May 16, 2016

The Michigan Microbe Meeting, fungi in asthma exhaled breath, and fungi recovered after the California Rim Fire.

Events

Ongoing now: Michigan Meeting on Microbial Communities,  May 16-18. Follow on Twitter via #MiMicrobe

Functional Metagenomics 2016: 25-28 September 2016, Jægtvolden fjordhotell, Inderøy, Norway

Human respiratory microbiome

Analysis of the fungal microbiome in exhaled breath condensate of patients with asthma – Giovanna E. Carpagnano – Allergy and Asthma Proceedings

Human gut microbiome

Review: Antibiotic-Induced Changes in the Intestinal Microbiota and Disease – Simone Becattini- Trends in Molecular Medicine

Animal experiments

Stable host gene expression in the gut of adult Drosophila melanogaster with different bacterial mono-associations – Carolyn Elya – BioRxiv

Animal microbiome

Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina) – Daniela Numberger – Microbiology Open

Plant, root, and soil microbiome

Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot – Sydney I Glassman – The ISME Journal

Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles – Elisa Zampieri – Scientific Reports

The effect of different land uses on arbuscular mycorrhizal fungi in the northwestern Black Sea Region – Şahin Palta – Environmental Monitoring and Assessment

Plant powder teabags: A novel and practical approach to resolve culturability and diversity of rhizobacteria – Mohamed S. Sarhan – Physiologia Plantarum

Water and extremophile microbiome

Ecophysiological Distinctions of Haloarchaea from a Hypersaline Antarctic Lake as Determined by Metaproteomics – Bernhard Tschitschko – Applied and Environmental Microbiology

Waste and pollution microbiology

Effect of copper on the performance and bacterial communities of activated sludge using Illumina MiSeq platforms – Fu-Lin Sun – Chemospere

Microbes in the news

African scientists make headway in grasping persistent TB bacteria, offer hope for the future – Jomien Mouton – Mail & Guardian Africa

Bacteria are killing rainbow smelt in upper Lake Sakakawea, North Dakota – KFGO

The innovators: Irish lab develops coating to ward off superbug – Shane Hickey – The Guardian

Doctors are fist-bumping one another – here’s why – Richard Hartley-Parkinson – Metro UK
Doctors and nurses encouraged to swap handshakes for fist-bumps to reduce spread of bugs – John Paul Breslin – Sunday Post

Bacterium Blocks Zika’s Spread. Infecting mosquitoes with Wolbachia greatly reduces the insects’ abilities to transmit the virus – Tanya Lewis – The Scientist

Video: A National Poo Museum opened at the Isle of Wight Zoo in the UK

Satire: “Microbiome of Wounds” to be renamed “Infection” – The Allium

Science, publishing, and career

Opinion: Reimagining the Paper. Breaking down lengthy, narrative-driven biomedical articles into brief reports on singular observations or experiments could increase reproducibility and accessibility in the literature – Ahmed Alkhateeb – The Scientist

May 14, 2016

Your weekend microbiome update.

Human Respiratory microbiome

The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid – Kentaro Akata – BMC Pulmonary Medicine

The cystic fibrosis lower airways microbial metagenome – Patricia Moran Losada – ERJ Open Research

Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk – Christian Rosas-Salazar – American Journal of Respiratory and Critical Care Medicine

Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry – Jessica A. P. Carlson-Jones – PLOS ONE

Human ear microbiome

MALDI-TOF mass spectrometry reveals a highly complex bacterial profile of otitis media with effusion – Zoltán Papp – International Journal of Pediatric Otorhinolaryngology

Human gut microbiome

Editorial: Heartbeat: The gut microbiota and heart failure – Catherine M Otto – Heart

Editorial: Dietary metabolism, gut microbiota and acute heart failure – WH Wilson Tang – Heart

Trimethylamine N-oxide and prognosis in acute heart failure – Toru Suzuki – Heart

Animal experiments

Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium – Ting-Chin David Shen – PLOS ONE

Effects of alternative plant-based feeds on hepatic and gastrointestinal histology and the gastrointestinal microbiome of sablefish (Anoplopoma fimbria) – Linda D. Rhodes – Aquaculture

Addendum: Rebooting the Microbiome – Sean Munoz – Gut Microbes

Typos, horrible experiment, and controversial findings. Proceed with care: An investigation into blood microbiota and its potential association with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers – Rabindra K. Mandal – Scientific Reports

Animal microbiome

Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits – Yuliaxis Ramayo-Caldas – The ISME Journal

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta) – Genevieve Bennett – American Journal of Primatology

Jellyfish: Aurelia aurita ephyrae reshape a coastal microbial community – Luca Zoccarato – Frontiers in Microbiology

Mosquito C-type lectins maintain gut microbiome homeostasis – Xiaojing Pang – Nature Microbiology

Plant, root, and soil microbiome

D-Amino Acid Catabolism Is Common Among Soil-Dwelling Bacteria – Atanas D Radkov – Microbes and Environments

MycoDB, a global database of plant response to mycorrhizal fungi – V. Bala Chaudhary – Scientific Data

Effects of soil substrate quality, microbial diversity and community composition on the plant community during primary succession – Jan Frouz – Soil Biology and Biochemistry

Deciphering the Bacterial Microbiome in Huanglongbing-Affected Citrus Treated with Thermotherapy and Sulfonamide Antibiotics – Chuanyu Yang – PLOS ONE

Fire-severity effects on plant–fungal interactions after a novel tundra wildfire disturbance: implications for arctic shrub and tree migration – Rebecca E. Hewitt – BMC Ecology

Water and extremophile microbiome

The symbiotic relationship of sediment and biofilm dynamics at the sediment water interface of oil sands industrial tailings ponds – T. Reid – Water Research

Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough – Taiki Katayama – FEMS Microbiology Ecology

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions – Sergei V. Bukin – Frontiers in Microbiology

The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale – Zhang, Binglin – Environmental Research Letters

Microbial dynamics of the extreme-thermophilic (70 °C) mixed culture for hydrogen production in a chemostat – Fang Zhang – International Journal of Hydrogen Energy

Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles – Fumito Shiraishi – Earth and Planetary Science Letters

Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge – Likui Zhang – Scientific Reports

Biofilm transplantation in the deep sea – Irene Wagner-Döbler – Molecular Ecology

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

Food microbiology

Composition and function of sourdough microbiota: From ecological theory to bread quality – Michael Gänzle – International Journal of Food Microbiology

Comparison of DNA-based techniques for differentiation of production strains of ale and lager brewing yeast – J. Kopecká – Journal of Applied Microbiology

Infection microbiology

Review: Polymicrobial-Host Interactions During Infection – Hong Tay Wei – Journal of Molecular Biology

Bioinformatics and metagenomics

A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology – Jesús A. Ballesteros – Molecular Biology and Evolution

Evaluating techniques for metagenome annotation using simulated sequence data (CC) – Richard J. Randle-Boggis – FEMS Microbiology Ecology

Computational methods for predicting genomic islands in microbial genomes – Bingxin Lu – Computational and Structural Biotechnology Journal

Microbial ecology

Quorum Sensing Communication Modules for Microbial Consortia – Spencer R. Scott – ACS Synthetic Biology

Ecological Opportunity, Evolution, and the Emergence of Flea-borne Plague – B. Joseph Hinnebusch – Infection and Immunity

Microbes in the news

NOAA Research on Microbial Communities Contributes to National Microbiome Initiative – Edward Pritchard – NOAA

Parasites Influence Makeup of Human Gut Microbiome, BoG Speaker Reports – GenomeWeb

May 13, 2016

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

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

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

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

EditorialTranskingdom 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

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

EditorialCaenorhabditis 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

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

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

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

OpinionMirror, 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