Author Archives: eliesbik

May 13, 2016

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Today brought us great news from the White House Office of Science and Technology Policy (OSTP): the National Microbiome Initiative (NMI). Look on Twitter for our tweets tagged with #NMI.

National Microbiome Initiative and news coverage

Fact Sheet: Announcing the National Microbiome Initiative – The White House Office of Science and Technology Policy

Microbes shape our world – and a new White House initiative will figure out how – Rachel Feltman – The Washington Post

Obama administration to launch microbiome initiative, heeding scientists’ calls – David Nather – STAT News

The White House Launches the National Microbiome Initiative: Half a billion dollars are being pledged to study the microbes in humans, crops, soils, oceans, and more – Ed Yong – The Atlantic

Pleasantly surprised by the National Microbiome Initiative – Jonathan Eisen – The Tree of Life

New microbiome center to combine UChicago, Marine Biological Laboratory, Argonne expertise – EurekAlert

Events

Bioinformatics for the Microbiome – Stanford – Friday May 27th, with talks by Rob Knight, Ami Bhatt, Susan Holmes, Tomer Altman, Justin Sonnenberg, Sharon Greenblum, Ben Callahan and more.

Pint of Science Festival, May 23-25, San Francisco: Science talks in the finest watering holes of the Bay Area. Several microbiology talks!

Time is Running Out for “Culture as Medium” exhibit at Baltimore Under Ground Science Space (BUGSS) – Anne M. Estes – Mostly Microbes

Festival of Genomics – 27-29 June 2016 Boston

General microbiome

Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges – Martin J. Blaser – mBio

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis – Marco Fondi – Genome Biology and Evolution

Pregnancy and birth

News: Antibiotics, gut bugs and the young – Hilary Browne – Nature Reviews Microbiology

Human skin microbiome

Cross your legs before reading this one: Genital anaerobic bacterial overgrowth and the PrePex male circumcision device, Rakai, Uganda – Cindy M. Liu -The Journal of Infectious Diseases

Human gut microbiome

Gut microbiota in early pediatric multiple sclerosis: a case−control study – H. Tremlett – European Journal of Neurology

Review: Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle – Christopher M. Jakobson – PLOS Pathogens

Plant, root, and soil microbiome

The Sphagnum microbiome: new insights from an ancient plant lineage – Joel E. Kostka – New Phytologist

Bioinformatics and metagenomics

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R – Timothy G. Stephens – PeerJ

Microbes in the news
Is a Disrupted Gut Microbiome at the Root of Modern Disease?—with Dr. Justin Sonnenburg – Chris Kresser – Revolution Health Radio

Fatal attachment: How pathogenic bacteria hang on to mucosa and avoid exfoliation – EurekAlert

This MIT professor is using bee poop to map an invisible world – Melia Robinson – TechInsider

Microbes and art

ASM Agar Art 2016 People’s Choice voting – vote for the best contribution.

Science, publishing, and career

Top Medical Journals Give Women Researchers Short Shrift – Lauren Silverman – NPR

May 12, 2016

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Dandruff, archaeological dental calculus methanogens, extreme longevity, UK twins, and dissemination of human-derived bacteria into the Antarctic microbiome.

Pregnancy and birth microbiome

Early-life gut microbiome composition and milk allergy resolution – Supinda Bunyavanich – Journal of Allergy and Clinical Immunology

Human skin microbiome

Dandruff is associated with the conjoined interactions between host and microorganisms – Zhijue Xu – Scientific Reports

Human oral microbiome

Restricted diversity of dental calculus methanogens over five centuries, France – Hong T. T. Huynh – Scientific Reports

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer – Kaitlin J. Flynn – mSphere

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study – Vanessa Sousa – Clinical Oral Implants Research

Human respiratory microbiome

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study – Moana Mika – The Lancet Respiratory Medicine

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR – Joshua R. Stokell – Antonie van Leeuwenhoek

Human gut microbiome

Gut Microbiota and Extreme Longevity – Elena Biagi – Current Biology

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study – C Walton – European Journal of Clinical Nutrition

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study – Christian Milani – Scientific Reports

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing – Emily Vogtmann – PLOS ONE

Review: Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection – Caná L. Ross – Anaerobe

Preview: What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease – Taylor Feehley – Cell Host & Microbe

Review: Koch’s postulates, microbial dysbiosis and inflammatory bowel disease – Benjamin P. Willing – Clinical Microbiology and Infection

Review: Impact of gut microbiota on diabetes mellitus – G. Blandino – Diabetes & Metabolism

Review: Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD – David Briskey – Nitric Oxide

Review: Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract – Jenessa A. Winston – Anaerobe

Review: The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases – Rodney R. Dietert – Reproductive Toxicology

Animal experiments

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica) – Eduardo Crisol-Martínez – PeerJ

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide – Qingsen Shang – Macromolecules

Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease – Jennifer K. Spinler – Anaerobe

Editorial: Immunology: You Remind Me of a Microbe I Know – Ray Soto and June Round – Current Biology

Forum: Human Microbiota-Associated Mice: A Model with Challenges – Marie-Claire Arrieta – Cell Host & Microbe

Plant, root, and soil microbiome

Geography and agronomical practices drive diversification of the epiphytic mycoflora associated with barley and its malt end product in western Canada – Wen Chen – Agriculture, Ecosystems & Environment
http://www.sciencedirect.com/science/article/pii/S0167880916301669

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere –
Alec Cobban – MicrobiologyOpen
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.374/abstract

 

Water and extremophile microbiome

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome – Michelle L. Power – Environmental Pollution

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands – Felix Oloo – Scientific Reports

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants – Ghada A. Mustafa – Environmental Pollution

Conference Highlight: Decoding Microbial “Relationship Statuses” at OSM 2016 – Kelsey Ellis – Bulletin Limnology and Oceanography

Phages and viruses

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology – Angela L. Rasmussen – Cell Host & Microbe

Techniques

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface – Pranjul Shah – Nature Communications

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome

Video: Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – JOVE

Microbial Ecology

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments – Scott W. Olesen – PLOS ONE

More microbiology

Self-driven jamming in growing microbial populations – Morgan Delarue – bioRxiv

Review: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics – Elizabeth Klemm – Cell Host & Microbe

Microbes in the news

Osel, Inc.’s Lead Product LACTIN-V Enters Phase 2b Study to Prevent Recurrence of Bacterial Vaginosis– Digital Journal

Bacteria Battle Can Lead to Dandruff – Jennifer Viegas – Discovery
Bacteria the yin and yang of dandruff, says study – MedicalXpress

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development
– PR Newswire

Experts react to ‘waste of money’ headlines against probiotics – Adi Menayang – NutraIngredients

How scientists are harnessing the ice-making powers of bacteria – Zach St. George – The Week

Researchers Engineer Bacteria to Streamline Biofuel Production Process – IndiaWest

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development – PR Newswire

Twin study finds that gut microbiomes run in families – EurekAlert

From the American Urological Association meeting: Gut Bugs Differ in Chronic Prostatitis. Difference in taxa may aid biomarker, researchers say – MedPageToday

In Infants With Necrotizing Enterocolitis, Gut Dysbiosis Precedes Disease – Julie A. Jacob – JAMA

Science, publishing, and career

Reminder to deposit DNA sequences – Mark Blaxter – Science

Unexpected revelations for study volunteer: What health information do researchers owe the volunteers in their studies – Jennifer Couzin-Frankel – Science

Bik’s Picks

WATCH: What happened to astronaut Scott Kelly’s DNA during his year in space – Carl Zimmer – STAT News

May 11, 2016

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Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.

Events

The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news

May 10, 2016, 2nd edition

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Nitrate and oral microcosms, microbial tryptophan metabolism effects on astrocytes, creating germ free plants, a systematic review of the (lack of) effect of probiotics on the gut microbiome, and a phage/host prediction tool.

Event

Starts today: Food-Microbiome Interaction: Implications for Health & Disease – New York Academy of Sciences and the Quadram Institute at The Royal Society in London

Pregnancy and birth

Prenatal and post-natal exposure to antibiotics and risk of asthma in childhood – J. Metsälä – Clinical & Experimental Allergy

Review: Obesity and overweight: Impact on maternal and milk microbiome and their role for infant health and nutrition – Izaskun Garcia-Mantrana – Molecular Nutrition and Food Research

Human respiratory microbiome

Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities – Marcos Pérez-Losada – AIMS Microbiology

Human oral microbiome

Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms – Jessica E. Koopman – Microbial Ecology

Human skin microbiome

A systematic review and meta-analysis on Staphylococcus aureus carriage in psoriasis, acne and rosacea – J. E. E. Totté – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups – Deepak Yadav – Gut Pathogens

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials – Nadja B. Kristensen – Genome Medicine

Tissue Microbiome Profiling Identifies An Enrichment of Specific Enteric Bacteria In Opisthorchis viverrini Associated Cholangiocarcinoma – Kern Rei Chng – EBioMedicine

Editorial: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Could physical exercise help modulate the gut microbiota in chronic kidney disease? – Marta Esgalhado – Future Microbiology

Review: The Gut Microbiota and Immune System Relationship in Human Graft-versus-Host Disease – Lucrezia Laterza – Mediterranean Journal of Hematology and Infectious Diseases

Review: Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions? – David Endesfelder – Current Diabetes Reports

Animal experiments

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions – Alejandro Salgado-Flores – PLOS ONE

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants – Sheerli Kruger Ben Shabat – The ISME Journal

Book Chapter: Germ-Free Mice Model for Studying Host–Microbial Interactions – Yogesh Bhattarai – Mouse Models for Drug Discovery – Springer

Animal microbiome

Review: Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds – Anak Agung Gede Indraningrat – Marine Drugs

Plant, root, and soil microbiome

Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes – Rebekah J. Robinson – Scientific Reports

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils – Jean-Baptiste Ramond – Journal of Basic Microbiology

Plants of the Fynbos biome harbour host species-specific bacterial communities – Tsakani Miyambo – FEMS Microbiology Letters

Extremophile microbiome

In situ hydrogen dynamics in a hot spring microbial mat during a diel cycle – Niels Peter Revsbech – Applied and Environmental Microbiology

Metabolomics

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor – Veit Rothhammer – Nature Medicine

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands – Bruno Lamas – Nature Medicine

Review: Urolithins, the rescue of ‘old’ metabolites to understand a ‘new’ concept: metabotypes as a nexus between phenolic metabolism, microbiota dysbiosis and host health status – Francisco A. Tomás-Barberán – Molecular Nutrition & Food Research

Metagenomics and bioinformatics –

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – J. A. Frank – Scientific Reports

OrfM: A fast open reading frame predictor for metagenomic data – Ben J. Woodcroft – Bioinformatics

Phages and viruses

HostPhinder: A Phage Host Prediction Tool – Julia Villarroel – MDPI Viruses

More microbiology

Nonclinical Safety Assessment of SYN-004: An Oral β-lactamase for the Protection of the Gut Microbiome From Disruption by Biliary-Excreted, Intravenously Administered Antibiotics – John F. Kokai-Kun – International Journal of Toxicology

Rapid identification of health care–associated infections with an integrated fluorescence anisotropy system – Ki Soo Park – Science Advances

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans – Narasimha Anaganti – Journal of Biosciences

Microbes in the news

Stool Bank OpenBiome Is Expanding to Somerville. The bank wants more Boston-area residents to donate – Jamie Ducharme

Do probiotics have an effect on healthy adults? It’s too early to tell – EurekAlert

The Microbiome in Pediatric Rheumatic Diseases – Matthew Stoll – The Rheumatologist

May 10, 2016

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A very selective antibiotic that does not disturb the microbiota, metabolic pathways of the Deepwater Horizon spill, and GI microbiome role in acute myeloid leukemia.

Jobs and events

Postdoc funding opportunity “Microbiology of the built environment”, Alfred P. Sloan Foundation

The 4th Microbiome R&D and Business Collaboration Forum: USA – 3-4 October 2016, La Jolla, San Diego, USA

Human gut microbiome

The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Animal experiments

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model – Philipp Dirksen – BMC Biology

Editorial: Caenorhabditis microbiota: worm guts get populated – Laura C. Clark – BMC Biology

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome – Jiangwei Yao – Antimicrobial Agents and Chemotherapy

Waste, pollution, and water treatment microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states – I.B. Gomes – Science of the Total Environment

Microbes in the news

Gut Microbiome Startup CeMeT Aims to Build Reference Database from 10K Volunteers in Germany – Julia Karow – Genome Web

Microbiome linked to infectious complications in AML – Medical Xpress

Narrow-Spectrum Antibiotic Could Spare the Microbiome. A drug that singles out Staphylococcus aureus leaves gut-dwelling microbiota largely intact, a mouse study shows – Amanda B. Keener – The Scientist

Genetic potential of oil-eating bacteria from the BP oil spill decoded – University of Texas at Austin

Fooling the test: Antibiotic-resistant bacteria that look susceptible – Phys.org

A new industry that uses bacteria to remediate old mines? – Jonathan Migneault – Sudbury

The Mighty Microbes of Yellowstone – Scalding water is home to what microbiologists call extremophiles, heat-loving creatures that have figured in many scientific breakthroughs – David Quammen – National Geographic

Science, publishing, and career

John Oliver exposes how the media turns scientific studies into “morning show gossip”
– German Lopez – Vox

Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action – Elizabeth A. Silva – PLOS Biology

With quotes from me: Image manipulation in biomedical papers is commonplace – Maria Burke – Chemistry World

Open-access index delists thousands of journals. Many publications did not reapply after leading directory tightened its quality criteria – Monya Baker

May 9, 2016

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Reanalysis of plaque microbiome using Minimum Entropy Decomposition, decomposing cow dung, antimicrobial peptides in Drosophila, and distinct microbiomes in US landfills.

Human oral microbiome

Individuality, Stability, and Variability of the Plaque Microbiome – Daniel R. Utter – Frontiers in Microbiology

Human gut microbiome

Long-term changes of bacterial and viral compositions in the intestine of a recovered Clostridium difficile patient after fecal microbiota transplantation – Felix Broecker – Cold Spring Harbor Molecular Case Studies

Colonization with the enteric protozoa Blastocystis is associated with increased diversity of human gut bacterial microbiota – Christophe Audebert – Scientific Reports

Not sure what is novel here: Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics – Juan Jovel – Frontiers in Microbiology

Review: Local and Long-Distance Calling: Conversations between the Gut Microbiota and Intra- and Extra-Gastrointestinal Tract Infections – Joshua E. Denny – Frontiers in Cellular and Infection Microbiology

Animal and in vitro experiments

Selection of Lactobacillus strains as potential probiotics for vaginitis treatment
– Carolina M. A. Santos – Microbiology

Nod2 deficiency leads to a specific and transmissible mucosa-associated microbial dysbiosis which is independent of the mucosal barrier defect – Ziad Al Nabhani – Journal of Crohn’s and Colitis

The bacteriocin bactofencin A subtly modulates gut microbial populations – Caitriona M. Guinane – Anaerobe

Intestinal microecology associated with fluoride resistance capability of the silkworm (Bombyx mori L.) – Guan-Nan Li – Applied Microbiology and Biotechnology

Animal microbiome

Rapid Microbiome Changes in Freshly Deposited Cow Feces under Field Conditions –
Kelvin Wong – Frontiers in Microbiology

Microbial Diversity in the Gut of Cashew Stem Girdler, Analeptes trifasciata Fabricius (Coleoptera: Cerambycidae), in Ibadan, Nigeria – A.V. Oyedokun – International Journal of Insect Science

Includes eukaryotic microbes: Please mind the gap – Visual census and cryptic biodiversity assessment at central Red Sea coral reefs – John K. Pearman – Marine Environmental Research

Review: Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions – Nichole A. Broderick – Philosophical Transactions of the Royal Society B

Plant, root, and soil microbiome

Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides – Boris Jakuschkin – Microbial Ecology

Distribution of bacterial communities across plateau freshwater lake and upslope soils – Yihui Chen – Journal of Environmental Sciences

Water microbiome

What causes the inverse relationship between primary production and export efficiency in the Southern Ocean? – Frédéric A. C. Le Moigne – Geophysical Research Letters

Waste and pollution microbiology

Municipal Solid Waste Landfills Harbor Distinct Microbiomes – Blake W. Stamps – Frontiers in Microbiology

Yeasts and fungi

Review: Invasive candidiasis: from mycobiome to infection, therapy, and prevention – L. Lagunes – European Journal of Clinical Microbiology & Infectious Diseases

Viruses and phages

Pseudo-nitzschia Challenged with Co-occurring Viral Communities Display Diverse Infection Phenotypes – Michael C. G. Carlson – Frontiers in Microbiology

Techniques

Single cell stable isotope probing in microbiology using Raman microspectroscopy – Yun Wang – Current Opinion in Biotechnology

Microbes in the news

Is Obesity Infectious? Study Suggests Our Gut Microbes Can ‘Spread’ To Others – Alyssa Navarro – Tech Times

Bik’s Picks

If Dung Beetles (Scarabaeidae: Scarabaeinae) Arose in Association with Dinosaurs, Did They Also Suffer a Mass Co-Extinction at the K-Pg Boundary? – Nicole L. Gunter – PLOS ONE

Lab Stock Photos: The Inside Job

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A biosafety cabinet is essentially a big box with a window and opening on the front, and an airflow from above that creates a “curtain” of air, to protect both the worker from the materials they are handling, as well as the materials from the worker. It is used for tissue culture, handling biohazardous materials, and sterile work.

It is usually not recommended that photographers crawl into biosafety cabinet to make that perfect shot. But that does not prevent the stock photo industry from doing just that!

So here we go: photos from inside biosafety cabinets. Note that some cabinets have windows on the side, which could explain some of these images. Other pictures might be perfectly explained by a little tripod or a selfie stick. But in most of these pictures, just pretend that the photographer is crawled up in a corner, for a good laugh.

The first photo is from the SafetyAtWorkBlog, where the caption reads: “A researcher works with materials in a biosafety cabinet in the Biosecurity Research Institute at Kansas State University. A biosafety cabinet is a safety enclosure that uses HEPA filters and directional airflow to contain pathogens.”

brisafety.jpg

Shutterstock: “Young asian scientist pipetting samples in lab”, Copyright: KYTan:stock-photo-young-asian-scientist-pipetting-samples-in-lab-391395604.jpg

A photo from the same lab worker shows up in Dreamstime, entitled “Young asian scientist performing microbial tests in lab” – credit: Tan Kian Yong:young-asian-scientist-performing-microbial-tests-lab-series-biosafety-cabinet-68361375.jpg

Getty Images, credit: Javier Larrea. The caption reads: “Salmonella cultures in biosafety cabinet, Laboratory of Diagnosis, Departamento de Produccion y Sanidad Animal, Neiker Tecnalia, Instituto de Investigacion y Desarrollo Agrario, Ganadero, Forestal y del Medio Natural, Derio, Bizkaia, Euskadi, Spain”:Screen Shot 2016-05-08 at 9.42.19 PM.png

Penn State News:  “Tyler Goralski, a graduate student studying biochemistry and molecular biology at Penn State, streaks out a bacteria sample at the Pell Laboratory for Advanced Biological Research.” – Image: Patrick Mansell:Screen Shot 2016-05-08 at 9.47.53 PM.png

AFP Getty Images, found on Daily Mail, in an article about Indonesia and HIV. The caption reads: “Awareness about HIV in Indonesia remains poor despite the fact that more than 660,000 people are estimated to be living with the virus. Pictured is a medical laboratory technician at an HIV care hospital in Indonesia”:Screen Shot 2016-05-08 at 10.05.00 PM.png

From 123RF: “Female scientist researching in laboratory, pipetting cell culture medium samples in laminar flow. Life science professional grafting bacteria in the pettri dishes. Photo taken from laminar interior.”. Copyright : kasto:Screen Shot 2016-05-08 at 10.13.48 PM.png

Also from 123RF possibly the same model: “Female scientist researching in laboratory, pipetting cell culture samples on LB agar medium in laminar flow. Life science professional grafting bacteria in the petri dishes.” Copyright : kasto:Screen Shot 2016-05-08 at 10.17.49 PM.png

From Alamy, “Plate culture in laminar flow cabinet. Biological test laboratory. Fundacion Inasmet-Tecnalia. Donostia, San Sebastian”:Screen Shot 2016-05-08 at 10.20.51 PM.png

May 7, 2016

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Drosophila male-killing spiroplasma, chitin in potting soil, temperature constraints for complex life, a book on microbial diversity, and monitoring sewer health.

General microbiome

Review: Design, analysis and application of synthetic microbial consortia – Xiaoqiang Jia – Synthetic and Systems Biotechnology

Review: Metabolic network modeling of microbial interactions in natural and engineered environmental systems – Octavio Perez-Garcia – Frontiers in Microbiology

Opinion: Mirror, mirror on the wall: which microbiomes will help heal them all? – Renuka R. Nayak – BMC Medicine

Hypothesis: Do microbiotas warm their hosts? – Eugene Rosenberg – Gut Microbes

Human respiratory microbiome

Microbiome diversity in the sputum of patients with pulmonary tuberculosis – P. Krishna – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Literature review: The gut microbiota: a major player in the toxicity of environmental pollutants? – Sandrine P Claus – NPJ Biofilms and Microbiomes

Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study – Zoltan Pataky – Digestive Diseases and Sciences

n=1: Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report – Bumjo Oh – Clinical Nutrition Research

Conference abstract: Associations Between Physical Activity and the Intestinal Microbiome of College Freshmen – Corrie M Whisner – The FASEB Journal

Animal experiments

Male-Killing Spiroplasma Alters Behavior of the Dosage Compensation Complex during Drosophila melanogaster Embryogenesis – Becky Cheng – Current Biology

Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities – Kevin D. Kohl – Frontiers in Microbiology

Conference abstract: Soy positively impacts cecal microbiota of ovariectomized rats selectively bred for low aerobic capacity – Tzu-Wen Liu – the FASEB Journal

Animal microbiome

Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response – Jianhua Zhang – PLOS ONE

Plants, roots, and soil microbiome

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology – Jane Debode – Frontiers in Microbiology

Litter microbial and soil faunal communities stimulated in the wake of a volcanic eruption in a semiarid woodland in Patagonia, Argentina – Paula Berenstecher – Functional Ecology

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China – Jianli Ding – Applied Soil Ecology

Conference abstract: Multi-omics of the Soil Microbiome – Janet K Jansson – The FASEB Journal

Review: Life cycle specialization of filamentous pathogens — colonization and reproduction in plant tissues – Janine Haueisen – Current Opinion in Microbiology

Review: Interspecific hybridization impacts host range and pathogenicity of filamentous microbes – Jasper RL Depotter – Current Opinion in Microbiology

Water and extremophile microbiome

From climate models to planetary habitability: temperature constraints for complex life – Laura Silva – arXiv preprint

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems – Roberto Danovaro – Science Advances

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer – Robert Danczak – Frontiers in Earth Science

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling – Kenneth Wasmund – mBio

Book: Their World: A Diversity of Microbial Environments – Editors: Christon J. Hurst – Springer

Review: Marine microorganisms as a promising and sustainable source of bioactive molecules – G. Romano – Marine Environmental Research

Waste and pollution microbiology

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed – Elliott P. Barnharta – International Journal of Coal Geology

Review: Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments? – Viviana Fonti – Science of The Total Environment

Review: Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure – Sevcan Aydin – Applied Microbiology and Biotechnology

Viruses and phages

Editorial overview: The megaviromes – Didier Raoult – Current Opinion in Microbiology

More microbiology

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development – Ryan H. Hansen – PLOS ONE

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria – Kelly C Wrighton – The ISME Journal

Research Highlight: A time to gather chromosomes together – Naomi Attar – Nature Reviews Microbiology

Conference abstract: Metabolic Exchange In Microbial Communities – Andrei Osterman – The FASEB Journal

Microbes in the news

Pipe Dreams: Tapping into the Health Information in Our Sewers – Carrie Arnold – Environmental Health Perspectives

Deep sea microbes may be key to oceans’ climate change feedback – Howard Lee – The Guardian

Exploiting Male Killing Bacteria Could Control Insect Pest Species in the Future – SciCasts

Fifty people warned about possible exposure to drug-resistant bacteria at University of Alberta Hospital – Keith Gerein

May 6, 2016

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A quiet day, this Friday. The main stories of today are about Bacteroides vesicles that interact with certain genes implicated in Crohn’s disease (in a mouse model), and duplications in Pseudomonas genomes associated with novel traits.

Human respiratory microbiome

Evaluation of Malassezia and Common Fungal Pathogens in Subtypes of Chronic Rhinosinusitis – Jonathan T. Gelber – International Forum of Allergy & Rhinology

Animal models
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease – Hiutung Chu – Science

Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons – Elisa Deriu – PLOS Pathogens

Techniques

A Novel Computerized Cell Count Algorithm for Biofilm Analysis – Mareike Klinger-Strobel – PLOS ONE

Other microbiology

Fungal Genomics Challenges the Dogma of Name-Based Biosecurity – Alistair R. McTaggart – PLOS Pathogens

Duplication drives novelty: The Genomic Basis of Evolutionary Innovation in Pseudomonas aeruginosa – Macarena Toll-Riera – PLOS Genetics

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe – David M. Aanensen – mBio

Microbes in the news

Get cozy with your skin bacteria — they’re not going anywhere – Rachel Feltman – Washington Post

Breast Milk Primes Gut for Microbes. Maternal antibodies engender a receptive gut environment for beneficial bacteria in newborn mice – Ruth Williams – The Scientist

Genetic variants in patients with Crohn’s disease prevent ‘good’ gut bacteria from working – Science Daily

How did birds get their wings? Bacteria may provide a clue, say scientists – University of Oxford

Leonardo da Vinci’s DNA: Experts unite to shine modern light on a Renaissance genius – Phys.org

May 5, 2016

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Leptin and insulin levels in breast milk influence infant gut microbiome, temporal stability of the human skin microbiome, gut microbiota in children with CF, and the cocobiota (for the chocolate lovers).

Thank you all for your support! It means a lot to me, and I hope that I will be able to continue the work I put into this blog.
Jobs and events

Postdoctoral Fellow – Senior Bioinformatician : Cambridge, United Kingdom – Nature Jobs

General microbiome
Review: Microbiome Therapeutics – Advances and Challenges – Mark Mimee – Advanced Drug Delivery Reviews

Pregnancy and birth

Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome – Dominick J Lemas – The American Journal of Clinical Nutrition

Human skin microbiome
Weird illustration (worth another blog post?) Editorial: Microbial Skin Inhabitants: Friends Forever – Pieter C. Dorrestein – Cell

Temporal Stability of the Human Skin Microbiome – Julia Oh – Cell

Human respiratory microbiome

Community dynamics and the lower airway microbiota in stable chronic obstructive pulmonary disease, smokers and healthy non-smokers – G G Einarsson – Thorax

Human reproductive tract microbiome

Review: The vaginal microbiota, host defence and reproductive physiology – Steven B Smith, Jacques Ravel

Human gut microbiome
Disrupted progression of the intestinal microbiota with age in children with cystic fibrosis – Shaun Nielsen – Scientific Reports

Molecular characterization and meta-analysis of gut microbial communities illustrate enrichment of Prevotella and Megasphaera in Indian Subjects – Shrikant Bhute – Frontiers in Microbiology

“Actinomyces ihumii”, a new bacterial species isolated from the digestive microbiota of a HIV-infected patient – Sokhna Ndongo – New Microbes and New Infections

Conference abstract that looks promising: Assessing Relationships Between Dietary Intake, Gut Microbiota and Weight Among a Diverse Cohort of College Freshmen – Elizabeth Journey – The FASEB Journal

Editorial: The Mucosal Microbiome and Recurrence After Surgery for Crohn’s Disease – Alastair J.M. Watson – Gastroenterology

Review: Microbiome in Brain Function and Mental Health – Paul J. Kennedy – Trends in Food Science & Technology

Review: Can exercise affect the course of inflammatory bowel disease? Experimental and clinical evidence – Jan Bilski – Pharmacological Reports

Review: Emerging Concepts on the Gut Microbiome and Multiple Sclerosis – Justin D. Glenn – Journal of Interferon & Cytokine Research

Review: The Intestinal Microenvironment and Functional Gastrointestinal Disorders – Giovanni Barbara – Gastroenterology

Editorial: Frozen faecal matter works as well as fresh for transplantation in C difficile patients – Jacqui Wise – The BMJ

Animal experiments

Comparison of microbial communities isolated from feces of asymptomatic Salmonella-shedding and non-Salmonella shedding dairy cows – Bradd J. Haley – Frontiers in Microbiology

Food microbiology

Review about chocolate production: Cocobiota: Implications for Human Health
Ivan M. Petyaev – Journal of Nutrition and Metabolism

Metagenomics and bioinformatics

Bracken: Estimating species abundance in metagenomics data – Jennifer Lu – bioRxiv preprint

Techniques

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Microbes in the news

Review on Techniques for Protecting Cultural Heritage Materials from Microbes – Alex Alexiev – MicroBEnet

Bacteria Block Mosquitoes from Transmitting Zika, Brazilian Study Says
Wolbachia bacteria have already been used to control dengue – Julie Steenhuysen – Scientific American

Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus – Carl Zimmer – New York Times

Vancouver students win more awards for discovering bacteria that destroys polluting plastics – Jeff Lee – Vancouver Sun

Our personal skin microbiome is surprisingly stable – EurekAlert

Disparities in Gut Microbiome Could Lead to Biomarkers for Estrogen-driven Breast Cancer – Kathy Boltz – Oncology Nurse Advisor

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight – Science Daily

Stephen O’Hara, chief executive of OptiBiotix talks to TPL, develops compounds to modulate the human microbiome – The Pharma Letter

Gut check: Study may shed new light on sleep deprivation: team received $7.5 million grant from DoD – University of Colorado Boulder