November 16, 2017

Today we have a very nice serving to digest, with some impactful gut microbiome studies for human health/therapeutics, a whitepaper on the challenges of clinical microbiome research.  We also have clusters of related studies on the environment, drinking water, and antibiotic resistance.  There are even a few studies on the microbiota found in caves!  Give these all a read, there is a lot of amazing research today.  Don’t forget to have yourself a few extra side servings of my own non-microbial picks, in honor of the upcoming Thanksgiving US holiday.

Human oral microbiome

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

Human respiratory microbiome

The microbiota protects against respiratory infection via GM-CSF signaling – Rebecca L. Brown – Nature

Human gut microbiome

Microbiota: A high-pressure situation for bacteria – David A. Relman – Nature

Quantitative microbiome profiling links gut community variation to microbial load – Doris Vandeputte – Nature

Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature

A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li – PLOS ONE

Plant, root, and soil microbiome

[Doctoral Thesis] Plant biomass-degrading microbial consortia: Ecology, lignocellulolytic machinery and biotechnological potential – Jiménez Avella – University of Groningen

Direct evidence for the enhanced acquisition of phosphorus in the rhizosphere of aquatic plants: A case study on Vallisneria natans – Xigang Xing – Science of the Total Environment

Effect of Phosphate Solubilization Microorganisms and Plant Growth Promoting Rhizobacteria on Yield and Yield Components of Corn – Amin Fathi – Scientia Agriculturae

Water and extremophile microbiome

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients – Alyse K. Hawley – Nature

Comparison of bacterial and archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary) – Dóra Anda – Journal of Cave and Karst Studies

Comparisons of Soil Properties, Enzyme Activities and Microbial Communities in Heavy Metal Contaminated Bulk and Rhizosphere Soils of Robinia pseudoacacia L. in the Northern Foot of Qinling Mountain – Yurong Yang – Forests

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data – Stéphane Pfendler – Science of the Total Environment

Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system – Lingwei Meng – Journal of Environmental Sciences

Field assessment of bacterial communities and total trihalomethanes: Implications for drinking water networks – Carolina Montoya-Pachongo – Science of the Total Environment

Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water – Hao-Chang Su –  Science of the Total Environment


Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene – Yifei Zhang – PLOS ONE

Microbes in the news

Probiotics: Health boost or waste of cash?

Microbes on the market

* uBiome Launches HPV, STD, Vaginal Microbiome Test for Self-Collected Samples – genomeweb

* [Whitepaper] The Microbiome in Clinical Trials: Opportunities and Challenges – Brian Murphy – MedPace

Bacteria Hysteria

Fort Mitchell woman attacked by flesh-eating bacteria back home after 45 days in hospital

Fecal Bacteria Discovered In Public Well Serving Seymour, Oxford

Ed’s non-microbiology picks

Epistemic rationality: Skepticism toward unfounded beliefs requires sufficient cognitive ability and motivation to be rational – Tomas Ståhl – Personality and Individual Differences

Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing – Hao Yin – Nature

Increased food production and reduced water use through optimized crop distribution – Kyle Frankel Davis – Nature Geoscience

* Fructan, Rather Than Gluten, Induces Symptoms in Patients With Self-reported Non-celiac Gluten Sensitivity – Gry I. Skodje – Gastroenterology

* Does Money Matter in the Long Run? Effects of School Spending on Educational Attainment – Joshua Hyman – American Economy Journal: Economic Policy

* Hippocampal GABA enables inhibitory control over unwanted thoughts – Taylor W. Schmitz – Nature

Daytime variation of perioperative myocardial injury in cardiac surgery and its prevention by Rev-Erbα antagonism: a single-centre propensity-matched cohort study and a randomised study – David Montaigne – The Lancet Cardiac Surgery

The reminiscence bump: why America’s greatest year was probably when you were young

Study: Americans are retiring later, dying sooner and sicker in-between


November 14, 2017

Today seems unusually quiet. But, a few highlights still stand out. Scientists discover a new mechanism of antibiotic resistance. The HHS in the US released a progress report on fighting against antibiotic resistance. Finally, please enjoy the stunning beauty of microbes under the microscope.


Grants Alert – Federal Grants & Contracts


Technologist (Microbiology) – Tampa Florida

General microbiology

New issue of Global Change Biology Bioenergy

* The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity – Prateek Sharma et al. – Nature Communications

Press: New mechanisms discovered that bacteria use to protect themselves from antibiotics –

* National Action Plan Drives Progress in Fight Against Antibiotic-Resistant Bacteria – Christopher M. Jones – HHS

Na+-induced structural transition of MotPS for stator assembly of the Bacillus flagellar motor – Naoya Terahara et al. – Science Advances

Press: How bacteria get their groove: Mechanism behind flagellar motility – Osaka University – Science Daily

Phages and viruses

Phage Genome Annotation Using the RAST Pipeline – Katelyn McNair et al. – Bacteriophages

Microbes in the news

* Seeing the Beautiful Intelligence of Microbes – John Rennie & Lucy Reading-Ikkanda – Quanta Magazine

FDA Acts to Advance Potential Inhaled Treatment of Resistant Bacteria Tied to Lung Infections – Janet Stewart – Cystic Fibrosis News Today

Strong Evidence Emerging That Gut Microbiome Is a Key Variable in Immunotherapy Efficacy – Theodore Bosworth – Medscape

How the Gut Microbiome Affects Outcomes in HIV – Jeannette Y. Wick – Special Pharmacy Times

Microbes on the market

With a grain of salt: Would you put bacteria on your face? This brand thinks you should – Victoria Hall – Telegraph


November 13, 2017

Today’s digest is concise but exciting- how electric bandages decrease biofilm formation and highlights on immune response and microbiome interactions

General microbiome

Differences in bacterial composition between men’s and women’s restrooms and other common areas within a public building. Dobbler PCT. Antonie van Leeuwenhoek

Gut microbiome 

The Intestinal Microbiome in Nonalcoholic Fatty Liver Disease.Puri P. Clinics in Liver Disease

Lung microbiome

Highlights in immune response, microbiome and precision medicine in allergic disease and asthma. Sokolowska M. Current Opinion in Immunology

Animal microbiome

Evidence from the gut microbiota of swarming alates of a vertical transmission of the bacterial symbionts in Nasutitermes arborum (Termitidae, Nasutitermitinae). Diouf M- Antonie van Leeuwenhoek

Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals. Chiarello M,

Microbiome News

Electric bandages help to fight infection– Digital Journal

November 7, 2017

Here’s your daily Digest. Highlights include an attempt to establish the causal link between gut microbiota and colorectal cancer in mice, an electric bandage to fight biofilm and antimicrobial resistance, and a group B Streptococcus vaccine that could save tens of thousands of babies per year.

General microbiology

Oral epithelial cells orchestrate innate type 17 responses to Candida albicans through the virulence factor candidalysin – Akash H. Verma et al. – Science Immunology

Methicillin Resistant Staphylococcus aureus Sequence Type (ST) 5 Isolates from Health Care and Agricultural Sources Adhere Equivalently to Human Keratinocytes – Samantha J. Hau et al. – Applied and Environmental Microbiology

Human gut microbiome

Human microbiome signatures of differential colorectal cancer drug metabolism – Leah Guthrie et al. – npj Biofilms and Microbiomes

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial – Henrik Munch Roager et al. – Gut

Multi-site human microbiome

Review: Human microbiome, infections, and rheumatic disease – Ana Clara Camine et al. – Clinical Rheumatology

Review: The Microbiome and Bone and Joint Disease – Christopher J. Hernandez – Current Rheumatology Reports

Animal experiments

Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional mice – Sunny H. Wong and Liuyang Zhao – Gastroenterology

Animal microbiome

An integrative study on biologically recovered polyhydroxyalkanoates (PHAs) and simultaneous assessment of gut microbiome in yellow mealworm – Su Yean Ong et al. – Journal of Biotechnology

Plant, root and soil microbiome

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3 – Peng Wang et al. – Scientific Reports

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization – Luis H. Orellana et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

High altitude, hyper-arid soils of the Central-Andes harbor mega-diverse communities of actinobacteria – Alan T. Bull et al. – Extremophiles

Sediment nitrogen cycling rates and microbial abundance along a submerged vegetation gradient in a eutrophic lake – Lu Yao et al. – Science of The Total Environment


Electric Field Based Dressing Disrupts Mixed-Species Bacterial Biofilm Infection and Restores Functional Wound Healing – Barki, Kasturi Ganesh et al. – Annals of Surgery

Press: Study shows electric bandages can fight biofilm infection, antimicrobial resistance – MedicalXpress


Preprint: A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing – Samuel I. W. Lipworth et al. – bioRxiv

Microbes in the news

Your Eyes Have Their Own Microbiome. Here’s What You Need To Do To Take Care Of It – Sam Berne – MBG Health

Does a Healthy Gut Equal a Long, Healthy Life? – Jim Pietrangelo – Healthline

Unlocking the Secrets of the Microbiome – Jane E. Brody – New York Times

Specific gut bacteria can help or hinder cancer treatments – Rich Haridy – New Atlas

Proprietary Prebiotic Fiber Tested in National Institutes of Health Pilot Study with End-Stage Renal Disease Patients – Kimberly J. Decker – Nutritional Outlook

Briny pool bacteria can clean up and power up – King Abdullah University of Science & Technology – EurekAlert

2 million Chinese mothers carry strep bacteria that can be fatal to newborns, study finds – Laurie Chen – South China Morning Post

* Vaccine for bacteria carried by 20% of pregnant women ‘could prevent 100,000 baby deaths’ – Sarah Boseley – The Irish Times

Research finds link between gut fungi, bacteria and obesity – Camille Bienvenu –

Microbes on the market

Microbiome Therapeutics prepares to launch ‘microbiome modulator’ – Stephen Daniells – NutraIngredients


October 31, 2017

Today’s Digest is short, but not without highlights. The highlights all go to antibiotics. Ed Yong wrote about the history of methicillin resistance, colistin resistance was found to be increasing in Chinese hospitals, and fox poop could save us from vegetable and fruit waste.

General microbiology

A CRISPR–Cas9-based gene drive platform for genetic interaction analysis in Candida albicans – Rebecca S. Shapiro et al. – Nature Microbiology

Reduction of bacterial burden by copper alloys on high-touch athletic center surfaces – Zina Ibrahim et al. – American Journal of Infection Control

Press: New Study Shows Copper Surfaces on Athletic Equipment Reduce Bacteria by 94 Percent – Business Wire

Plant, root and soil microbiome

Assessing and characterising the repertoire of constitutive promoter elements in soil metagenomic libraries in Escherichia coli – Caua Antunes Westmann et al. – bioRxiv


Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan Raju et al. – bioRxiv

Microbes in the news

Flesh-eating bacteria kills man helping repair Harvey-damaged homes – Claire Z. Cardona – Dallas News

Gut bacteria found to have a role in both PTSD and Alzheimer’s disease – Rich Haridy – New Atlas

* Bacteria Can Evolve Resistance to Drugs Before Those Drugs Are Used – Ed Yong – The Atlantic

* New Study Detects Increase in MCR-1 Positive Multidrug-Resistant Bacteria in Humans – Samar Mahmoud – Contagion Live

Vaginal Microbiota Profile Predictive of Chlamydia Susceptibility – Jessica Martin – Infectious Disease Advisor

* War on waste: Antimicrobial borne by feral foxes slows decay saving food and money – Jennifer Nichols – ABC News

Microbes on the market

Video: Bioengineers recreated spider silk by fermenting E. Coli bacteria – Mashable

Kane Biotech Inc. Provides Overview of Biofilm Industry, Clinical Development and Growth Drivers in New SNNLive Video Interview with – Global Newswire

Evivo™ Gains Health Canada Approval, Providing First International Expansion Opportunity – Global Newswire


October 27, 2017

A dynamic Digest today. A variety of articles in human and other microbiome research. The ongoing discussion on reproducible research and P value. For us junior scientists, what are our career prospects?

General microbiology

Review: Development and regulation of single- and multi-species Candida albicans biofilms – Matthew B. Lohse et al. – Nature Reviews Microbiology

Preprint: Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal et al. – bioRxiv

Human skin microbiome

Review: Staphylococcal Biofilms in Atopic Dermatitis – Tammy Gonzalez et al. – Current Allergy and Asthma Reports

Human oral microbiome

Sociodemographic variation in the oral microbiome – Audrey Renson et al. – bioRxiv

Human lung microbiome

Review: New opportunities for managing acute and chronic lung infections – William O. C. M. Cookson et al. – Nature Reviews Microbiology

Human gut microbiome

Gut microbiota and host metabolism: what relationship? – Mithieux G – Neuroendocrinology

Review: Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen and Yan Yan Jin et al. – Molecules

Review: The Gastrointestinal Tract as an Integrator of Mechanical and Hormonal Response to Nutrient Ingestion – Adrian Vella and Michael Camilleri – Diabetes

Molecular, microbiological and clinical characterization of Clostridium difficile isolates from tertiary care hospitals in Colombia – Clara Lina Salazar et al. – PLoS One

Animal experiments

Polyphenol- and caffeine-rich post-fermented Pu-er tea improves diet-induced metabolic syndrome by remodeling intestinal homeostasis in mice – Xiaoyu Gao et al. – Infection and Immunity

Animal microbiome

Exogenous dietary lysozyme improves the growth performance and gut microbiota in broiler chickens targeting the antioxidant and non-specific immunity mRNA expression – Mervat A. Abdel-Latif et al. – PLoS One

Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine – Jun-Yeong Lee et al. – PLoS One

Plant, root and soil microbiome

Effects of stand age and soil properties on soil bacterial and fungal community composition in Chinese pine plantations on the Loess Plateau – Peng Dang et al. – PLoS One

Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle – Magalí S. Marcos et al. – Microbial Ecology

Phages and viruses

Preprint: Diagnostic Potential & the Interactive Dynamics of the Colorectal Cancer Virome – Geoffrey D. Hannigan et al. – bioRxiv

Microbes in the news

Does Chinese Urbanization Change the Microbiome? – Usha B. Nair – Medical News Bulletin

*Healthy ageing? Microbiome study shows same patterns irrespective of age – Nathan Gray – Nutra

Modified bacteria convert petroleum directly into building blocks for plastics – Wageningen University

Releasing the Antibiotics That Lie Dormant in Bacteria – Micronow

Bacteria have a sense of touch – EurekAlert

How Dog and Cat ‘Kisses’ Can Turn Deadly – Erika Engelhaupt – National Geographic

Xin’s non-microbiology picks

*Many junior scientists need to take a hard look at their job prospects – Nature Editorial

*Preprint: The Reproducibility Of Research And The Misinterpretation Of P Values – David Colquhoun – bioRxiv


October 26, 2017

In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology


Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)


‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE