle E. Mulcahy – Trends in Microbiology

Human skin and tissue microbiome

Forensic analysis using microbial community between skin bacteria and fabrics – So-Yeon Lee – Toxicology and Environmental Health Sciences

Not a word about extraction controls, so proceed with caution: Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis – Elvira E. Ziganshina – PLOS ONE

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Gut Microbiota and Risk of Developing Celiac Disease – Cenit, Maria C. – Journal of Clinical Gastroenterology

Editorial: What’s in Your GI Microbiome? – Martin H. Floch – Journal of Clinical Gastroenterology

Animal and in vitro models

Study of the Ability of Bifidobacteria of Human Origin to Prevent and Treat Rotavirus Infection Using Colonic Cell and Mouse Models – Mélanie Gagnon – PLOS ONE

Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism – Limin Zhang – mSystems

A mixture of milk and vegetable lipids in infant formula changes gut digestion, mucosal immunity and microbiota composition in neonatal piglets – Isabelle Le Huërou-Luron – European Journal of Nutrition

An Advanced In Vitro Technology Platform to Study the Mechanism of Action of Prebiotics and Probiotics in the Gastrointestinal Tract – Marzorati, Massimo – Journal of Clinical Gastroenterology

Animal microbiome

Sea lions: Protein and RNA extraction from mucosal swabs: a minimally invasive source of ecological data for studies of natural populations – W Espinosa-de Aquino – Methods in Ecology and Evolution

Mycobacteria in aquarium fish: results of a 3-year survey indicate caution required in handling pet-shop fish – D Kušar – Journal of Fish Diseases

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts – Amanda M. V. Brown – Scientific Reports

Plant, root, and soil microbiome

Disentangling interactions between microbial communities and roots in deep subsoil – Martina I. Gocke – Science of the Total Environment

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock – Alexandre Bagnoud – Nature Communications

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area – Isabella Gandolfi – Environmental Pollution

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation – Xihui Xu – Environmental Science and Pollution Research

Impact of urban land use on the bacterial phyllosphere of ivy (Hedera sp.) – Wenke Smets – Atmospheric Environment

Water and extremophile microbiome

Periodic change in coastal microbial community structure associated with submarine groundwater discharge and tidal fluctuation – Eunhee Lee – Limnology and Oceanography

Microbial Community Dynamics in Two Polar Extremes: The Lakes of the McMurdo Dry Valleys and the West Antarctic Peninsula Marine Ecosystem – Jeff S. Bowman – BioScience

Diversity and physiological and biochemical properties of heterotrophic bacteria isolated from Lake Baikal neuston – A. D. Galach’yants – Microbiology

Phylogenetic and functional prokaryotic diversity in the Hoito-Gol mesothermal mineral spring (Eastern Sayan Mountains, Buryat Republic) – E.S. Kashkak – Microbiology

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water – Xiao-Ming Lu – Microbial Ecology

Built environment microbiome

How do we make indoor environments and healthcare settings healthier? – Jack A. Gilbert – Microbial Biotechnology

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats – Daniel Petras – Analytical Chemistry

Food microbiology

Raw Ready-to-Eat Seafood Safety: Microbiological Quality of the Various Seafood Species Available at Fishery, Hyper, and Online Market – H.W. Kim – Letters in Applied Microbiology

Bioinformatics and metagenomics

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources – Nicolas Tsesmetzis – Standards in Genomic Sciences

IMG/M: integrated genome and metagenome comparative data analysis system
I-Min A. Chen – Nucleic Acids Research

Review: The present and future of de novo whole-genome assembly – Jang-il Sohn – Briefings in Bioinformatics

Microbes in the news

Soaking A Bunch Of Toads In Their Own Bacteria Could Save Their Lives – Krista Langlois – Five Thirty Eight

Bacteria Hysteria

Why your office could be making you sick: Keyboards ‘contain 20,000 MORE bacteria than a toilet bowl’– Stephen Matthews – Daily Mail

How to clean and disinfect your keyboard and mouse – Ed Rhee – CNET

Science, publishing, and career

A Tale of Two Women and Their Careers in Science – Anna Katie – YouTube

Promoting Responsible Scientific Research – American Society for Microbiology

October 14, 2016

Posted on by

The pubic hair microbiome, lung transplant virome, IBS microbiome signature, coprolites, antibacterial molecules for babies the Tasmanian Devil pouch, Archaea in Mars simulation, white pudding, functional mapping pipeline,

Human oral microbiome

Clinical, Immune, and Microbiome Traits of Gingivitis and Peri-implant Mucositis – G.P. Schincaglia – Journal of Dental Research

The microbial community shifts of subgingival plaque in patients with generalized aggressive periodontitis following non-surgical periodontal therapy: a pilot study – Jing Hang – Oncotarget

Review: The Autoimmunity-Oral Microbiome Connection – N Nikitakis – Oral Diseases

Human respiratory microbiome

The Perioperative Lung Transplant Virome: Torque Teno Viruses are Elevated in Donor Lungs and Show Divergent Dynamics In Primary Graft Dysfunction – A. A. Abbas – American Journal of Transplantation

Composition and immunological significance of the upper respiratory tract microbiota – L. Patrick Schenck – FEBS Letters

Human skin and hair microbiome

Individualization of pubic hair bacterial communities and the effects of storage time and temperature – Diana W. Williams – Forensic Science International: Genetics

Gram-positive anaerobe cocci (GPAC) are underrepresented in the microbiome of filaggrin-deficient human skin – Patrick L.J.M. Zeeuwen – The Journal of Allergy and Clinical Immunology

Review: Microbiome in healthy skin, update for dermatologists – B. Dréno – Journal of the European Academy of Dermatology and Venereology

Human reproductive tract microbiome

Challenging dogma: the endometrium has a microbiome with functional consequences! – Linda C. Giudice – American Journal of Obstetics & Gynecology

Human gut microbiome

Intestinal microbiota in adult patients with Short Bowel Syndrome: Preliminary results from a pilot study – Stefania Boccia – Clinical Nutrition

Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome – Julien Tap – Gastroenterology

The dual role of Escherichia coli in the course of ulcerative colitis – Magdalena Pilarczyk-Zurek – BMC Gastroenterology

Review: The gut microbiota and gastrointestinal surgery – Kristina Guyton – Nature Reviews Gastroenterology & Hepatology

Review: Dysbiosis in the ICU: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Parasites, microbiota and metabolic disease – Sonakshi Bhattacharjee – Parasite Immunology

Review: Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

Review: Human Coprolites as a Source for Paleomicrobiology – Sandra Appelt – Microbiology Spectrum

Animal models

Behavioural and Neurochemical Consequences of Chronic Gut Microbiota Depletion during Adulthood in the Rat – A.E. Hoban – Neuroscience

Changes in the rumen microbiome and metabolites reveal the effect of host genetics on hybrid crosses – Zhipeng Li – Environmental Microbiology Reports

Microbial community mapping in intestinal tract of broiler chicken – Yingping Xiao – Poultry Science

Animal microbiome

Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria – Jeroen A. J. M. van de Water – Microbial Ecology

Cathelicidins in the Tasmanian devil (Sarcophilus harrisii) – E. Peel – Scientific Reports

Plant, root, and soil microbiome

Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems – S. Uroz – Soil Biology and Biochemistry

Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea – Ludovic Henneron – Oikos

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat – Akitomo Kawasaki – PLOS ONE

Review: Recent Developments in Systems Biology and Metabolic Engineering of Plant–Microbe Interactions – Vishal Kumar – Frontiers in Plant Science

Water microbiome

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes – M. Romina Schiaffino – Environmental Microbiology

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake – Patricia M. Valdespino-Castillo – Microbial Ecology

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River – Wenhui Wang – Scientific Reports

Microbes in space

Survivability and Growth Kinetics of Methanogenic Archaea at various pHs and Pressures: Implications for Deep Subsurface Life on Mars – Navita Sinha – Planetary and Space Science

Food microbiology

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: The example of white pudding – Emilie Cauchie – International Journal of Food Microbiology

Microbial diversity in pitted sweet cherries (Prunus avium L.) as affected by high-hydrostatic pressure treatment – Julia Toledo del Árbol – Food Research International

Built environment microbiology

Bioaerosol assessment in the library of Istanbul University and fungal flora associated with paper deterioration – Duygu Göksay Kadaifciler – Aerobiologia

Techniques / Fungi

Accurate Estimation of Fungal Diversity and Abundance Through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing – D. Lee Taylor – Applied and Environmental Microbiology

Bioinformatics and metagenomics

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli – Minseung Kim – Nature Communications

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies – Jiwoong Kim – BMC Bioinformatics

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets – Rico Lucas – FEMS Microbiology Ecology

Microbes in the news

Extremophiles found in a lake, and this is great news for biotech – Colm Gorey – Silicon Republic

‘I want my teeth back’: Kids infected with jaw-eating bacteria after dental treatment – Katie Mettler – Sacramento Bee

Microbiome biotech joins Peter Thiel’s Breakout Labs project – Fierce Biotech

Science, publishing, and career

Book:  Fungible Life: Experiment in the Asian City of Life – Aihwa Ong – Amazon

October 13, 2016

Posted on by

Ethics and microbiome research, oversimplifying microbiome studies, viruses destroy archaea in the deep seafloor, Clostridium difficile in patients sharing hospital beds.

General microbiome

Perspective: Ethical issues in microbiome research and medicine – Rosamond Rhodes – BMC Medicine

Interview: Science communication: the dangers of oversimplifying microbiome studies – Interview with Lauren Freeman and Saray Ayala – Ben Johnson – NPJ Biofilms Community

Human gut microbiome

Preview: Making It Stick: A Compelling Case for Precision Microbiome Reconstitution – David Berry – Cell Host & Microbe

Preview: A Commensal Protozoan Strikes a Balance in the Gut – P’ng Loke – Cell Host & Microbe

Animal models

Intestinal microbiota could transfer host Gut characteristics from pigs to mice – H. Diao – BMC Microbiology

Plant, root, and soil microbiome

Review: How lichens impact on terrestrial community and ecosystem properties – Johan Asplund – Biological Reviews

Water (and coral) microbiology

Virus-mediated archaeal hecatomb in the deep seafloor – Roberto Danovaro – Science Advances

Press: Deep-Sea Viruses Destroy Archaea. Viruses are responsible for the majority of archaea deaths on the deep ocean floors, scientists show – Ruth Williams – The Scientist

Multifaceted impacts of the stony coral Porites astreoides on picoplankton abundance and community composition – Sean P. McNally – Limnology and Oceanography

Food microbiology

Ultrasound improves chemical reduction of natural contaminant microbiota and Salmonella enterica subsp. enterica on strawberries – Denes Kaic Alves do Rosário – International Journal of Food Microbiology

Techniques

Greater than X kb: a quantitative assessment of preservation conditions on genomic DNA quality, and a proposed standard for genome-quality DNA – Daniel G. Mulcahy – PeerJ

Metagenomics

Diverse Intestinal Bacteria Contain Putative Zwitterionic Capsular Polysaccharides with Anti-inflammatory Properties – C. Preston Neff – Cell Host & Microbe

Other microbiology

Division of labour in microorganisms: an evolutionary perspective – Stuart A. West – Nature Reviews Microbiology

Receipt of Antibiotics in Hospitalized Patients and Risk for Clostridium difficile Infection in Subsequent Patients Who Occupy the Same Bed – Daniel E. Freedberg – JAMA

Press: Antibiotics Encourage Spread of C.diff To Subsequent Patients Who Occupy the Same Bed and Haven’t Received Antibiotics: Interview with Daniel Freedberg – Medical Research

Microbes in the news

The Conversation Gut Series:

RI Hospital receives $500,000 CDC grant to research new approach for combating antibiotic resistance. Microbiome research will help prevent ongoing spread of multi-drug resistant bacteria – EurekAlert

Science, publishing, and career

How Are Scientists Using Social Media in the Workplace? – Kimberley Collins – PLOS ONE

5 retractions and a sack for Pfizer lead cancer researcher Min-Jean Yin – Leonid Schneider – For Better Science
Pfizer fires employee, requests five retractions – Alison McCook – Retraction Watch

Bik’s non-microbiology Picks

Genomics is failing on diversity – Alice B. Popejoy & Stephanie M. Fullerton – Nature
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations – Swapan Mallick – Nature

October 10, 2016

Posted on by

A Mostly Male Microbiome meeting, host genetics and microbiota in IBD, dysbiosis in dogs and humans, airport door handles, and surfing the world for microbes. I’m back!

Events

I wish I could recommend this, but it has only 2 of the 27 invited speakers are women. This is so sad. See Jonathan Eisen’s blog post about this. Second Annual Human Microbiome Congress in San Diego / North American Microbiome Congress – 24/25 January 2017 – San Diego.

Human gut microbiome

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease – Floris Imhann – Gut

Effect of dietary interventions on the intestinal microbiota of Mongolian hosts – Jing Li – Science Bulletin

Animal models

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks – Yoshiki Vázquez-Baeza – Nature Microbiology

Acute Infectious Gastroenteritis Potentiates a Crohn’s Disease Pathobiont to Fuel Ongoing Inflammation in the Post-Infectious Period – Cherrie L. Small – PLOS Pathogens

Press: Diarrhea-Causing Bacteria Promote Growth of Crohn’s-Linked Microbe in Mice – ET Healthworld

Neonatal androgen exposure causes persistent gut microbiota dysbiosis related to metabolic disease in adult female rats – Isabel Moreno-Indias – Endocrinology

Exposure to the Functional Bacterial Amyloid Protein Curli Enhances Alpha-Synuclein Aggregation in Aged Fischer 344 Rats and Caenorhabditis elegans – Shu G. Chen – Scientific Reports

Press: Gut microbiota may have role in neurodegenerative diseases: study – CTV News

Plant, root, and soil microbiome

Review: Too much or not enough: Reflection on two contrasting perspectives on soil biodiversity – Philippe C. Baveye – Soil Biology and Biochemistry

Built environment microbiology

Airport door handles and the global spread of antimicrobial-resistant bacteria: a cross sectional study – Frieder Schaumburg – Clinical Microbiology and Infection

Press: Are Airport Bathrooms Spreading Antibiotic-Resistant Bacteria Globally? – Alex Berezow – American Council on Science and Health

Food microbiology

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria – Kevin S. Bonham – bioRxiv

Does fingerprinting truly represent the diversity of wine yeasts? A case study with interdelta genotyping of S. cerevisiae strains – Walter P. Pfliegler – Letters in Applied Microbiology

Microbes in the news

This Surfer/PhD Student Is Scraping Bacteria off Surfers Around the World for Science – Dylan Heyden – The Inertia
Surfing the world for microbes – Erika Johnson, UC San Diego – University of California

Weethinking the role of bacteria in incontinence. Researchers look at the role of bacteria in incontinence – EurekAlert

The Unseen Cloud Makers From The Ocean – Jennifer – The Microbial Menagerie

Marine bacteria are the climate’s wild card – ScienceNordic

Researchers Hunt for a Link Between Microbiome and Autism – KQED

The natural wonder that holds the key to the origins of life – and warns of its destruction – Michael Slezak – The Guardian

Did his artificial hips put him at risk of infection when he saw the dentist? – David Lindley – Washington Post

Millions of craft paint units recalled over bacteria concerns – Morgan Maria Pawl – KDVR

Science, publishing, and career

Scientific Misconduct: The Elephant in the Lab. A Response to Parker et al. – Timothy D. Clark – Trends in Ecology & Evolution

Bik’s non-microbiology Picks

As DNA reveals its secrets, scientists are assembling a new picture of humanity – Carl Zimmer

September 30, 2016

Posted on by

When does a probiotic stick around, microbial diversity in 12 French cheese varieties, effects of field conditions on fecal microbiota.

Events

Microbiome Drug Development Summit Europe – 24-26 January 2017, Paris, France

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – Jessica E. Koopman – Archives of Oral Biology

Review: Role of oral microbiome on oral cancers, a review – Pourya Gholizadeh – Biomedicine & Pharmatherapy

Human skin microbiome

Novel volatiles of skin-borne bacteria inhibit the growth of Gram-positive bacteria and affect quorum-sensing controlled phenotypes of Gram-negative bacteria – Marie Chantal Lemfack – Systematic and Applied Microbiology

Human gut microbiome

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome – María X. Maldonado-Gómez – Cell Host & Microbe

Press: A Probiotic That Actually Lasts. The bacteria in yogurts have largely failed to live up to their hyped health benefits, but there are other microbes that might – Ed Yong – The Atlantic

Animal microbiome

Consequences of coinfection with protective symbionts on the host phenotype and symbiont titres in the pea aphid system – Mélanie Leclair – Insect Science

Corals: Bacterial community diversity of the deep-sea octocoral Paramuricea placomus – Christina A. Kellogg – PeerJ

Plant, root, and soil microbiome

Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps – Tommaso Bardelli – Science of the Total Environment

Food microbiology

Highlighting the microbial diversity of 12 French cheese varieties – Eric Dugat-Bony – International Journal of Food Microbiology

Microbial ecology and more microbiology

Macroecology for microbiology – Jay T Lennon – PeerJ Preprint

Review: Fungal Super Glue: The Biofilm Matrix and Its Composition, Assembly, and Functions – Kaitlin F. Mitchell – PLOS Pathogens

Techniques

Effects of field conditions on fecal microbiota – Vanessa L. Hale – Journal of Microbiological Methods

A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing – Henrik Krehenwinkel – Methods in Ecology and Evolution

Microbes in the news

The cost of cheap drugs? Toxic Indian lake is ‘superbug hotspot’ – Zeba Siddiqui – Reuters

Effects of maternal stress on newborn health: An Interview with Dr. Connie Mulligan of the University of Florida – DNA Genotek

Gene-engineered gut bacteria successfully treat sick mice — and could treat humans someday – Leah Samuel – STAT News

Microbiology retreat showcases research – Anamika Veeramani – Yale Daily News

Science, publishing, and career

Working life: Doing science while black – Edward J. Smith – Science

September 29, 2016

Posted on by

Two human skin microbiota papers, effects of eating chili powder, methanogens can tolerate Mars-like low pressure, gut microbiota signatures of longevity.

Human skin microbiome

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults – Carey-Ann D. Burnham – Antimicrobial Agents and Chemotherapy

Evolutionary and Functional Implications of Hypervariable Loci Within the Skin Virome – Geoffrey D Hannigan – bioRxiv

Human gut microbiome

Healthy subjects differentially respond to dietary capsaicin correlating with the specific gut enterotypes – Chao Kang – Journal of Clinical Endocrinology & Metabolism

Gut microbiota signatures of longevity – Fanli Kong – Current Biology

Shifts in the fecal microbiota associated with adenomatous polyps – Vanessa L Hale – Cancer Epidemiology, Biomarkers & Prevention

When pathogenic bacteria meet the intestinal microbiota – Nathalie Rolhion – Philosophical Transactions of the Royal Society B

Review: From homeostasis to pathology: decrypting microbe–host symbiotic signals in the intestinal crypt – Thierry Pédron – Philosophical Transactions of the Royal Society B

Review: Human microbiome as therapeutic intervention target to reduce cardiovascular disease risk – Annefleur M. Koopen – Current Opinion in Lipidology

Review: The microbial epigenome in metabolic syndrome – Marlene Remely – Molecular Aspects of Medicine

Animal and in vitro models

Probiotic legacy effects on gut microbial assembly in tilapia larvae – Christos Giatsis – Scientific Reports

D-Tryptophan from probiotic bacteria influences the gut microbiome and allergic airway disease – Inge Kepert – The Journal of Allergy and Clinical Immunology

Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice – Iain A. Murray – Scientific Reports

Animal microbiome

The chicken tracheal microbiome: unexpected preliminary data – Tim Johnson Lab

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae) – Charles J. Mason – Scientific Reports

Plant, root, and soil microbiome

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine – Yuanqing Chao – Environmental Science & Technology

Fungal endophytes as priority colonizers initiating wood decomposition – Zewei Song – Functional Ecology

Water and extremophile microbiome

Culture-independent study of bacterial communities in tropical river sediment  –
Honglada Thoetkiattikul – Bioscience, Biotechnology, and Biochemistry

Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms – Eunsoo Kim – Environmental Microbiology

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars – R. L. Mickol – Origins of Life and Evolution of Biospheres

Microbes and robots

Did not quite grasp the abstract, but cool picture of a small robot: Bioinspired decision architectures containing host and microbiome processing units – K C Heyde – Bioinspiration & Biomimetics

Microbes in the news
Research Breakthrough Could Help Diagnose, Treat Biofilm Infections – Lorena Anderson – UC Merced

Profile: Dr. Bonnie Bassler, a pioneer who’s investigating how bacteria communicate – Joe Tyrrell – New Jersey Spotlight

World’s Largest MS Research Conference Highlights Advances in Progressive MS, Gut Microbiome, Managing Symptoms, and New Approaches to Restoring Function – National MS Society

Assembly Biosciences Announces Key Additions to Microbiome Team – Globe Newswire

Can’t lose weight? You might be able to blame it on your parents—and their gut bacteria – Akshat Rathi – Quartz
Are Your Genes Making It Hard To Get Into Your Jeans? – Julie Taylor – uBiome blog

Deadly Mud-Dwelling Bacteria Melioidosis Stirs In The Northern Territory – Cayla Dengate – Huffington Post Australia

 

Science, publishing, and career

Young researchers thrive in life after academia. Alternative career paths should be celebrated, not seen as a compromise. – Nature

September 28, 2016

Posted on by

Twins, body fat, and bacteria, dietary zinc and C. diff infections, honey inhibits biofilm formation, microbial life in a Great Lake sinkhole.

Pregnancy and early life

Review: The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life -William B. Miller Jr. – Frontiers in Pediatrics

Human gut microbiome

Heritable components of the human fecal microbiome are associated with visceral fat – Michelle Beaumont – Genome Biology

Press: Body fat link to bacteria in faeces – BBC
How Gut Bacteria May Predict Belly Fat – Alice Park – Time

Characterisation of the faecal microbiota in Japanese patients with paediatric-onset primary sclerosing cholangitis – Kentaro Iwasawa – Gut

Commentary: Thinking with your stomach? Gut feelings on microbiome modulation of brain structure and function (Commentary on Luczynski et al.) – Anthony J. Hannan – European Journal of Neuroscience

Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection – Joseph P Zackular – Nature Medicine

Editorial: Devil in the detail: A closer look at childhood obesity and the gut microbiota – Michael W. Taylor – Environmental Microbiology

News and views: Culturing: Looking it up in our gut – Clarisse Marotz – Nature Microbiology

Animal microbiome

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice – Taichi A. Suzuki – PLOS ONE

Plant, root, and soil microbiome

Using a Control to Better Understand Phyllosphere Microbiota – Andrea R. Ottesen – PLOS ONE

Caves: Microbial contributions to subterranean methane sinks – J. T. Lennon – Geobiology

Diatom blooms and associated vegetation shifts in a subarctic peatland: responses to distant volcanic eruptions? – U. Kokfelt – Journal of Quaternary Science

The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant – Gianna Pitsch – The Journal of Eukaryotic Microbiology

Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi – Xihui Xu – PLOS ONE

Fungal Endophytes as a Metabolic Fine-Tuning Regulator for Wine Grape – Ming-Zhi Yang – PLOS ONE

Water and extremophile microbiome

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole – L. E. Kinsman-Costello – Geobiology

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments – Patrick J. Kearns – Nature Communications

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes – Jan-Hendrik Hehemann – Nature Communications

Proteomics

The impact of sequence database choice on metaproteomic results in gut microbiota studies – Alessandro Tanca – Microbiome

More microbiology

Diluted honey inhibits biofilm formation: potential application in urinary catheter management? – Somadina Emineke – Journal of Clinical Pathology

Press: Manuka honey may help prevent life-threatening urinary infections – Simon Hendel – The Conversation
Honey May Be a Natural Way to Beat Bacteria – Alexandra Sifferlin – Time

Personalized therapeutic cocktail of wild environmental phages rescues mice from A. baumannii wound infections – James M. Regeimbal – Antimicrobial Agents and Chemotherapy

Press: A Cocktail Of Wild Viruses Treats Bacterial Wound Infections In Mice – Alex Berezow – American Council on Science and Health

Microbes in the news

Chicago Shedd Aquarium Studies Microbes’ Effect on Sea Life – Illumina

The 3 Robs: NIH Funds Research to See if Gut Microbiomes of Hispanics/Latinos Influence Their Diabetes Risk – Albert Einstein College of Medicine

Antibiotic resistance can occur naturally in soil bacteria – Science Daily

Science, publishing, and career / Peer review

Author affiliation can bias peer review: Single-blind vs Double-blind Peer Review in the Setting of Author Prestige – Kanu Okike – JAMA

September 24, 2016

Posted on by

Eye microbiome, malnutrition and rotavirus, edible insects, vineyard management, and drones.

Human eye / skin microbiome

Impact of Microbiota on Resistance to Ocular Pseudomonas aeruginosa-Induced Keratitis – Abirami Kugadas – PLOS Pathogens

Press (scroll to halfway the page to read this item): Lab chat: Eye bacteria and contact lenses  – Megan Thielking – STAT News

Human gut microbiome

Malnutrition Is Associated with Protection from Rotavirus Diarrhea: Evidence from a Longitudinal Birth Cohort Study in Bangladesh – Hans Verkerke – Journal of Clinical Microbiology

Animal models

Immunosuppression, peripheral inflammation and invasive infection from endogenous gut microbiota activate retinal microglia in mouse models – Victoria Maneu – Microbiology and Immunology

Animal microbiome

Phenological asynchrony between host plant and gypsy moth reduces insect gut microbiota and susceptibility to Bacillus thuringiensis – Vyacheslav V. Martemyanov – Ecology and Evolution

Plant, root, and soil microbiome

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management – Kayla N. Burns – Soil Biology and Biochemistry

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter – Ruibo Sun – Environmental Microbiology

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak – Gregory J. Pec – New Phytologist

Water microbiome

Dense water plumes modulate richness and productivity of deep sea microbes – Gian Marco Luna – Environmental Microbiology

Food microbiology

The microbiota of marketed processed edible insects as revealed by high-throughput sequencing – Cristiana Garofalo – Food Microbiology

Metagenomics reveals flavour metabolic network of cereal vinegar microbiota – Linhuan Wu – Food Microbiology

Techniques

Detection of food and skin pathogen microbiota by means of an electronic nose based on metal oxide chemiresistors – Estefanía Núñez Carmona – Sensors and Actuators B: Chemical

A one-step matrix application method for MALDI mass spectrometry imaging of bacterial colony biofilms – Bin Li – Journal of Mass Spectrometry

Microbial ecology

The biogeography of kin discrimination across microbial neighbourhoods – Susanne A. Kraemer – Molecular Ecology

More microbiology

Microbes can fly: Drone Transport of Microbes in Blood and Sputum Laboratory Specimens – Timothy K. Amukele – Journal of Clinical Microbiology

Microbes in the news

New CDC Report Shows One Quarter of Contact Lens-related Eye Infections Due to Improper Use, Modifiable Factors – PR Web

Extremely rare US leprosy case found in California elementary school student – Andrew Dalton – STAT News

How Can Science Benefit from Microbes on the ISS? – Jessica F – Nature World News

New Research Indicates Alzheimer’s and Other Neurodegenerative Diseases Are Contagious – PR Newswire

Deadly Viruses and Bacteria Mistakenly Shipped 21 Times – R. Jeffrey Smith – The Daily Beast

Science, publishing, and career

Meet the world’s top peer reviewer: Jonas Ranstam – Ivan Oransky and Adam Marcus – STAT News