Category Archives: Plant Root Soil microbiome

January 8, 2017

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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

Metabolomics

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

Bioinformatics

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

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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

Transcriptomics

* 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

Biofilms

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 5, 2017

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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

Bioinformatics

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

Metabolomics

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

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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

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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

Fungi

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

Phages

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

Metabolomics

* 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 1, 2017

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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

Metabolomics

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

December 31, 2016

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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

Proteomics

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

December 30, 2016

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Vancomycin treatment preceding fecal transplantation, a diet for IBD, dieting and gut microbiome diversity, halotolerant extremophiles for recycling pollutants, mass spectrometry on medical swabs.

Human vaginal microbiome

Genital injury signatures and microbiome alterations associated with depot medroxyprogesterone acetate usage and intravaginal drying practices – Kenzie D. Birse – The Journal of Infectious Diseases

Human gut microbiome

Oral Vancomycin Followed by Fecal Transplantation Versus Tapering Oral Vancomycin Treatment for Recurrent Clostridium difficile Infection: An Open-Label, Randomized Controlled Trial – Susy S. Hota – Clinical Infectious Diseases

Fecal Fixation: Fecal Microbiota Transplantation for Clostridium difficile Infection – Stuart Johnson – Clinical Infectious Diseases

SCD diet: Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease – David L. Suskind – Journal of Clinical Gastroenterology

Press: Changes With Diet Therapy in Active Inflammatory Bowel Disease – Science Daily

Review: From bugs to brains: The microbiome in neurological health – Kyla A. McKay – Multiple Sclerosis and Related Disorders

Animal experiments

Prior Dietary Practices and Connections to a Human Gut Microbial Metacommunity Alter Responses to Diet Interventions – Nicholas W. Griffin – Cell Host & Microbe

Press: Your Crappy American Diet Might Leave Your Gut Bacteria Stunted – Ryan F. Mandelbaum – Gizmodo
Your microbiota’s previous dining experiences may make new diets less effective – EurekAlert

Intestinal Serotonin Transporter Inhibition by Toll-Like Receptor 2 Activation. A Feedback Modulation – Eva Latorre – PLOS ONE

Press: Gut microorganisms affect our physiology – EurekAlert

Alterations in the gut microbiota can elicit hypertension in rats – Sareema Adnan – Physiological Genomics

Plant, root, and soil microbiome

Impact of plant growth-promoting rhizobacteria on root colonization potential and life cycle of Rhizophagus irregularis following co-entrapment into alginate beads -P. Loján – Journal of Applied Microbiology

Review: Soil Bacteria Alter Plant Physiology to Mitigate Salinity Stress Effects in Glycophytes – Ramalingam Radhakrishnan – Frontiers in Plant Science

Presentation abstract: Soil microbial community structures and activities in relation to nitrogen cycling in two contrasting soils in Malawi – community responses to added carbon – Akane Chiba – International Nitrogen Initiative

Waste and pollution microbiology

Pyrosequencing reveals microbial community dynamics in integrated simultaneous desulfurization and denitrification process at different influent nitrate concentrations
– Chuan Chen – Chemosphere

Microbiological water quality in the medical device industry in Italy – Emilio D’Ugo – Microchemical Journal

Halotolerant extremophile bacteria from the Great Salt Lake for recycling pollutants in microbial fuel cells – Matteo Grattieri – Journal of Power Sciences

Functionality of microbial communities in constructed wetlands used for pesticide remediation: Influence of system design and sampling strategy – Tao Lv – Water Research

Metagenomic Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments as Revealed by Functional Taxonomic Strategies – Arghya Mukherjee – bioRxiv

Food microbiology

Saccharomyces uvarum is Responsible for the Traditional Fermentation of Apple CHICHA in Patagonia – ME Rodríguez – FEMS Yeast Research

Metabolomics

Medical swab analysis using desorption electrospray ionization mass spectrometry (DESI-MS) – a non-invasive approach for mucosal diagnostics – Pamela Pruski – Analytical Chemistry

Coping with inevitable accidents in metabolism – Antoine Danchin – Microbial Biotechnology

Techniques

Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing – Morag Taylor – Journal of Clinical Pathology

Microbes in the news

Short podcast: Academic Minute – Diversifying Your Microbiome. Jack Gilbert details how the sharing of bacteria from person to person could make us healthier in the long run. – Inside Higher Ed

Ancient ‘Eternal Life’ bacteria leaves Russian scientist ‘Illness-Free’ – Harry Walker – Express

Bacteria evolution offers insights into human protein interactions – Brooks Hays – UPI

High school students discover new phages: Genomics research gives youth a leg up on education – Tonya S. Grace – Kentucky New Era

Fermentation expert Sandor Katz on why we shouldn’t fear bacteria – Andrew Sun – SCMP

Novel diet therapy helps children with crohn’s disease and ulcerative colitis reach remission – Science Daily

Prebiotics for your skin: The La Roche-Posay Toleriane Double Repair Moisturizer Could Be the Secret to Better Skin – Sarah Kinonen – Allure

December 29, 2016

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A foundational coral, bacteria in tree hollows, mining and visualizing microbiome data with Calypso, viral metagenomics in aquaculture.

General microbiome

Editorial: You are not alone – M. Ludwig – Acta Physiologica

Human ear microbiome

The Relationship of the Middle Ear Effusion Microbiome to Secretory Mucin Production in Pediatric Patients with Chronic Otitis Media – Krueger, Anna – The Pediatric Infectious Disease Journal

Animal experiments

Improvement of Intestinal Immune Cell Function by Lactic Acid Bacteria for Dairy Products – Tomonori Kamiya – Microorganisms

In poultry: Zeolite food supplementation reduces abundance of enterobacteria – Tanka P. Prasai – Microbiological Research

Animal microbiome

* Effects of predation and nutrient enrichment on the success and microbiome of a foundational coral – Elizabeth C. Shaver – Ecology

By their own devices: invasive Argentine ants have shifted diet without clear aid from symbiotic microbes – Yi Hu – Molecular Ecology

Gut content microbiota of introduced bigheaded carps (Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe – Andrea K. Borsodi – Microbiological Research

Plant, root, and soil microbiome

Ericoid Roots and Mycospheres Govern Plant-Specific Bacterial Communities in Boreal Forest Humus – Sari Timonen – Microbial Ecology

Benzo(a)pyrene degradation and microbial community responses in composted soil – Fengxiao Zhu – Environmental Science and Pollution Research

* Bacteria and Hoverflies (Diptera: Syrphidae) in Tree Hollows From the Iberian Mediterranean Forest – I. R. Sánchez-Galván – Environmental Entomology

Cd immobilization and reduced tissue Cd accumulation of rice (Oryza sativa wuyun-23) in the presence of heavy metal-resistant bacteria – Ya Li – Ecotoxicology and Environmental Safety

Water microbiome

* Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control – Hetron M. Munang’andu – Frontiers in Microbiology

Food microbiology

Microbial Ecology Dynamics in Portuguese Broa Sourdough – João M. Rocha – Journal of Food Quality

Bioinformatics and metagenomics

* Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions – Martha Zakrzewski – Bioinformatics

DACE: A Scalable DP-means Algorithm for Clustering Extremely Large Sequence Data – Linhao Jiang – Bioinformatics

A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases – Xing Chen – Bioinformatics

Measuring the diversity of the human microbiota with targeted next-generation sequencing – Francesca Finotello – Briefings in Bioinformatics

More microbiology

Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation – Robin A. Sorg – PLOS Biology
Microbes in the news

Circadian rhythms and the microbiome – Cosmos Magazine

You Don’t Even Want To Know About Bacteria On The Space Station – Trace Dominguez – Seeker

Rabbits, Bacteria and Calcium – Carl Palazzolo – Long Beach Post

Bacteria evolving more sophisticated antibiotic resistance – Brooks Hays – UPI

December 28, 2016

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Human gut microbiome

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling – Andrew M. Thomas – Frontiers in Cellular and Infection Microbiology

Gastrointestinal neuromuscular apparatus: An underestimated target of gut microbiota – Michele Pier Luca Guarino – World Journal of Gastroenterology

Immune Response of Healthy Adults to the Ingested Probiotic Lactobacillus casei Shirota
– L. S. Harbige – Scandinavian Journal of Immunology

Review: Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine – Alejandra V. Contreras – Frontiers in Physiology

Review: IL-17: overview and role in oral immunity and microbiome – L Abusleme – Oral Diseases

Animal experiments

Bacillus sp. QSI-1 Modulate Quorum Sensing Signals Reduce Aeromonas hydrophila Level and Alter Gut Microbial Community Structure in Fish – Shuxin Zhou – Frontiers in Cellular and Infection Microbiology

Use of Asian selected agricultural byproducts to modulate rumen microbes and fermentation – Yasuo Kobayashi – Journal of Animal Science and Biotechnology

Correlation of Gut Microbiota Composition with Resistance to Experimental Autoimmune Encephalomyelitis in Rats – Suzana Stanisavljević – Frontiers in Microbiology

Comparative Analysis of the Rats’ Gut Microbiota Composition in Animals with Different Ginsenosides Metabolizing Activity – Wei-Wei Dong – Journal of Agricultural Food Chemistry

Animal microbiome

Potential for Nitrogen Fixation in the Fungus-Growing Termite Symbiosis – Panagiotis Sapountzis – Frontiers in Microbiology

Impact and Influence of the Natural Vibrio-Squid Symbiosis in Understanding Bacterial–Animal Interactions – Mark J. Mandel and Anne K. Dunn – Frontiers in Microbiology

Plant, root, and soil microbiome

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification – Yuan Yun – Frontiers in Microbiology

Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs – Xiaofang Wang – Evolution

Review: The Plant as Metaorganism and Research on Next-Generation Systemic Pesticides – Prospects and Challenges – Zisis Vryzas – Frontiers in Microbiology

Extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Outdoor and indoor microbiome

Bacterial characterization in ambient submicron particles during severe haze episodes at Ji’nan, China – Caihong Xu – Science of The Total Environment

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

Waste and pollution microbiome

Effect of the chemical composition of filter media on the microbial community in wastewater biofilms at different temperatures – Iffat Naz – RSC Advances

Phages and viruses

Inferring phage–bacteria infection networks from time-series data – Luis F. Jover – Royal Society Open Science

Microbes in the news

How hospitals, nursing homes keep lethal ‘superbug’ outbreaks secret – Deborah J. Nelson, David Rohde, Benjamin Lesser and Ryan McNeill – Reuters

Causes Of Rheumatoid Arthritis: Gum Disease Bacteria Triggers Joint Inflammation, Latest Research Suggests – Lizette Borreli – Medical Daily

Genome Sequencing Sheds Light On Shigella Outbreaks In California – Saranya Palanisamy – Tech Times

Now, dental implants that kill bacteria and anchor to bone – The Tribune India

Antibiotic resistance just became more complex – EurekAlert

How Germs, Dirt and Hookworms Can Boost Your Health – Ruben Castaneda – US News