January 8, 2017

Human mouth microbiome

Comparison of sputum microbiome of legionellosis-associated patients and other pneumonia patients: indications for polybacterial infections – Hila Mizrahi – Scientific Reports

Human reproductive tract microbiome

Investigation of the microbiota of the reproductive tract in women undergoing a total hysterectomy and bilateral salpingo-oopherectomy – Shana M. Miles – Fertility and Sterility

Human skin microbiome

Review: Performing Skin Microbiome Research: A Method to the Madness – Heidi H. Kong – Journal of Investigative Dermatology

Human gut microbiome

Sleeve gastrectomy drives persistent shifts in the gut microbiome – Cyrus Jahansouz – Surgery for Obesity and Related Diseases

Review: Gut microbiota in vascular disease: Therapeutic target? – Anbazhagan AN – Current Vascular Pharmacology

Review: Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Reviews in Gastroenterology Clinics of North America
Diet and the Microbiome – Nida Murtaza
The Gut Microbiota in Inflammatory Bowel Disease – Donal Sheehan
The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan
Biology of the Microbiome : Interactions with the Host Immune Response – Sylwia Smolinska
Biology of the Microbiome 2: Metabolic Role – Jia V. Li

Animal experiments

Structural and functional alterations in the colonic microbiome of the rat in a model of stress induced irritable bowel syndrome – Nicolaas H Fourie – Gut Microbes

Animal microbiome

Greater Species Richness of Bacterial Skin Symbionts Better Suppresses the Amphibian Fungal Pathogen Batrachochytrium Dendrobatidis – Jonah Piovia-Scott – Microbial Ecology

Plant, root, and soil microbiome

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters – Riegardt M. Johnson – Extremophiles

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere – Adil Essarioui – Microbial Ecology

Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency – Hyunjun Cho – Microbial Ecology

Water and extremophile microbiome

Effect of salinity on mercury methylating benthic microbes and their activities in Great Salt Lake, Utah – Eric S. Boyd – Science of the Total Environment

Waste and pollution microbiology

Low temperature MBBR nitrification: Microbiome analysis – Bradley Young – Water Research

Microbes in space

MELiSSA the minimal biosphere: Human life, waste and refuge in deep space – Jeremy Walker – Future


Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology


An Informative Approach on Differential Abundance Analysis for Time-course Metagenomic Sequencing Data – Dan Luo – Bioinformatics

Microbial ecology

Cheating fosters species co-existence in well-mixed bacterial communities – Anne Leinweber – ISME Journal

Microbes in the news

Life after death: the science of human decomposition – Mo Costandi

Japan’s fantastic emerald green algae. These great balls of fuzz, look lovely, are zero maintenance and keep water clean – James Wong

Cavities Are Contagious: Kissing And 3 Other Ways Harmful Bacteria Spreads And Causes Tooth Decay – Lizette Borreli – Medical Daily

Same bacteria found in Indian River Lagoon killed 10 in Florida in 2016 | Map – Tyler Treadway – TC Palm

Wake up, wipe out: How oxygen can help take down antiobiotic-resistant bacteria – Cordis

Your child’s microbiome, and why its health matters – Jennifer Graham – The Washington Times

January 7, 2017

3D modeling of endometrial interaction with vaginal bacteria, insect symbiont determined by host plants, 2011 tsunami effects on  phytoplankton, virus taxonomy, Microbiome Helper and microRNA sensitivity in intestinal stem cells.

Human vaginal microbiome

Human three-dimensional endometrial epithelial cell model to study host interactions with vaginal bacteria and Neisseria gonorrhoeae – Paweł Łaniewski – Infection and Immunity

Human gut microbiome

Workshop Proceedings: Nutrition Across the Lifespan for Healthy Aging – Proceedings of a Workshop—in Brief – NAS

Review: Gut–brain axis in 2016: Brain–gut–microbiota axis — mood, metabolism and behaviour – Timothy G. Dinan & John F. Cryan – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis – Franziska Faber – PLOS Pathogens

Comparative Analysis of Drosophila melanogaster Gut Microbiota with Respect to Host Strain, Sex, and Age – Gangsik Han – Microbial Ecology

Impact of birth weight and postnatal diet on the gut microbiota of young adult guinea pigs – Kait Al – PeerJ

* Host plant species determines symbiotic bacterial community mediating suppression of plant defenses – Seung Ho Chung – Scientific Reports

Animal microbiome

Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges – Gerald Lackner – PNAS

Plant, root, and soil microbiome

Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria – Jana Klikno – Protoplasma

Diversity and composition of rhizospheric soil and root endogenous bacteria in Panax notoginseng during continuous cropping practices – Yong Tan – Journal of Basic Microbiology

Subsurface Microbial Ecosystems: A Photon Flux and a Metabolic Cascade – Alexander P. Petroff – Journal of Statistical Physics

Water microbiome

* Retrospective analysis of phytoplankton assemblages on the Iwate coast before and after the 2011 tsunami using cryopreserved DNA samples – Yutaka Okumura

Effects of iron deficiency on the growth and photosynthesis of three bloom-forming cyanobacterial species isolated from Lake Taihu – Kui Xu – Phycological Research

Patterns of bacterial diversity in the marine planktonic particulate matter continuum
Mireia Mestre – The ISME Journal

Bioreactor, waste, and pollution microbiology

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant – Applied and Environmental Microbiology

Enhanced methane production via repeated batch bioaugmentation pattern of enriched microbial consortia – Zhiman Yang – Bioresource Technology

Accelerated acidification by inoculation with a microbial consortia in a complex open environment – Jiadong Yu – Bioresource Technology

Effects of a bacterial consortium from acid mine drainage on cadmium phytoextraction and indigenous soil microbial community – Jin-tian Li – Plant and Soil

Can DNA sequencing show differences between microbial communities in Polish and Danish wastewater treatment plants? – A. Miłobędzka – Water Science & Technology

Frequency dependent microbial growth during cycles of feast and famine – Jason Merritt – arXiv

Viruses and phages

* Consensus statement: Virus taxonomy in the age of metagenomics – Peter Simmonds – Nature Reviews Microbiology

Genomic evolution of bacterial populations under coselection by antibiotics and phage
– Johannes Cairns – Molecular Ecology

Bioinformatics and metagenomics

* Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research – André M. Comeau – mSystems


Functional transcriptomics in diverse intestinal epithelial cell types reveals robust microRNA sensitivity in intestinal stem cells to microbial status – Bailey C.E. Peck – Journal of Biological Chemistry


Tackling Fungal Resistance by Biofilm Inhibitors – Shanchao Wu – Journal of Medical Chemistry

Microbes in the news

Featuring our research: The Secret Lives of Marine Mammal Microbes – Probing the mystery of what goes on inside the guts of dolphins and whales – Emma Hiolski – Scientific American

That cold you have might actually be the worst Bay Area flu outbreak in a decade – Kristin Hanes – SF Gate

Microbiomes in far-flung places: characterizing the arctic Inuit gut microbiome – Stephen Ornes – ASM

Microbes on the market

MoBio’s Microbiome News is back!

OptiBiotix Release: Microbiome Technology Powers The Healthy Weight Loss Company Expansion – BioSpace

Bik’s Non-Microbiology Picks

The crack in this Antarctic ice shelf just grew by 11 miles. A dramatic break could be imminent – Chris Mooney – Washington Post

Citizen Science: It’s that time of year: the annual bird count – Shawn Price – Los Angeles Times

January 6, 2017

The second Bay Area Microbiome Meetup, urban finches have more feather-damaging bacteria than rural birdies, metagenomic analysis of children with IBD, airborne fungi in a hospital.

Second San Francisco Bay Area Microbiome Meetup @Illumina. January 31, 2017, San Francisco. Theme: Tools & Techniques. Sign up for this free event.

Pregnancy and early life microbiome

Letter: Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome – Martin Gotteland – The American Journal of Clinical Nutrition

Human eye microbiome

Review: Gut microbiota as a source of a surrogate antigen that triggers autoimmunity in an immune privileged site – Carlos R Zárate-Bladés – Gut Microbes

Human respiratory microbiome

Eosinophilic airway inflammation in asthma is associated with an altered airway microbiome – Asger Sverrild- Journal of Allergy and Clinical Immunology

Anaerobic Bacteriological Microbiota in Surface and Core of Tonsils in Chronic Tonsillitis – Meera Niranjan Khadilkar – Journal of Clinical and Diagnostic Research

Human urinary tract microbiome

Review: Microbiota in 2016: Associating infection and incontinence with the female urinary microbiota – Linda Brubaker – Nature Reviews Urology

Human gut microbiome

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition – a metagenomic analysis – Rebecca Luise Knoll – American Journal of Physiology – Gastrointestinal and Liver Physiology

Irritable Bowel Syndrome-Like Symptoms Following Fecal Microbiota Transplantation: A Possible Donor-Dependent Complication – Bianca W Chang – American Journal of Gastroenterology

Review: The potential impact of gut microbiota on your health: Current status and future challenges – Stitaya Sirisinha – Asian Pacific Journal of Allergy and Immunology

Review: Gut microbiome, surgical complications and probiotics – George Stavrou – Annals of Gastroenterology

Review: Perceptions of fecal microbiota transplantation for Clostridium difficile infection: factors that predict acceptance – Leslie Park – Annals of Gastroenterology

Review: Analysis of Gut Microbiota – an ever changing landscape – Michael J. Sadowsky – Gut Microbes

Animal experiments

GAS6 is a key homeostatic immunological regulator of host–commensal interactions in the oral mucosa – Maria Nassar – PNAS

Bacteria isolated from lung modulate asthma susceptibility in mice – Aude Remot – The ISME Journal

Epimural bacterial community structure in the rumen of Holstein cows with different responses to a long-term subacute ruminal acidosis diet challenge – S.U. Wetzels – Journal of Dairy Science

Effect of faecal microbiota transplantation on mouse gut colonization with carbapenemase-producing Escherichia coli – R. Mahieu – Journal of Antimicrobial Chemotherapy

Changes in Intestinal Motility and Gut Microbiota Composition in a Rat Stress Model
Murakami T – Digestion

Animal microbiome

* House finches: Plumage micro-organisms and preen gland size in an urbanizing context – Mathieu Giraudeau – Science of The Total Environment

Impacts of canine distemper virus infection on the giant panda population from the perspective of gut microbiota – Na Zhao – Scientific Reports

From Seoul Zoo: Comparison of fecal microbiota of three captive carnivore species inhabiting Korea – Choa AN – Journal of Veterinary Medical Science

Yeast: An Overlooked Component of Bactrocera tryoni (Diptera: Tephritidae) Larval Gut Microbiota – Ania T. Deutscher – Journal of Economic Entomology

Symbiotic bacterial communities in ants are modified by invasion pathway bottlenecks and alter host behavior – Philip J. Lester – Ecology

Plant, root, and soil microbiome

Microbial Response to Soil Liming of Damaged Ecosystems Revealed by Pyrosequencing and Phospholipid Fatty Acid Analyses – Ramya Narendrula-Kotha – PLOS ONE

Microbial taxa and functional genes shift in degraded soil with bacterial wilt – Hongchun Zhang – Scientific Reports

Review: Can plant microbiome studies lead to effective biocontrol of plant diseases? – Jeffrey Ellis – Molecular Plant-Microbe Interactions

Water and extremophile microbiome

Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents – Sayaka Mino – ISME Journal

Earth analogues for past and future life on Mars: isolation of perchlorate resistant halophiles from Big Soda Lake – Toshitaka Matsubara – International Journal of Astrobiology

Bacterial growth tolerance to concentrations of chlorate and perchlorate salts relevant to Mars – Amer F. Al Soudi – International Journal of Astrobiology

Built environment microbiome

High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis – Xunliang Tong – Scientific Reports

Food microbiology

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes – A Gomba – Journal of Applied Microbiology

Waste and pollution microbiology

Heavy metal bioleaching and sludge stabilization in a single stage reactor using indigenous acidophilic heterotrophs – Akanksha Mehrotra – Environmental Technology

Integrated Anaerobic-Aerobic Biodegradation of Multiple Contaminants Including Chlorinated Ethylenes, Benzene, Toluene, and Dichloromethane – Miho Yoshikawa – Water, Air, & Soil Pollution

Arsenic resistance genes of As-resistant purple nonsulfur bacteria isolated from As-contaminated sites for bioremediation application – Phitthaya Nookongbut – Journal of Basic Microbiology

Metagenomics and bioinformatics

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics – Léa Siegwald – PLOS ONE

Negative binomial mixed models for analyzing microbiome count data – Xinyan Zhang – BMC Bioinformatics


Impact of Glycosidic Bond Configuration on Short Chain Fatty Acid Production from Model Fermentable Carbohydrates by the Human Gut Microbiota – Hannah C. Harris – Nutrients

The Fumarate Reductase of Bacteroides thetaiotaomicron, unlike That of Escherichia coli, Is Configured so that It Does Not Generate Reactive Oxygen Species – Zheng Lu – mBio

Microbial ecology

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community – Aisling J. Daly – Chaos

Review: Multispecies Swarms of Social Microorganisms as Moving Ecosystems – Eshel Ben-Jacob – Trends in Microbiology

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems – Sergei Maslov – Scientific Reports

Prebiotics and probiotics

Extensively hydrolysed casein formula containing L. rhamnosus GG reduces the occurrence of other allergic manifestations in children with cow’s milk allergy: 3-year randomized controlled trial – Roberto Berni Canani – Journal of Allergy and Clinical Immunology


Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes – Tatsuhiko Hoshino – PLOS ONE

Microbes in the news

Roadkill Animals Are Surprising Sources of Drug Discovery – Jamie Durrani – Scientific American

Inspecting the genomic link between Archaea and Eukaryota – Tom O. Delmont – Meren Lab

Mealworms’ gut bacteria possible plastic pollution reduction solution, specialist says – Olivier Rey – ReddirtReport

‘The Doctors’ star talks about good gut bacteria – Alyssa Harvey – BG Daily News
How the brain helps the body fight bacteria – Jesmond Dalli – The Conversation

Will the Bacteria Wear Hardhats? – Charles Osgood – The Osgood File

Indigestion pills taken by millions of Britons could triple stomach bug risk by reducing acid that help fight off the bacteria – Victoria Allen – Daily Mail

Book review: Microbe, 2nd edition (2016) – ASM Science

Bacteria Hysteria

Killer bacteria, drugs and even white rhino DNA: Researchers reveal dollar bills have up to 3,000 different types of organism on them – Daily Mail

Microbes on the market

uBiome Appoints Boston Children’s Hospital Genomics Expert, Dr. Olaf Bodamer, to its Advisory Board – Benzinga

uBiome Review: What Does Your Gut Have to Say About You? – Sally Jones – Exploring Life’s Mysteries

French Microbiome Biotech enters its First Clinical Trial – Labiotech

CosmosID Launches Metagenomic and Antibiotic Resistance Application in Thermo Fisher Cloud – Benzinga

AOBiome Partners with iCarbonX and Secures $30 Million Investment for Drug Development – PR Newswire

January 5, 2017

Microbiome of Inuit, centenarians, microbes showing differential expression when they are grown with sound, taxonomy of prokaryotic viruses.

Human gut microbiome

Gut Microbiome of the Canadian Arctic Inuit – Catherine Girard – mSphere

The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile – Biagi Elena – Mechanisms of Ageing and Development

Review: Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota – Jun Xu – Medicinal Research Reviews

Editorial: The microbiome as a source of new enterprises and job creation: Considering clinical faecal and synthetic microbiome transplants and therapeutic regulation – Daniel van der Lelie – Microbial Biotechnology

Animal experiments

Effect of dietary kefir on the growth performance, feed utilization and fatty acid profile of juvenile rainbow trout, Oncorhynchus mykiss – E. Gümüş – Aquaculture Nutrition

Plant, root, and soil microbiome

The Pseudomonas putida T6SS is a plant warden against phytopathogens – Patricia Bernal – The ISME Journal

Mycorrhizal Colonization Status and Rhizosphere Soil Properties of BCSIR Reserve Forest Rajshahi, Bangladesh – M. Halder – Current World Environment

Waste and pollution microbiology

Batch and continuous removal of heavy metals from industrial effluents using microbial consortia – F. Migahed – International Journal of Environmental Science and Technology

Musical microbes

Frequency-dependent response of Chromobacterium violaceum to sonic stimulation, and altered gene expression associated with enhanced violacein production at 300 Hz – Chinmayi Joshi – bioRxiv


Book: Molecular Data Analysis Using R – Csaba Ortutay

Viruses and phages

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee – Evelien M. Adriaenssens – Archives of Virology


Optimal allocation of metabolic functions among organisms in a microbial ecosystem – Qi Zhao – Decision and Control (CDC), 2016 IEEE 55th Conference on

Microbes in the news

CDC keeps secret its mishaps with deadly germs: CDC blacked-out information from lab incident reports – Alison Young – USA Today

Single fecal transplant no more effective than standard of care in treating C. diff – MedicalXpress

Alaska gulls are picking up antibiotic-resistant bacteria that could infect humans – Yereth Rosen – ADN

Man-made lake near Linganore drained to kill toxic pink bacteria: pink-colored cyanobacterium releases a toxin – Samantha Hogan – The Frederick News Post

Bacteria Hysteria

Dirty Money. The public health case for a cashless society – Dina Fine Maron – Scientific American
The Money in Your Wallet Might Be Covered With Poop, Mold, and Cocaine – Brad
– Money
The 5 Dirtiest Things You Touch Every Day – Markham Heid – Time

Microbes in the market

Israeli Gut Microbiome Startup Lands Mayo Clinic Venture Backing – TwinCities Business

Ritter Pharmaceuticals Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published in Proceedings of the National Academy of Sciences – Yahoo

Cambridge BioMarketing Announces Five Predictions for 2017 – Yahoo

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business – PR Newswire

Science integrity

Bavarian court sentences me to prison if I dare repeat unwelcome facts of Walles’ trachea transplants – Leonid Schneider – For Better Science


January 4, 2017

Short-chain sugars and lactose intolerance, NEC and bile salts, gut microbiome in women with Polycystic Ovary Syndrome, Brucella in frogs. And since this is a quiet time on the microbiome literature front,  I also included some other interesting microbes in the news.

Pregnancy and early life

Fecal Bile Salts and the Development of Necrotizing Enterocolitis in Preterm Infants – Christian V. Hulzebos – PLOS ONE

Human respiratory microbiome

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation – Linh Do Ngoc Nguyen – PLOS ONE

Human gut microbiome

Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals – M. Andrea Azcarate-Peril – PNAS

Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study – Lisa Lindheim – PLOS ONE

Review: Modulation of alloimmune response by commensal gut microbiota and potential new avenues to influence the outcome of allogeneic transplantation by modification of the ‘gut culture’ – S. Kanangat – International Journal of Immunogenetics

Editorial: Gut Microbiota, Diet and Health. (We and our gut microbes) – Juan Carlos Espín – Molecular Nutrition & Food Research

Editorial: Hot Topics in 2017 – Gut Microbiota, Whole Grains and Health – Hans-Ulrich Humpf – Molecular Nutrition & Food Research

Microbiology of nearly sterile sites

Pseudomonas aeruginosa Microcolonies in Coronary Thrombi from Patients with ST-Segment Elevation Myocardial Infarction – Gorm Mørk Hansen – PLOS ONE

Animal microbiome

The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs – Holger C. Scholz – PLOS ONE

Synbiotics for Broiler Chickens—In Vitro Design and Evaluation of the Influence on Host and Selected Microbiota Populations following In Ovo Delivery – Aleksandra Dunislawska – PLOS ONE

Plant, root, and soil microbiome

Frontiers for research on the ecology of plant-pathogenic bacteria: fundamentals for sustainability. Challenges in Bacterial Molecular Plant Pathology – Cindy E. Morris – Molecular Plant Pathology

Water and extremophile microbiome

Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment – Christophe Leboulanger – PLOS ONE

Food microbiology

Crystal Ball: Exciting strain-level resolution studies of the food microbiome – Danilo Ercolini – Microbial Biotechnology

Viruses / phages / bioinformatics / metagenomics

Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data – Guillaume Carissimo – PLOS ONE

Microbial Ecology

Effects of Spatial Localization on Microbial Consortia Growth – Michael Venters – PLOS ONE

More microbiology / Microbes in the news

RelA Mutant Enterococcus faecium with Multiantibiotic Tolerance Arising in an Immunocompromised Host– Erin S. Honsa – mBio

Inhibition of CRISPR-Cas9 with Bacteriophage Proteins – Benjamin J. Rauch – Cell

50 Years of Journal of Virology: Classic Spotlight, 1969 and 1970: Articles of Significant Interest Selected from the Journal of Virology Archives by the Editors – Journal of Virology

Research Highlight: Building a bacterial ribosome – Ashley York – Nature Reviews Microbiology

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria – Nancy L. Burritt – PLOS ONE

Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian clock – Anna M Puszynska – bioRxiv

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Bisphenol-A Linked to Endocrine Disorders in Pets, Humans – CBS Local

Microbes on the market

Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Clive Cookson – Financial Times

Marina Biotech Granted European Claims Covering Bacteria Mediated Gene Silencing – Market Wired

A Bright Future for Bacteria – Betsy Davis – Pharma Elsevier

Synthetic Biologics to Present at the Biotech Showcase™ 2017 Conference – PR Newswire

Bacteria Hysteria

The Bacteria We’ve Got to Beat: Nasty germs lurk on cell phones, doorknobs, ketchup bottles — here’s how to fight ’em this flu season – Carleen Wild – Lifezette

January 3, 2017

Denture microbiome, insulin resistance and appendix microbiome in obesity, raw milk microbiome, subtropical forest soils, biofilms in drinking water systems, metabolomics of a Mediterranean diet, cell shape and biofilms.

Human oral microbiome

The Denture-Associated Oral Microbiome in Health and Stomatitis – Baochen Shi – mSphere

Commentary: A novel strategy for diagnosing viral versus bacterial infection: implications for oral diseases – Nataly Kravchenko-Balasha – Oral Diseases

Human gut microbiome

*  Insulin resistance is associated with specific gut microbiota in appendix samples from
morbidly obese patients – Isabel Moreno-Indias – American Journal of Translational Research

Microbiology of nearly sterile sites

Improving molecular diagnosis of neonatal septicaemia: Comparative evaluation of different protocols for extraction of bacterial and fungal DNA from blood samples – Gargi Dangre-Mudey – International Journal of Current Research in Medical Sciences

Animal microbiome

Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study – Conor J. Doyle – Applied and Environmental Microbiology

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula – Maren Ziegler – Journal of Biogeography

Plant, root, and soil microbiome

Colonization and community structure of arbuscular mycorrhizal fungi in maize roots at different depths in the soil profile respond differently to phosphorus inputs on a long-term experimental site – Chao Wang – Mycorrhiza

Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest – Merlin Sheldrake – New Phytologist

Modeling of mineral nutrient uptake of spruce tree roots as affected by the ion dynamics in the rhizosphere: Upscaling of model results to field plot scale – H. Nietfeld – Ecological Modelling

Competition between rhizobia under different environmental conditions affects the nodulation of a legume – Zhao Jun Ji – Systematic and Applied Microbiology


Altered precipitation seasonality impacts the dominant fungal but rare bacterial taxa in subtropical forest soils – Qian Zhao – Biology and Fertility of Soils

Cultivable bacterial communities associated with roots of rose-scented geranium (Pelargonium graveolens) with the potential to contribute to plant growth – Thais Freitas da Silva – Applied Soil Ecology

Isolation of Soil and Endophytic Fungi from Rice (Oryza sativa L.) – Thianrat Leewijit – Journal of Agricultural Technology

Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition – A. Blaud – Advances in Agronomy

Book chapter: The Significance of Plant-Associated Microbial Rhizosphere for the Degradation of Xenobiotic Compounds – Durgesh Kumar Jaiswal – Plant Responses to Xenobiotics

Review: Plant Communication With Associated Microbiota in the Spermosphere, Rhizosphere and Phyllosphere – P. Lemanceau – Advances in Botanical Research

Review: Plant growth promoting Rhizobacteria: Biocontrol potential for pathogens – Roomina Mazhar – Pure Appl Biol

Water and extremophile microbiome

* Spatial and temporal analogies in microbial communities in natural drinking water biofilms – I. Douterelo – Science of The Total Environment

Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments – Rituja Saxena – Frontiers in Microbiology

Response of the microbial community to bioturbation by benthic macrofauna on intertidal flats – Hui Shen – Journal of Experimental Marine Biology and Ecology

Review: Biotechnological Applications of Marine Enzymes From Algae, Bacteria, Fungi, and Sponges – S. Parte – Advances in Food and Nutrition Research

Waste and pollution microbiology

Inhibitory effects of sodium azide on microbial growth in experimental resuspension of marine sediment – Cabrol Léa – Journal of Microbiological Methods

Effect of various chemical oxidation agents on soil microbial communities – Eva Kakosová – Chemical Engineering Journal

Shifts in microbial community structure and function in surface waters impacted by unconventional oil and gas wastewater revealed by metagenomics – N.L. Fahrenfeld – Science of the Total Environment

Changes in the microbial community during bioremediation of gasoline-contaminated soil – Aline Jaime Leal – Brazilian Journal of Microbiology

Performance and microbial communities of completely autotrophic denitrification in a bioelectrochemically-assisted constructed wetland system for nitrate removal – Dan Xu – Bioresource Technology

Screening selectively harnessed environmental microbial communities for biodegradation of polycyclic aromatic hydrocarbons in moving bed biofilm reactors – Marc A. Demeter – Bioresource Technology

Review: Resource recovery from wastewater by biological technologies: opportunities, challenges and prospects – Daniel Puyol – Frontiers in Microbiology


A Review of the Ubiquity of Ascomycetes Filamentous Fungi in Relation to Their Economic and Medical Importance – Mary Augustina Egbuta – Advances in Microbiology


Editorial: Filamentous Bacteriophage in Bio/Nano/Technology, Bacterial Pathogenesis and Ecology – Jasna Rakonjac – Frontiers in Microbiology


Adherence to a Mediterranean diet influences the fecal metabolic profile of microbial-derived phenolics in a Spanish cohort of middle-age and older people – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemistry

MASTR-MS: a web-based collaborative laboratory information management system (LIMS) for metabolomics – Adam Hunter – Metabolomics

More microbiology

* Cell morphology drives spatial patterning in microbial communities – William P. J. Smith – PNAS

Microbes in the news

A Gut Makeover for the New Year – Roni Caryn Rabin – The New York Times

Keys plan field trial for bacteria-infected mosquitoes – Associated Press

Salmonella bacteria threatens Mudumalai: cattle and elephants died – Times of India

How your gut’s circadian rhythm affects your whole body – Richard G. “Bugs” Stevens – The Conversation

Eat Dirt… It’s Good For You (So Are Worms) – Tanya Mead – The Alternative Daily

January 2, 2017

A short Microbiome Digest today. Because of the winter break there are not many new papers. Enjoy the quiet times as long as they last!

Animal microbiome

Comparative analysis of the gut microbiota of black bears in China using high-throughput sequencing – Can Song – Molecular Genetics and Genomics

Food microbiology

Microbial Quality, Safety, and Pathogen Detection by Using Quantitative PCR of Raw Salad Vegetables Sold in Dhanbad City, India – Sujeet K. Mritunjay – Journal of Food Production

Microbes in the news

A year of microbes – Jennifer – The Microbial Menagerie

Bacteria strain named by Clemson students – Nancy Spitier – Clemson World

Science meets fiction: the microbiome and super powers – Srimathy Sriskantharajah – Bug Bitten

Forget the normal new year resolutions: think microbiome instead – David Dodwell – South China Morning Post

Researchers Say Gut Microbiota Affects Our Physiology – Sci-News

Boulder City bighorn herd still ailing as ‘insidious’ bacteria spreads – Henry Brean – Review Journal


January 1, 2017

Happy New Year, everyone! May 2017 be good for you and your microbes!

Multiple human site microbiome

Disruption of the microbiota across multiple body sites in critically ill children – Matthew B. Rogers – Microbiome

Pregnancy and early life

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease – Christopher J. Stewart – Microbiome

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants – Katherine E. Gregory – Microbiome

The developing hypopharyngeal microbiota in early life – Martin Steen Mortensen – Microbiome

Review: Maternal health and the placental microbiome – Elise Pelzer – Placenta

Human respiratory microbiome

Study of the Lung Microbiome. Have We Reached the End of the Beginning? – Alison Morris – American Journal of the Respiratory and Critical Care Medicine

Human urinary tract microbiome

Review: Impact of polymicrobial biofilms in catheter-associated urinary tract infections – Andreia S. Azevedo – Critical Reviews in Microbiology

Human gut microbiome

The gut microbiota in conventional and serrated precursors of colorectal cancer – Brandilyn A. Peters – Microbiome

Interaction between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort – Stephanie A. Flowers – Pharmacotherapy

Book chapter: The Role of the Gastrointestinal Microbiota in Visceral Pain – Kieran Rea – Handbook of Experimental Pharmacology

Review: Microbial nutrient niches in the gut – Fátima C. Pereira – Environmental Microbiology

Animal and bioreactor experiments

Autochthonous probiotic Lactobacillus sp. in the diet of bullfrog tadpoles Lithobates catesbeianus improves weight gain, feed conversion and gut microbiota – S.A. Pereira – Aquaculture Nutrition

The effect of pullulan on the growth and acidifying activity of selected stool microflora of human – Anna Chlebowska-Śmigiel – Current Pharmaceutical Biotechnology

Animal microbiome

Effects of diet type, developmental stage, and gut compartment in the gut bacterial communities of two Cerambycidae species (Coleoptera) – Jeong Myeong Kim – Journal of Microbiology

Metagenomic approach to study the bacterial community in clinical and subclinical mastitis in buffalo – Reena J. Patel – Meta Gene

Plant, root, and soil microbiome

Analysis of copper tolerant rhizobacteria from the industrial belt of Gujarat, western India for plant growth promotion in metal polluted agriculture soils – Murali Sharaff – Ecotoxicology and Environmental Safety

High-Performing Windowfarm Hydroponic System: Transcriptomes of Fresh Produce and Microbial Communities in Response to Beneficial Bacterial Treatment – Seungjon Lee – Molecular Plant-Microbe Interactions

Using soil microbial inoculations to enhance substrate performance on extensive green roofs – Chloe J. Molineux – Science of the Total Environment

Rhizospheric iron and arsenic bacteria affected by water regime: Implications for metalloid uptake by rice – Sarah Zecchin – Soil Biology and Biochemistry


Stability of Cross-Feeding Polymorphisms in Microbial Communities
– Ivana Gudelj – PLOS Computational Biology

Microbes in the news

Rochester using ‘pickle juice’ to reduce nitrogen – Liz Markhlevskaya – Seacoast Online

Bacteria in soil has antidepressant effects – Jessica Damiano – News Day

10 New Year resolutions for your vaginal health – Cosmopolitan

Heart surgery patients warned about possible exposure to bacteria – Tammy Palmer – Local Syracuse

Winners of the “Best Microbiome Papers of 2016”

The voting results are in, and we have a surprising winner. Not a paper I would have predicted to win, but one that definitely had a huge fan base. Thank you all for voting, and all the best wishes for 2017. Happy New Year!

The winner of the “Best Microbiome Paper of 2016” is……

Second place:

Shared third/fourth place:

Fifth place:

Shared 6th-10th place:


December 31, 2016

Human lung microbiome

Study of the Lung Microbiome. Have We Reached the End of the Beginning?  – Alison Morris – American Journal of Respiratory and Critical Care Medicine

Microbes at nearly sterile sites

The Clinical Impact of Rapid, Direct MALDI-ToF Identification of Bacteria from Positive Blood Cultures – Kathryn French – PLOS ONE

Animal experiments

Impacts of resistant starch and wheat bran consumption on enteric inflammation in relation to colonic bacterial community structures and short-chain fatty acid concentrations in mice – Janelle A. Jiminez – Gut Pathogens

Animal microbiome

A Review of Bacterial Interactions With Blow Flies (Diptera: Calliphoridae) of Medical, Veterinary, and Forensic Importance – Jeffery K. Tomberlin – Annals of the Entomological Society of America

Comparative community structure of archaea in rumen of buffaloes and cattle – Shyam S Paul – Journal of the Science of Food and Agriculture

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest – Martin Hartmann – Molecular Ecology

Water and extremophile microbiome

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor – Chang-Hong Liu – Environmental Microbiology

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes – Vittorio Boscaro – Microbial Ecology

Microbial diversity and autotrophic activity in Kamchatka hot springs – Alexander Yu – Extremophiles

Cyanobacterial harmful algal blooms are a biological disturbance to western Lake Erie bacterial communities – Michelle A. Berry – Environmental Microbiology

Built environment microbiome

An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air

Sandpits as a reservoir of potentially pathogenic fungi for children – Anna Wójcik – Ann Agric Environ Med

Food microbiome

Microbiological characterization of vegetables and their rhizosphere soil in Eastern Poland – Teresa Kłapeć – Ann Agric Environ Med


Comparing genome versus proteome-based identification of clinical bacterial isolates
Valentina Galata – Briefings Bioinformatics

Microbes in the news

Now Sixty food poisoning cases ‘from farm’s trendy raw milk’ leads a judge to slap a ban on the business to block them from selling any more – Liz Hull – The Daily Mail

The Changing Face of American Forests. How pollution deposes dominant tree species and releases soil carbon – Nala Rogers – Inside Science

Can Bacteria Help Stop the Spread of Disease? – Infection Control Today

How Do Multidrug-Resistant Bacteria Survive Antibiotics Without Resistance Genes? – Contagion LIve

Easy, crunchy, healthy sauerkraut – Cindy Grace – AJC

Science, publishing, and career

Who Believes in the Storybook Image of the Scientist? – Coosje L. S. Veldkamp – Accountability in Research

What Scientists Think About Scientists – Neuroskeptic – Discover