Category Archives: Animal experiments

January 9, 2017

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Events

Reminder: Microbiome meetup (SF Bay Area) – Tools & Techniques for analysis
by SF Bay Area Microbiome Meetup – January 31, 2016, Illumina, San Francisco. Free.

Human gut microbiome

Water activity does not shape the microbiota in the human colon – Doris Vandeputte – Gut

Review: The thyroid, the eyes and the gut: a possible connection – D. Covelli – Endocrinological Investigation

Review: Role of intestinal microbiota and metabolites on gut homeostasis and human diseases – Lan Lin – BMC Immunology

Review: Gut microbiota and colorectal cancer – R. Gao – European Journal of Clinical Microbiology & Infectious Diseases

Review: How the Gut Affects Bone Metabolism – Marie-Hélène Lafage Proust – Joint Bone Spine

The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut – Julius Z.H. von Martels – Anaerobe

Animal experiments

Replacing corn with sorghum in the diet alters intestinal microbiota without altering chicken performance – N. S. Fagundes – Journal of Animal Physiology and Animal Nutrition

Quantitative analyses of the bacterial microbiota of rearing environment, tilapia and common carp cultured in earthen ponds and inhibitory activity of its lactic acid bacteria on fish spoilage and pathogenic bacteria – Pierre Marie Kaktcham – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado – Ademir Sergio Ferreira de Araujo – Antonie van Leeuwenhoek

Soil microbial communities are shaped by vegetation type and park age in cities under cold climate – Nan Hui – Environmental Microbiology

Water and extremophile microbiome

The effect of coagulants and antiscalants discharged with seawater desalination brines on coastal microbial communities: A laboratory and in situ study from the southeastern Mediterranean – Natalia Belkin – Water Research

DNA metabarcoding reveals that 200 μm size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes – Lemian Liu – Molecular Ecology Resources

Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam – Tatsuya Nakayama –

Waste and pollution research

Microbial community redundancy in anaerobic digestion drives process recovery after salinity exposure – Jo De Vrieze – Water Research

Proteomics

The rumen microbial metaproteome as revealed by SDS-PAGE – Timothy J. Snelling – BMC Microbiology

Microbes in the news

Deadly, Invisible Bacteria Melioidosis Spreads In Top End Monsoon – Cayla Dengate – The Huffington Post

I’m Fasting For Science: Will It Help Tame My Multiple Sclerosis? – Brandie Jefferson – NPR

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 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

December 27, 2016

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Cockatiel microbiome, a hibernating frog, Baltic Sea, a book about starter cultures, microbial divisions of labor.

Human oral/respiratory microbiome

Mycobiome in the Lower Respiratory Tract – a Clinical Perspective – Robert Krause – Frontiers in Microbiology

Review: A Review of Analytical Techniques and Their Application in Disease Diagnosis in Breathomics and Salivaomics Research – David J. Beale – Int J Mol Sci

Human gut microbiome

Impact of Amoxicillin/Clavulanate and Autologous Fecal Microbiota Transplantation (FMT) on the Fecal Microbiome and Resistome – Christopher Bulow – Open Forum Infectious Diseases

Review: The Development of Our Organ of Other Kinds—The Gut Microbiota – Shirong Liu – Frontiers in Microbiology

Review: Food Additives and Contaminants: Effects on Human Gut Microbiota—A Review – Paula Roca-Saavedra – Preprints

Animal experiments

Generation of Germ-Free Ciona intestinalis for Studies of Gut-Microbe Interactions – Brittany A. Leigh – Frontiers in Microbiology

Review: Emerging Sponge Models of Animal-Microbe Symbioses – Lucia Pita – Frontiers in Microbiology

Animal microbiome

Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural – Thijs De Mulder – FEMS Microbiology Ecology

Diversity of the Bacterial Microbiota of Anopheles Mosquitoes from Binh Phuoc Province, Vietnam – Chung T. Ngo – Frontiers in Microbiology

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples – Maozhang He – Frontiers in Microbiology

* Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet – Luis David Alcaraz – PeerJ

* Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation – Francis Cheng-Hsuan Weng – BMC Genomics

Plant, root, and soil microbiome

Long-term effects of aided phytostabilization on microbial communities of metal-contaminated mine soil– Olatz Garaiyurrebaso – FEMS Microbiology Ecology

Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection – Caroline De Tender – Frontiers in Microbiology

Expanding the Repertoire of Carbapenem-Hydrolyzing Metallo-ß-Lactamases by Functional Metagenomic Analysis of Soil Microbiota – Dereje D. Gudeta – Frontiers in Microbiology

High Diversity of Planctomycetes in Soils of Two Lichen-Dominated Sub-Arctic Ecosystems of Northwestern Siberia – Anastasia A. Ivanova – Frontiers in Microbiology

Editorial: Microbiota of Grapes: Positive and Negative Role on Wine Quality – Giuseppe Spano – Frontiers in Microbiology

Aspect has a greater impact on alpine soil bacterial community structure than elevation – Jieyun Wu – FEMS Microbiology Ecology

Water and extremophile microbiome

* Local Environmental Conditions Shape Generalist But Not Specialist Components of Microbial Metacommunities in the Baltic Sea – Markus V. Lindh – Frontiers in Microbiology

A High-Level Fungal Diversity in the Intertidal Sediment of Chinese Seas Presents the Spatial Variation of Community Composition – Wei Li – Frontiers in Microbiology

Viral induced microbial mortality in Arctic hypersaline spring sediments – Jesse Colangelo-Lillis – Frontiers in Microbiology

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study – Yulia A. Frank – Frontiers in Microbiology

Marine Subsurface Microbial Community Shifts Across a Hydrothermal Gradient in Okinawa Trough Sediments – Leah D. Brandt – Archaea

Waste and pollution microbiology

Temporal dynamics of microbial communities in microcosms in response to pollutants – Shuo Jiao – Molecular Ecology

Cultural heritage microbiology

Sloth: Survey of the state of conservation of the Mylodon listai (Xenarthra-Mylodontidae) skin fragment from the Pleistocene of Argentina kept at the Museum of La Plata (Argentina) – Daniela Silvana Nitiu – Ge-conservación

Food microbiology

* Book: Starter Cultures in Food Production – Barbara Speranza

Biofilm microbiome

Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes – Athenia L. Oldham – Journal of Industrial Microbiology & Biotechnology

Metagenomics and bioinformatics

Characterization of Uncultured Genome Fragment from Soil Metagenomic Library Exposed Rare Mismatch of Internal Tetranucleotide Frequency – Yunpeng Liu – Frontiers in Microbiology

RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys – Chao Xie – BMC Bioinformatics

More microbiology

Review: Chronic infections with viruses or parasites: breaking bad to make good – Andrew Godkin – Immunology

Biocontrol of Burkholderia cepacia complex bacteria and bacterial phytopathogens by Bdellovibrio bacteriovorus – Damian McNeely – Canadian Journal of Microbiology

Fitness Impact of Obligate Intranuclear Bacterial Symbionts Depends on Host Growth Phase – Chiara Bella – Frontiers in Microbiology

* Review: Understanding Microbial Divisions of Labor – Zheren Zhang – Frontiers in Microbiology

Microbes in the news

How Does a Fatty Acid Protect Pathogenic Bacteria Against Antibiotics? – Nicola M. Parry – Contagion Live

How Microcosms help us understand ecology – James MacDonald – JSTOR Daily

Takuji Yamada – Early cancer intervention with gut bacteria – Tokyo Tech Researchers

How Probiotics Could Help Prevent Atopic Dermatitis – Kenneth Bender – Specialty Pharmacy Times