May 10, 2017

A short digest today, but not without interesting pieces. Largest study yet to demonstrate vertical transfer of bacteria from mother to infant, microbes could orchestrate plant ‘migration’, and many fascinating pieces of news on microbes. How may we make peace with microbes in and around us?

General microbiology

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance – Asunción Delgado et al. – Cell Reports

Press: Four-billion-year-old ‘fossil’ protein resurrected in bacteria protects them from viruses –

Infant Gut Microbiome

Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome – Pia S. Pannaraj et al. – JAMA Pediatrics

Press: Breastfeeding plays important role in ‘seeding’ infant microbiome with beneficial bacteria – Leigh Hopper – UCLA

Plant, root and soil microbiome

Microbial communities and diazotrophic activity differ in the root-zone of Alamo and Dacotah switchgrass feedstocks – Richard R. Rodrigues et al. – Global Change Biology Bioenergy

Divergent plant–soil feedbacks could alter future elevation ranges and ecosystem dynamics – Michael E. Van Nuland et al. – Nature Ecology and Evolution

Press: Microscopic soil creatures could orchestrate massive tree ‘migrations’ – University of Tennessee at Knoxville – Science Daily

Microbes in the news

Global warming is altering the microbiota of lizards – Brooks Hays – UPI

TOO much exercise causes a leaky gut and increases health risks, research shows (and be especially careful if you work in the military) – Claudia Tanner – Daily Mail

Be wary of the title: Bacteria in Yogurt Cures Depression, Study Shows – Lorie Johnson – CBN News

Anecdotal evidence: Faecal transplants boost mind-gut link – Sarah Wiedersehn – Yahoo News

Bacteria appears to be behind mysterious outbreak in Liberia – Mike Stobbe – ABC News

Scientists Battle Bacteria with Silver and Mucus – Shawn Radcliffe – Healthline News

Verify: Will I contract flesh-eating bacteria at the beach in Texas? – Brandon Jones – KVUE

BACTERIA could mean the end of the pothole: Radical self repairing road can ‘grow’ into cracks – Cecile Borkhataria – Daily Mail

I Survived Flesh-Eating Bacteria—and It Changed My Life Forever – Aimee Copeland – Time

Microbes on the market

Oral enzyme prevents C. difficile infection, VRE colonization – Healio Gastroenterology

May 5, 2017

A PLoS One paper, with Dr. Bik as one of the co-authors, to characterize human gut microbiome and compare certain taxa against healthy profiles, the relationship between diet, circadian rhythm and gut microbiome, and much more.


Webinar: Interactions between the Mycobiome and Bacteriome: Impact on Health and Disease – Zymo Research

The Real Impact of Rodent Diet on Microbiome and Gut Health Research Webinar Q&A – Taconic


PhD position in microbiology – Uppsala Universitet

Microbiology Technician – Pharmaceutical Industry – Runcorn

QC Microbiology/Environmental Control Associate – Yoh’s client – Phoenix

Human multi-site microbiome

Preprint: Microbial Metagenome Of Urinary Tract Infection – Ahmed Moustafa – bioRxiv

Human skin microbiome

Inhibition of fracture healing in the presence of contamination by Staphylococcus aureus: Effects of growth state and immune response – Krystle A. Blanchette et al. – Journal of Orthopaedic Research

Human gut microbiome

Conditional postnatal deletion of the neonatal murine hepatic circadian gene, Npas2, alters the gut microbiome following restricted feeding – Derek S. O’Neil et al. – American Journal of Obstetrics and Gynecology

Press: Study: Alterations to circadian clock change the body’s response to diet – Amy Wallace – UPI

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome – Daniel E. Almonacid and Laurens Kraal et al. (including our Elisabeth Bik) – PLoS One

Press: uBiome Publishes Peer-Reviewed Scientific Paper in PLOS ONE on First Version of Technology for Gut Health Screening Test – PRWeb

Commentary: The microbiota: an underestimated actor in radiation-induced lesions? – Harry Sokol and Timon Erik Adolph – Gut

Animal microbiome

Bacterial microbiota in small brown planthopper populations with different rice viruses – Shuo Li et al. – Journal of Basic Microbiology

Plant, root and soil microbiome

Small mammal activity alters plant community composition and microbial activity in an old-field ecosystem – Leigh C. Moorhead et al. – Ecosphere

Edaphic Conditions, Aboveground Carbon Stocks and Plant Diversity on Nickel Mine Tailings Dump Vegetated with Senegalia polyacantha (Willd.) Seigler & Ebinger – Edeth Mukaro et al. – Land Degradation & Development

Water and extremophile microbiome

Preprint: 290 Metagenome-assembled Genomes from the Mediterranean Sea: a resource for marine microbiology – Benjamin J Tully et al. – bioRxiv


Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli – Mojtaba Hasanpour and Akram Najafi – Journal of Microbiological Methods

New issue of the Journal of Microbiological Methods

Microbes in the news

Zika fight: Bacteria-laden mosquitoes unleashed in Florida to combat virus – Phil Keating – Fox News

Drought-quenching bacteria the future of farming? – Taylor Hartman – Daily Sun

Officials warn swimmers to avoid bacteria-laden parts of Lake Lanier – Ellen Eldridge – The Atlanta Journal-Constitution

Pathogenic bacteria train their defence in lakes and oceans –

Cross-sector collaboration needed in fight against antimicrobial resistance – Sara Wyant – Agri-Pulse

Microbes on the market

Taconic Biosciences Expands Microbiome Portfolio – P&T Community


Microbiology Career Profiles – Market Specialist at Pacific Biosciences with Melissa Smith, PhD – ASM

April 26, 2017

A series of commentary on the effects of microbiota on vaccines, a fascinating news release about a phage therapy against multi-drug resistant bacterial infection, and can our gut microbes tell us what to eat?

General microbiology

Evaluation of serotypes 5 and 8 capsular polysaccharides in protection against Staphylococcus aureus in murine models of infection – Brian L. Cheng – Human Vaccines & Immunotherapeutics

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? If So, Is There Potential for Efficacious Microbiota-Based Vaccines? – Dan R Littman – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Engaging Our Endogenous Adjuvants – Nicholas Collins1 and Yasmine Belkaid – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Issues of Sovereignty, Federalism, and Points-Testing in the Prokaryotic and Eukaryotic Spaces of the Host-Microbial Superorganism – Andrew J. Macpherson – Cold Spring Harbor Perspectives in Biology

Web alert: Microbial therapeutics – Microbial Biotechnology

Human multi-site microbiome

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015 – Marcus J. Drake – Neurourology and Urodynamics

Human gut microbiome

Doctoral Dissertation: The Effects of the Gut Microbiota on the Host Chromatin Landscape – Nicholas Paul Semenkovich – University of Washington, St. Louis

Tissue adaptation: Implications for gut immunity and tolerance – Ana M.C. Faria – Journal of Experimental Medicine

Animal experiments

Doctoral Dissertation, Mouse: The impact of malnutrition on host-microbe interactions in the intestine – Eric Brown – University of British Columbia

Mouse: Deciphering the mechanism of Huang-Lian-Jie-Du-Decoction on the treatment of sepsis by formula decomposition and metabolomics: enhancement of cholinergic pathways and inhibition of HMGB-1/TLR4/NF-κB signaling – Dingqiao Xu – Pharmacological Research

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats – Jing Chen – PLoS One

Commensal bacteria and essential amino acids control food choice behavior and reproduction – Ricardo Leitão-Gonçalves – PLoS Biology

Press: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh – Scientific American

Press: Are Gut Bacteria Driving Your Cravings? – Shayla Love – Vice

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice – Annadora J. Bruce-Keller – PLoS One

Animal microbiome

Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics – Can Song – Scientific Reports

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

New issue of Microbial Biotechnology is available online.

Plant, root and soil microbiome

Microbial communities associated with plants: learning from nature to apply it in agriculture – Fernando Dini Andreote and Michele de Cássia Pereira e Silva- Current Opinion in Microbiology

Life in earth – the root microbiome to the rescue? – Tim H Mauchline, Jacob G Malone – Current Opinion in Microbiology

Unique rhizosphere micro-characteristics facilitate phytoextraction of multiple metals in soil by the hyperaccumulating plant Sedum alfredii – Dandi Hou – Environmental Science & Technology

Water and extremophile microbiome

Doctoral Dissertation: Microbial community variation in an Arctic shelf seafloor – Tan Thi Nguyen – The Arctic University of Norway

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan – Ramganesh Selvarajan – Molecules

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis – Daniel Kurth – Scientific Reports


VSL#3 probiotic differently influences IEC-6 intestinal epithelial cell status and function – Benedetta Cinque – Journal of Cellular Physiology

Phages and viruses

Press Release: Novel phage therapy saves patient with multidrug-resistant bacterial infection – University of California, San Diego


Preprint: Assessing species biomass contributions in microbial communities via metaproteomics – Manuel Kleiner – bioRxiv

Microbes in the news

Are Probiotics the Answer to Acne? – Kristen Fischer – Healthline News

Are the microbes in our gut affecting how fast we age? – Vincent Maffei – OUPblog

Bacteria May be Reason Some Foods Cause Heart Disease, Stroke – Maggie Fox – NBC News

The Slow-Motion Bacteria Buried Deep in the Ocean’s Floor – Veronique Greenwood – The Atlantic

Bacteria from India’s hot springs could help contain oil spills – Dinesh C Sharma – Firstpost

Bacteria causing diarrhoea deaths in children resists key antibiotic – Syed Akbar – The Times of India

Fat rats, slow sperm, and unhealthy bacteria – Lee Evslin – The Garden Island

April 12, 2017

A pretty broad Digest today, with a promising phylogenetic marker for fungal community studies, a new issue of the Journal of Microbiological Methods, and several news pieces, including one about brain stimulating for weight loss.


Microbiology Technician – Lonza America Inc

BMS Microbiology – South West England

General microbiology

*A new promising phylogenetic marker to study the diversity of fungal communities: the GLYCOSIDE HYDROLASE 63 gene – L. Pérez-Izquierdo – Molecular Ecology Resources

pH-Controlled Cerium Oxide Nanoparticle Inhibition of Both Gram-Positive and Gram-Negative Bacteria Growth – Ece Alpaslan – Scientific Reports

Human oral microbiome

The probiotics in dentistry: a narrative review – A.M. Pujia – European Review for Medical and Pharmacological Sciences

Human ear microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

PrePrint: Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome – Jessica V. Ribado – bioRxiv

Corrigendum: Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific Reports

Seven versus 10 days antibiotic therapy for culture-proven neonatal sepsis: A randomised controlled trial – Smriti Rohatgi – Journal of Paediatrics and Child Health

Animal experiments

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice – Xiaoyu Gao – Applied Microbiology and Biotechnology

Bioactive Molecule from Streptomyces sp Mitigates MDR Klebsiella pneumoniae in Zebrafish Infection Model – Lalitha Cheepurupalli – Frontiers in Microbiology

Animal microbiome

Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing – Mao Li – Scientific Reports

Plant, root and soil microbiome

Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen (Acidovorax citrulli) with Rhizosphere Associated Bacteria – Mahesh Adhikari – The Plant Pathology Journal

Book Chapter: Ecological Restoration Techniques for Management of Degraded, Mined-Out Areas and the Role Played by Rhizospheric Microbial Communities – Prashant Pant & Pratibha Pant – Green Technologies and Environmental Sustainability

Abstract: Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales – Hendershot JN – Ecology

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere – Sadaf Kalam – Journal of Basic Microbiology

Water and extremophile microbiome

Abstract: Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon – P. Behera – Science of the Total Environment

PDF: The Effects of Soil Environmental Factors on the Colonization of Marine Biocontrol Bacteria – Zenghai Bao – Journal of Residuals Science & Technology

Book chapter: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad & Juan M. Gonzalez – Microbial Applications Vol.1

Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance – Weixiong Lin – Ecotoxicology and Environmental Safety

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Microbes in space

Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions – Giorgio Casaburi – Scientific Reports

Phages and viruses

iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus – Songbai Yang – Scientific Reports


Release of a new issue of the Journal of Microbiological Methods, with various technical articles of potential interest.


The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models – Chao Ye – Scientific Reports

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding – Panu Somervuo – Methods in Ecology and Evolution

Microbes in the news

DIRTY PINTS One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly – Sara Kamouni – The Sun

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge – Eleni Rousos – ABC News

*Magnetic brain stimulation causes weight loss – Tim Sandle – Digital Journal

5 Ways to Ruin Wine Before It’s Even Bottled – Laura Burgess – Vine Pair

A public health failure – Otago Daily Times

Study to develop faster detection of antibiotic resistance – Scoop

Microbes on the market

Superbugs receive a dual drug attack – Kate Dearling – The Badger Online

Breast Milk Helps In The Growth Of Microbes Beneficial To Human Colon, Best For Babies Too – Jezreel Smith – The Science Times

March 28, 2017

A brief digest today, but with several interesting news pieces, including one about 3D-printing bacteria and one about ammonia-digesting bacteria in urinals. Also worth reading are the relationship between human papillomavirus, cancers and the impact of land-based pollution on coral reefs and how clean do you think your home is?

General microbiology

Preprint: Primary souring: a novel bacteria-free method for sour beer production – Kara Osburn – bioRxiv

Human gut microbiome

Low FODMAP in 2017: Lessons learned from clinical trials and mechanistic studies – S. Eswaran – Neurogastroenterology and Motility

Animal experiments

Mouse: Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties – Jason D Guss – Journal of Bone and Mineral Research

Water and extremophile microbiome

Review: New insights into a hot environment for early life – Jianhong Dai – Environmental Microbiology Reports

*A Next-Generation Sequencing Approach to Characterize the Impacts of Land-based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs – Christopher Staley – Applied and Environmental Microbiology

Effect of salinity on the microbial community and performance on anaerobic digestion of marine macroalgae – Yi Zhang – Journal of Chemical Technology and Biotechnology

Phages and viruses

*Human papillomavirus in cervical cancer and oropharyngeal cancer: One cause, two diseases – Tara A. Berman and John T. Schiller – Cancer

Microbes in the news

On World Tuberculosis Day, Doctors Warn Of New Drug-Resistant Bacteria – Henry Ridgwell – VOA News
Bad breath: Study find array of bacteria when orcas exhale – Phuong Le – ABC News

*Creating materials in a novel way by 3-D printing bacteria – Bob Yirka –

Mumbai airport goes green: replaces water in urinals with ammonia-breaking bacteria – DNA web team – DNA India

Gonad-chomping bacteria to be unleashed on dengue virus – Anusha Venkat – Asia Times

Gut bacteria new weapon in fight against asthma – Thoracic Society for Australia and New Zealand Annual Scientific Meeting

*The Dirtiest Things In The Home Don’t Include The Toilet – Zye Angiwan – Immortal News

March 14, 2017

A short Digest today, many news pieces, a new bioinformatics tool from the Rob Knight lab, and papers on genome-scale metabolic models.

General microbiology

Pentamidine sensitizes Gram-negative pathogens to antibiotics and overcomes acquired colistin resistance – Jonathan M. Stokes – Nature Microbiology

Press: Antiprotozoal drug, Pentamidine, used with antibiotics effective against ‘superbugs’: McMaster research – Outbreak News Today

Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis – Gang Luo – Environmental Science & Technology

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families – Ana Popovic – Scientific Reports

Animal experiments

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis – Huijuan Jia – Scientific Reports

Animal microbiome

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants – Jon G. Sanders – bioRxiv

Plant, root, and soil microbiome

Book chapter – Chapter 16: Growth Promotion Features of the Maize Microbiome: From an Agriculture Perspective – Ubiana de Cássia Silva – Plant-Microbe Interaction: An Approach to Sustainable Agriculture


Evaluating the Capabilities of Microbial Chemical Production Using Genome-Scale Metabolic Models – Hugh M. Purdy and Jennifer L. Reed – Current Opinion in Systems Biology

Model-based quantification of metabolic interactions from dynamic microbial-community data – Mark Hanemaaijer – PLoS One

Review: Current state and applications of microbial genome-scale metabolic models – Won Jun Kim – Current Opinion in Systems Biology


Deblur: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping – Amnon Amir – mSystems

Deblur: Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns – Amnon Amir – mSystems

Microbes in the news

Common Bacteria May Control Disease-Carrying Insects – Jessica Berman – VOA

Study finds new evidence that viruses and bacteria may be found in some public water supply wells – Home Town Source

Your mobile phone has more germs than a toilet seat, but should you worry? – The News Minute

Mining nature for the next groundbreaking antibiotic – Julia Franz – PRI

February 22, 2017

Here’s your daily routine. Autoregressive and non-autoregressive regimes in the human gut microbiome. The interaction between diet, microbiota and personalized nutrition. More topics to think about: reproducibility in the microbiome studies, intellectual property in the microbiome industry, and heavy rain brings fatal bugs to northern Californian dogs.

Events and jobs

The 3rd Annual Translational Microbiome Conference – April 11-13, 2017 – Boston, MA

Microbiology Laboratory Technician – ALS Life Sciences – Ireland

Field Sales Manager, Microbiology, Molecular Biology, Chemistry – Cromwell and Clark – UK

General microbiology

Vancomycin displays time-dependent eradication of mature Staphylococcus aureus biofilms – Virginia Post – Journal of Orthopaedic Research

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment – James E. Gomez – eLife

Press: Genetic mutations that drive antibiotic resistance in bacteria – Science Daily

Global Proteomic Analyses of Macrophage Response to Mycobacterium tuberculosis Infection – Valerie Poirier – BioRxiv

Human gut microbiome

*Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Human intestinal microbiota: Role in development and functioning of the nervous system – O. V. Averina and V. N. Danilenko – Microbiology

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Review: The Influence of the Microbiome on Early-Life Severe Viral Lower Respiratory Infections and Asthma—Food for Thought? – Jason P. Lynch – Frontiers in Immunology

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Review: “We are what our bacteria eat”: The role of bacteria in personalizing nutrition therapy in gastrointestinal conditions – Ruth Harvie – Journal of Gastroenterology and Hepatology

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLoS One

Animal experiments

Not peer reviewed: Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructooligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Mouse: The influence of rosuvastatin upon the gastrointestinal microbiota and host gene expression profiles – James A. Nolan – American Journal of Physiology – Gastrointestinal and Liver Physiology

High-cholesterol diet does not alter gut microbiota composition in mice – Lidiya G. Dimova – Nutrition & Metabolism

The effect of gut microbiome on tolerance to morphine mediated antinociception in mice – Minho Kang – Scientific Reports

Mouse: Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites – Rongsong Li – Scientific Reports

Editorial: Sources of variation: Animal microbiota – Alexandra A. Mushegian – Science Signaling

The effects of amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses, growth and ampicillin resistance of intestinal coliform bacteria in weaned pigs – Jinhyeon Yun – PLoS One

Animal microbiome

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilised by these intracellular bacteria – Alyce Taylor-Brown – Environmental Microbiology

Corals: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach – Edward G Smith – The ISME Journal

Prevalence of AmpC- and Extended-Spectrum β-Lactamase-Harbouring Enterobacteriaceae in Faecal Flora of a Healthy Domestic Canine Population – D. A. Mathys – Zoonoses and Public Health

Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken – Marcio C. Costa – PLoS One

Plant, root and soil microbiome

A Plant Bacterial Pathogen Manipulates Its Insect Vector’s Energy Metabolism – Nabil Killiny – Applied and Environmental Microbiology

Effective control of root-knot nematode disease with Pseudomonad rhizobacteria filtrate – Ishwar Prakash Sharma and A.K. Sharma – Rhizosphere

Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow region – E. N. Kaparullina – Microbiology

Epiphytic microorganisms degrading aromatic hydrocarbons from the phyllosphere of urban woody plants – O. I. Sazonova – Microbiology

Book chapter: Improving Soil Fertility and Soil Functioning in Cover Cropped Agroecosystems with Symbiotic Microbes – Yang Zhou – Agro-Environmental Sustainability

Book chapter: Role of Phosphate-Solubilising Microorganisms in Sustainable Agricultural Development – Rajesh Kumar and Beenu Shastri – Agro-Environmental Sustainability

Influence of rhinoceros beetle (Trypoxylus dichotomus septentrionalis) larvae and temperature on the soil bacterial community composition under laboratory conditions – Jinu Eo – Soil Biology and Biochemistry

Water and extremophile microbiome

Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India – A. Sharma – Microbiology

Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment – Dong Xu – AMB Express

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens – Jessica Chopyk – Microbiome

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints – Stéphane Greff – Scientific Reports


MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data – Christopher Noune and Caroline Hauxwell – Biology


DNA Barcoding for Fractured Reservoir Analysis – An Initial Investigation – Yuran Zhang – PROCEEDINGS, 42nd Workshop on Geothermal Reservoir Engineering

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR – Claudio Foschi – PLoS One

Microbes in space

The Effect of High-Dose Ionizing Radiation on the Isolated Photobiont of the Astrobiological Model Lichen Circinaria gyrosa – Joachim Meeßen – Astrobiology

Phages and viruses

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats – Pu Han and Michael W. Deem – Journal of the Royal Society Interface

Microbes in the news

Probiotics: IP Perspectives on the Microbiome – Jing Liu and Daniel Yarbrough – JDSupra

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s – Carolyn Gregoire – The Huffington Post

Space Bacteria Draws Focus of Researchers – Robert Lee Hotz – Wall Street Journal (subscription required)

Irish experts key to battling bacteria – Niall Murray – Irish Examiner

Heavy Rains Bring Dog-Killing Bacteria to Northern California – Tex Dwokin – Care2