Category Archives: Animal experiments

January 9, 2016

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Microbiomes of musk deer, Tasmanian Devils, Panamanian frogs, roots of truffle-associated Douglas firs, and the Great Barrier Reef lagoon.

General human microbiome

Editorial: Getting fat from an inflamed relationship? The revenge of the holobiont
Andrew Moore – BioEssays

Perspective: Has provoking microbiota aggression driven the obesity epidemic? – Benoit Chassaing – BioEssays

Pregnancy and birth

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data – Erica Plummer- OMICS Proteomics & Bioinformatics

Review: Infection and preterm birth – Hugh C.G. Nadeau – Seminars in Fetal and Neonatal Medicine

Human gut microbiome

Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects – Radilla-Vázquez R.B. – Obesity Facts

Animal models

The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice – Jinyu Xu – Scientific Reports

Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation – Allison Agus – Scientific Reports

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior – Mark Lyte – PLOS ONE

Effects of BmCPV Infection on Silkworm Bombyx mori Intestinal Bacteria – Zhenli Sun – PLOS ONE

Antibiotic-treated versus germ-free rodents for microbiota transplantation studies – Randi Lundberg – Gut Microbes

Animal microbiome

The musk chemical composition and microbiota of Chinese forest musk deer males
Diyan Li – Scientific Reports

Pasteurellaceae bacteria from the oral cavity of Tasmanian Devils (Sarcophilus Harrisii) show high MIC values towards aminoglycosides and clindamycin – Nicole Gutman – Letters in Applied Microbiology

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis – Eria A Rebollar – The ISME Journal

Plant, root, and soil microbiome

Prokaryotic diversity in biodeteriorated wood coming from the Bükkábrány fossil forest – Katerina Nikolouli – International Biodeterioration & Biodegradation

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia – Alyssa Cornall – Environmental Toxicology and Chemistry

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum) – Gian Maria Niccolò Benucci – Mycorrhiza

Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils – Patrick L. Tomco – Environmental Toxicology and Chemistry

Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months – Daquan Sun – Applied Soil Ecology

Water and extremophile microbiome

Deep Microbial Life in High-Quality Granitic Groundwater from Geochemically and Geographically Distinct Underground Boreholes – Kohei Ino – Environmental Microbiology Reports

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication – Jesse Colangelo-Lillis – Environmental Microbiology Reports

Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community – Richard A. White III – Frontiers in Microbiology

Partitioning of fungal assemblages across different marine habitats – T.C. Jeffries – Environmental Microbiology Reports

Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities – Stéphane Jomini – Environmental Pollution

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions – Hon Lun Wong – MDPI Microorganisms

Microbial genetic diversity in soils along salinealkaline gradients at the coast of Laizhou Bay – Feng Zhao – Protistology

Influence of Zinc on Bacterial Populations and their Proteolytic Enzyme Activities in Freshwater Environments: A Cross-Site Comparison – Lauren Rasmussen – Canadian Journal of Microbiology

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events – Florent E. Angly – Peer J

Food microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Infection microbiology

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh – Shafiqul Alam Sarker – EBioMedicine

Book Chapter: Reducing pathobiomes could slow arms race between man and microbes
S. Romano-Bertrand – Microbiology 5

Bioinformatics and metagenomics

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery – Eric Marinier – BioRxiv

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities – Lisa Oberding – MDPI Microorganisms

Conference abstracts from the 2015 IEEE International Conference onBioinformatics and Biomedicine (BIBM):
Leveraging the k-Nearest Neighbors classification algorithm for Microbial Source Tracking using a bacterial DNA fingerprint library – Jeffrey D McGovern
A computational framework for integrative analysis of large microbial genomics data – Erliang Zeng
Computational challenges in microbiome research – Mihai Pop

Microbes in the news

New Year’s Resolutions for your Microbiome – Anne Estes – Mostly Microbes

West Hartford Children Museum Starts Scientific Discussion Series – Kristin Stoller – Hartford Courant

Balbriggan pair named Young Scientists of the Year: Maria Louise Fufezan and Diana Bura claim first place for research into soil fertility and nematodes – Dick Ahlstrom – The Irish Times

Body’s bacteria don’t outnumber human cells so much after all – Tina Hesman Saey – Science News

Are we really made up of more bacteria than human cells? – Lindsey Kratochwill – Popular Science

P&G granted patent for prebiotic agent-containing composition targeting skin microbiome – Andrew McDougall – Cosmetic Design-Europe.com

Science, publishing, and career

Nobel winner pulls out of Melb conference run by controversial Indian company (OMICS, EB) – Andrew Masterson – The Age

Cheer up, my academic colleagues! We’re so lucky to do this job – Anonymous Academic – The Guardian

Publishers to require ORCID identifiers for authors – EurekAlert

Bik’s Picks

Healthy Diet Helps 183-Year-Old Tortoise Feel Young Again – Jason Bittel – National Geographic

 

January 8, 2016

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Breast milk microbiota profiles, what did the Romans ever do for us, it was only a matter of thyme, and going down the wrong clay.

Pregnancy and birth

Human milk microbiota profiles in relation to birthing method, gestation and infant gender – Camilla Urbaniak – Microbiome

Early Gut Colonization of Preterm Infants: Effect of Enteral Feeding Tubes – Gómez, Marta – Journal of Pediatric Gastroenterology and Nutrition

Review: Role of the Placenta in Preterm Birth: A Review – Terry K. Morgan – American Journal of Perinatology

Human oral microbiome

Long-term efficacy of microbiology-driven periodontal laser-assisted therapy – F. S. Martelli – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human parasites in the Roman World: health consequences of conquering an empire – Piers D. Mitchell – Parasitology

Animal models

Microbiota-induced obesity requires farnesoid X receptor – Ava Parséus – Gut

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome – Scott T. Kelley – PLOS ONE

Animal microbiome

Heterogeneous size datasets of broiler intestinal microbial communities can be analyzed without normalization – I. Aranda-Olmedo – Poultry Science

Plant, root, and soil microbiome

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches
Javier Pascual – PLOS ONE

Image-based modelling of nutrient movement in and around the rhizosphere – Keith R. Daly – Journal of Experimental Botany

Unearthing the Antibacterial Mechanism of Medicinal Clay: A Geochemical Approach to Combating Antibiotic Resistance – Keith D. Morrison – Scientific Reports

Water and waste microbiology

Virome-associated antibiotic-resistance genes in an experimental aquaculture facility – Stefano Colombo – FEMS Microbiology Ecology

Biodiversity patterns of plankton assemblages at the extremes of the Red Sea – J.K. Pearman – FEMS Microbiology Ecology

Food microbiology

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes – Sebastian Liebe – FEMS Microbiology Ecology

Bioinformatics and metagenomics

Antibiotic resistance genes across a wide variety of metagenomes – David Fitzpatrick – FEMS Microbiology Ecology

Microbes in the news

You’re Probably Not Mostly Microbes – Ed Yong – The Atlantic

Scientists discover how blue and green clays kill bacteria – National Science Foundation

Heartburn pills may help grow infection-causing bacteria in gut – Lisa Rapaport – News Daily

Good Bacteria In, Bad Bacteria Out: Biofilms In Water Pipes Filter Dangerous Pathogens Out Of Drinking Water – Lizette Borreli – Medical Daily

The Next Food Fad Is Coming: Feed Your Microbiome – Andrea Hayley, Epoch Times

Enterome Announces Collaboration with Johnson & Johnson Innovation Focused on the Discovery of Novel Targets and Therapeutics for Crohn’s Disease – PR Newswire

From the gut to the eye: commensal microbes as potential triggers of autoimmune uveitis – Atlas of Science

Changes coming with QIIME 2 – Greg Caporaso – Qiime

Science, publishing, and career

DATA CHECK: For female scientists, mixed funding results at U.S. agencies – Jeffrey Mervis – Science
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January 7, 2016

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A new estimate of the ratio microbial:human cells in our bodies, a 5300-year old Helicobacter genome, antibiotics alter bile metabolism, microbiota from 59 bird species, and fecal contamination of Kathmandu drinking water.

Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, which will take place in London, on the 11th and 12th of April, 2016. Early registration closes Jan 15th.

Mysterious Microbes Webinar Series 1 of 3: Microbes and the miracle of compost tea, with Noah Fierer and Ryan Heiland, on Jan 14. Learn how and why microbes are the natural secret to green lawns, lush flowers, and abundant produce

General human microbiome

Revised estimates for the number of human and bacteria cells in the body – Ron Sender – bioRxiv

Review: The human microbiota: the role of microbial communities in health and disease – Luz Elena Botero – Acta Biologica Columbiana

Pregnancy and birth microbiome

A comparative study of bifidobacteria in human babies and adults – Shadi Khonsari – Bioscience of Microbiota, Food and Health

Human oral microbiome

Salivary Antimicrobial Peptides in Early Detection of Periodontitis – Güliz N. Güncü – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

The 5300-year-old Helicobacter pylori genome of the Iceman – Frank Maixner – Science

Microbiome animal and other models

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine – Casey M. Theriot – mSphere

The Gut Microbiota Reduces Colonization of the Mesenteric Lymph Nodes and IL-12-Independent IFN-γ Production During Salmonella Infection – María Fernández-Santoscoy – Frontiers in Cellular and Infection Microbiology

Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health – Lonneke Onrust – Frontiers in Veterinary Science

Animal microbiome

Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology

Plant, root, and soil microbiome

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast –
Melike Balk – Frontiers in Microbiology

Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa – Hanan R. Shehata – Journal of Applied Microbiology

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants – Gerald Otti – Journal of Applied Microbiology

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria  – Max-Bernhard Ballhausen – Frontiers in Microbiology

Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150 – Lihua Li – MDPI Agriculture

Water and waste microbiome

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals – Galina Radeva – Canadian Journal of Microbiology

Master thesis: Evaluation of Two Culture-Independent Methods for Quantification of the Fraction of K-and r-Strategists within Water Microbial Communities – Brandsegg, Hege – Norges teknisk-naturvitenskapelige universitet

Built environment microbiome

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water – Abhilasha Karkey – PLOS Neglected Tropical Diseases

Application of the Environmental Relative Moldiness Index in Finland – Martin Täubel – Applied and Environmental Microbiology

Food microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology

Metagenomics and bioinformatics

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics – Alejandra Escobar-Zepeda – Frontiers in Genetics

Science, publishing, and career

Peer review: tips from field experts for junior reviewers – Sabina Alam – BMC Medicine

Microbes in the news

Gut bacteria from Otzi the Iceman reveals our intimate ties to one microbe – Rachel Feltman – Washington Post

Scientists unearth bacteria from stomach of 5,300-year-old iceman – Carl Zimmer – StatNews

The Famous Ancient “Iceman” Had Ulcer Bacteria In His Gut – Dan Vergano – BuzzFeed

High Stress Environments May Lead To Unhealthy Gut Microbiomes: How To Protect Yourself From The Consequences – Lecia Bushak – Medical Daily

Antibiotics Pave Way for C. Diff Infections – North Carolina State University

Jackson Laboratory Hosted Microbiome Symposium Related to Cancer and Immunology – Lexology

The Bacteria That May Be Causing Your Nasty Cold. “The most common one of them in Mycoplasma Pneumoniae Infection,” Martin explained. – Fox29

Bik’s Picks

A “Pedi” Cures All: Toenail Trimming and the Treatment of Ulcerative Dermatitis in Mice – Sean C. Adams – PLOS ONE
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January 6, 2016

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Microbes on catheters and skin, gastric microbiota and cancer risk, dholes, squirrels, and the brackish Caspian Sea.

Human skin microbiome

Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs – Md Abu Choudhury – PLOS ONE

Human gastric and gut microbiome

Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia – Ines Yang – Scientific Reports

Prebiotic Potential of a Maize-Based Soluble Fibre and Impact of Dose on the Human Gut Microbiota – Adele Costabile – PLOS ONE

HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria – Yang, Liying – AIDS

Review: Epidemiologic studies of the human microbiome and cancer – Emily Vogtmann – British Journal of Cancer

Review: The role of the intestinal microbiota in type 1 diabetes mellitus – Mikael Knip – Nature Reviews Endocrinology

Animal models

Fibrolytic Bacteria Isolated from the Rumen of North American Moose (Alces alces) and Their Use as a Probiotic in Neonatal Lambs – Suzanne L. Ishaq – PLOS ONE

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome – Scott T. Kelley – PLOS ONE

Disparate Metabolic Responses in Mice Fed a High-Fat Diet Supplemented with Maize-Derived Non-Digestible Feruloylated Oligo- and Polysaccharides Are Linked to Changes in the Gut Microbiota – Junyi Yang – PLOS ONE

Animal microbiome

Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels – Mason R. Stothart – Royal Society B

Comparison of the fecal microbiota of dholes high-throughput Illumina sequencing of the V3–V4 region of the 16S rRNA gene – Xiaoyang Wu – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas – Teresita M. Porter – PLOS ONE

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems – Oliver Grunert – Scientific Reports

Review: Arbuscular mycorrhizal fungal communities and root colonisation differ in relation to plant host and soil nutrients – Erla Olsen – Fróðskaparrit (Faroese Scientific Journal)

Review: Plant root-microbe communication in shaping root microbiomes – Andrew Lareen – Plant Molecular Biology

Water microbiome

Genome reconstruction from metagenomic datasets reveals novel microbes in the brackish waters of the Caspian Sea – Maliheh Mehrshad – Applied and Environmental Microbiology

Similarity of structure of taxonomic bacterial communities in the photic layer of Lake Baikal’s three basins differing in spring phytoplankton composition and abundance – I. S. Mikhailov – Doklady Biochemistry and Biophysics

Techniques

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB – Guohong Liu – PLOS ONE

Bioinformatics and metagenomics

The 2016 database issue of Nucleic Acids Research – Daniel J. Rigden – Nucleic Acids Research
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes – Samuel C. Forster
probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016 – Daniel Greuter
The MG-RAST metagenomics database and portal in 2015 – Andreas Wilke

Microbes in the news

Crohn’s Disease Treatments Alter Microbial Makeup – Rachel Lutz – HCP Live

B.C. teens invent ‘smart cutlery’ that scans for bacteria, allergens, nutrition – Emily Chan – CTV News

Skin bacteria help cancer cells grow – EurekAlert

Bacteria Hysteria

Bacteria found inside rare cooked beef burgers in restaurant – Daily Mail

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January 5, 2016

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Bacteria in breastmilk, nose/skin bacteria preventing pneumococcal infection, biofilms on pig carcasses in flowing water, Jurassic microbial mats, and Comammox Nitrospira-like bacteria in drinking water.

Pregnancy and birth

Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants – Kimberly Kozak – Gut Microbes

Review: Association Between the Gut Microbiota and Diet: Fetal Life, Early Childhood, and Further Life – D.A. Kashtanova – Nutrition

Human nose/skin microbiome

Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols – Lindsey Bomar – mBio

Human gut microbiome

A dysbiotic subpopulation of alcohol-dependent subjects – Philippe de Timary – Gut Microbes

Colorectal cancer: role of commensal bacteria and bystander effects – Xingmin Wang – Gut Microbes

Review: Gut inflammation and microbiome in spondyloarthritis – Jayakanthan Kabeerdoss – Rheumatology International

Review: Gut Microbiota and Celiac Disease – Giovanni Marasco – Digestive Diseases and Sciences

Animal models

Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice – Roman Dziarski – PLOS ONE

Plant, root, and soil microbiome

Dynamics of viral abundance and diversity in a Sphagnum-dominated peatland: temporal fluctuations prevail over habitat – Flore C. Ballaud – Frontiers in Microbiology

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession – Miao Wang – Frontiers in Plant Science

Early Jurassic microbial mats – a potential response to reduced biotic activity in the aftermath of the end-Triassic mass extinction event – Olof Peterffy – Palaeogeography, Palaeoclimatology, Palaeoecology

Water and extremophile microbiome

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals – Jennifer M. Lang – Microorganisms

Effect of water chemistry on zooplanktonic and microbial communities across freshwater ecotones in different macrophyte-dominated shallow lakes – Tomasz Mieczan – Journal of Limnology

Influences of microbial communities on groundwater component concentrations during managed artificial recharge – Wenjing Zhang – Environmental Earth Sciences

Complete metagenome sequencing based microbial diversity insights from Deccan basaltic hot spring of Unkeshwar, Maharashtra, India – Gajanan T. Mehetre – Genomics Data

Perspective: Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Built environment and waste microbiome

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System – Ameet J. Pinto – mSphere

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology – Juliana Cardinali-Rezende – Chemosphere

Food microbiology

Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration – E. Sattin – Food Microbiology

Microbes in the news

Outbreaks of Salmonellosis from Small Turtles – Maroya Spalding Walters – Pediatrics

Many of these are amazing because of microbes: 17 of the world’s weirdest water features – Marnie Hunter – CNN

Study details how good bacteria might help prevent middle ear infections and pneumonia – EurekAlert

Study: Bacteria, electrons spin in similar patterns. Bacteria streaming through a lattice behave like electrons in a magnetic material – EurekAlert
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December 31, 2015

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Last post of the year! Wishing you and all microbiomes a great, successful and healthy 2016!

Dead or alive in the sinus microbiome, early life exercise, feather degrading bacteria in the house sparrow, and fungi on public restroom floors.

Pregnancy and birth

Review: The Influence of Early Infant-Feeding Practices on the Intestinal Microbiome and Body Composition in Infants – Aifric O’Sullivan – Nutrition and Metabolic Insights

Human oral microbiome

Review: Advances in the microbial etiology and pathogenesis of early childhood caries –
Evlambia Hajishengallis – Molecular Oral Microbiology

Human respiratory tract microbiome

Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome – A.L. Williams – American Journal of Rhinology & Allergy

Human gut microbiome

Early life exercise may promote lasting brain and metabolic health through gut bacterial metabolites – Agnieszka Mika – Immunology & Cell Biology

Proton pump inhibitors alter the composition of the gut microbiota – Matthew A Jackson – Gut

Metagenomic Analysis Reveals Dynamic Changes of Whole Gut Microbiota in the Acute Phase of Intensive Care Unit Patients – Masahiro Ojima – Digestive Diseases and Sciences

Review: Dietary Emulsifiers, The Human Intestinal Mucus and Microbiome, and Dietary Fiber – Michael J. Glade – Nutrition

Review: Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

Review: Characterizing the Intestinal Microbiome in Infantile Colic. Findings Based on an Integrative Review of the Literature – Nancy E. Dubois – Biological Research For Nursing

Microbiome models

Variability in microbial population and fermentation traits at various sites within the forestomach and along the digestive tract as assessed in goats fed either grass or browse – J.O. Zeitz – Small Ruminant Research

Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis) – Neelam M. Nathani – BMC Genomics

The Effect of Immigration on the Adaptation of Microbial Communities to Warming – Diane Lawrence – The American Naturalist

Animal microbiome

Birds: Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe – Zoë L. Grange – Microbial Ecology

More birds: Feather-degrading bacteria, uropygial gland size and feather quality in House Sparrows Passer domesticus – Attila Fülöp – Ibis

Plant, root, and soil microbiology

The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria – Marjolaine Martin – Frontiers in Microbiology

Characterization of Arbuscular Mycorrhizal Fungus Communities of Aquilaria crassna and Tectona grandis Roots and Soils in Thailand Plantations – Amornrat Chaiyasen – PLOS ONE

Water and extremophile microbiome

Characterization of Halophilic Bacterial Communities in Turda Salt Mine (Romania) – Rahela Carpa – Origins of Life and Evolution of Biospheres

Built environment microbiome

Rapid assemblage of diverse environmental fungal communities on public restroom floors – Jennifer Fouquier – Indoor Air

A simple novel device for air sampling by electrokinetic capture – Julian Gordon – Microbiome

Infection microbiology

Review: The biogeography of polymicrobial infection – Apollo Stacy – Nature Reviews Microbiology

Microbes in the news

Gut Microbiome Influenced by Early-Life Exercise – GenEngNews

Celebrating the good viruses of 2015 – Jason Tetro – Popular Science

End of the year lists

Science: Best long reads of 2015 (part one) – BBC

Science: Best long reads of 2015 (part two) – BBC

Science, publishing, and career

“Women Who Don’t Give a Crap” – Holly Tabor – PLOS Genetics

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December 30, 2015

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Gut microbiomes of birds, mammals, and ray-finned fishes, metabolic pathways in the chicken cecum, fungi in sand dunes, and bacterioplankton in tilapia ponds.

Human gut microbiome

Role of the gut microbiota of children in diarrhea due to the protozoan parasite Entamoeba histolytica – Carol A. Gilchrist – The Journal of Infectious Diseases

Microbiome models

Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses – Darren Ruane – Journal of Experimental Medicine

Role of the Gut Microbiome in Obstructive Sleep Apnea–Induced Hypertension – David J. Durgan – Hypertension

Animal microbiome

Identification of specialists and abundance-occupancy relationships among intestinal bacteria of Aves, Mammalia, and Actinopterygii – Hyatt C. Green – Applied and Environmental Microbiology

Lactic Acid Bacteria Isolated from Bovine Mammary Microbiota: Potential Allies against Bovine Mastitis – Damien S. Bouchard – PLOS ONE

Characterisation of the most important metabolic pathways and biological processes expressed in chicken caecal microbiota – Ondrej Polansky – Applied and Environmental Microbiology

Bacterial Profiling Reveals Novel “Ca. Neoehrlichia”, Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks – Alexander W. Gofton – PLOS ONE

Fickle or Faithful: The Roles of Host and Environmental Context in Determining Symbiont Composition in Two Bathymodioline Mussels – Sven R. Laming – PLOS ONE

Plant, root, and soil microbiome

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis – Alice Roy-Bolduc – Ecology and Evolution

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome – Youry Pii – Plant Physiology and Biochemistry

Water and waste microbiome

Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing – Li Min Fan – World Journal of Microbiology and Biotechnology

Bioremediation of diesel contamination at an underground storage tank site: a spatial analysis of the microbial community – Marco Andreolli – World Journal of Microbiology and Biotechnology

Spatiotemporal variation of planktonic and sediment bacterial assemblages in two plateau freshwater lakes at different trophic status – Yu Dai – Applied Microbiology and Biotechnology

Microbial Ecology

In silico gene-level evolution explains microbial population diversity through differential gene mobility – Bram van Dijk – Genome Biology and Evolution

Microbes in the news

Genome watch: Viral fossils: increased availability of mammalian genomes provides new insights – Astrid Gall – Nature Reviews Microbiology

Drugs for your bugs: targeting the microbial enzymes involved in TMA metabolism – Cláudio Nunes-Alves – Nature Reviews Microbiology

Q&A: Cocktail maker: Tim Lu’s synthetic-biology research at Massachusetts Institute of Technology – Will Tauxe – Nature
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December 29, 2015

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Human respiratory microbiome

Culture-based and culture-independent bacteriologic analysis of cystic fibrosis respiratory specimens – Mona A. Mahboubi – Journal of Clinical Microbiology

Human gut microbiome

Review: Could the Gut Microbiota Reconcile the Oral Bioavailability Conundrum of Traditional Herbs? – Feng Chen – Journal of Ethnopharmacology

Chapter: Antimicrobial Peptides in the Gut – Maureen J. Ostaff – Antimicrobial Peptides

Review: Commensal ‘trail of bread crumbs’ provide pathogens with a map to the intestinal landscape – Deborah H Luzader – Current Opinion in Microbiology

Review: New frontiers in nanotoxicology: Gut microbiota/microbiome-mediated effects of engineered nanomaterials – Antonio Pietroiusti – Toxicology and Applied Pharmacology

Review: Nonalcoholic Fatty Liver Disease and the Gut Microbiome – Jerome Boursier – Clinics in Liver Disease

Review: Beneficial Microbes: The pharmacy in the gut – Daniel M. Linares – Bioengineered

Microbiome models

Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models – Deepak K. Rajpal – PLOS ONE

Animal microbiome

Microbial community of Pacific abalone (Haliotis discus hannai) juveniles during a disease outbreak in South China – Liu-yang Shi – Aquaculture Research

Plant, root, and soil microbiome

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil – O. Roger Anderson – The Journal of Eukaryotic Microbiology

Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China – Weigang Hu – PLOS ONE

Legacy effects of soil moisture on microbial community structure and N2O emissions – Samiran Banerjee – Soil Biology and Biochemistry

Water microbiome

High concentrations of bioavailable heavy metals impact freshwater sediment microbial communities – Caiying Ni – Annals of Microbiology

Techniques

Enhanced sequencing coverage with digital droplet multiple displacement amplification – Angus M. Sidore – Nucleic Acids Research

BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature – Steven J. Tuorto – PLOS ONE

Review: The A, C, G, T of Genome Assembly – Bilal Wajid – BioMed Research International

More Microbiology

Microbiology: A division of labour combined – Marcel M. M. Kuypers – Nature

PhD Thesis: Bacterial Predation in Host Microbiomes – Welsh, Rory M. – Oregon State

Microbes in the news

It’s Hard to Poop on Vacation – Why the holidays are a prime time for traveler’s constipation – Mollie Bloudoff-Indelicato – The Atlantic

Referring to a review based on debatable research: Babies in the Womb Aren’t So Sterile After All – Alice Park – Time

New Studies Suggest Microorganisms in the Womb Set Stage For Childhood and Adulthood Diseases – PR Web

Officials Expand Quarantine In Calif. To Battle Bug That Carries Bacteria Fatal To Citrus Trees – CBS Sacramento

Book reviews: ‘The Diet Myth,’ ‘The Good Gut’ and ‘The Hidden Half of Nature’ – Sonia Shah – The New York Times

http://news.co.cr/bacteria-from-antarctica-could-be-used-in-cancer-treatment/43621/Bacteria from Antarctica Could be Used in Cancer Treatment – Costa Rica Star

Activist Christopher Swain swims in ‘toilet bowl of bacteria’ – Scott Enman – Brooklyn Daily Eagle

Letters: We need a new strategy in the war against bacteria – The Independent
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December 26, 2015

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Gut microbiota of patients with and without abdominal bloating, probiotics to help with academic stress, and a copper gradient near a Canadian mine.

Pregnancy and birth

Review: The microbiome and childhood diseases: Focus on brain-gut axis –
Siobhain M. O’ Mahony – Birth Defects Research Part C: Embryo Today: Reviews

Human respiratory tract microbiome

Microbiological and Molecular Identification of Bacterial Species Isolated from Nasal and Oropharyngeal mucosa of Fuel Workers in Riyadh, Saudi Arabia – Suaad S. AlWakeel – Saudi Journal of Biological Sciences

Human gut microbiome

Molecular Characterization of the Intestinal Microbiota in Patients With and Without Abdominal Bloating – Tamar Ringel-Kulka – American Journal of Physiology

Microbiome models

Choline Diet and Its Gut Microbe–Derived Metabolite, Trimethylamine N-Oxide, Exacerbate Pressure Overload–Induced Heart Failure – Chelsea L. Organ – Circulation: Heart Failure

Bidirectional interactions between indomethacin and the murine intestinal microbiota
Xue Liang

A simple coculture system shows mutualism between anaerobic faecalibacteria and epithelial Caco-2 cells – Mehdi Sadaghian Sadabad – Scientific Reports

Animal microbiome

Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows – Dipti W. Pitta – Anaerobe

Age-Related Shifts in Bacterial Diversity in a Reef Coral – Alex D. Williams – PLOS ONE

Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches – Yislem Beltrán – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity – Martina Köberl – FEMS Microbiology Ecology

Locally adapted arbuscular mycorrhizal fungi improve vigor and resistance to herbivory of native prairie plant species – Elizabeth L. Middleton – Ecosphere

Root Exudation by Aphid Leaf Infestation Recruits Root-associated Paenibacillus spp. to Lead Plant Insect Susceptibility – Bora Kim – Journal of Microbiology and Biotechnology

Effects of the allelochemical coumarin on plants and soil microbial community – E. Niro – Soil Biology and Biochemistry

Water and waste microbiome

Microbiome analysis across a natural copper gradient at a proposed Northern Canadian mine site – Thea Van Rossum – Frontiers in Environmental Science

Evaluation of Community-Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds – Gerald L. Kurten – North American Journal of Aquaculture

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages – David H. Case – mBio

Microbial colonisation and litter decomposition in a Cerrado stream are limited by low dissolved nutrient concentrations – Adriana O. Medeiros – Limnetica

Diversity, community structure, and bioremediation potential of mercury-resistant marine bacteria of estuarine and coastal environments of Odisha, India – Hirak R. Dash – Environmental Science and Pollution Research

Review: Microbial Surface Colonization and Biofilm Development in Marine Environments – Hongyue Dang – Microbiology and Molecular Biology Reviews

Bioinformatics and metagenomics

Effect of k-tuple length on sample-comparison with high-throughput sequencing data – Ying Wang – Biochemical and Biophysical Research Communications

Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses – Hervé Seligmann – Current Opinion in Microbiology

Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data – Rohita Sinha – BMC Genomics

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis – Phelim Bradley – Nature Communications

Proteomics

Review: The challenge of metaproteomic analysis in human samples – Jonathan M Blackburn – Expert Review of Proteomics

Functional foods

Fermented milk containing Lactobacillus casei strain Shirota prevents the onset of physical symptoms in medical students under academic examination stress – A. Kato-Kataoka – Beneficial Microbes

Microbes in the news

Topical Mupirocin Changes Sinus Microbiome – Interview with Tara F. Carr – Medical Research

Is This Snowy Wonderland Or The World Inside A Petri Dish? – Meredith Rizzo – NPR

End of the year lists

From Blood Rain to Green Poo: 10 Weirdest Science Stories of 2015 – Elizabeth Palermo – Live Science

The Altmetric Top 100 Research Papers 2015 – Altmetric
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December 24, 2015

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Merry Christmas! The stream of microbiome research papers never appears to take a break, so I will keep on posting during the holidays. Today I found two nice review papers on the oral microbiome and cystic fibrosis microbiome, an upcoming hands-on workshop on mothur (Microbial Ecology software), the acne microbiome, and bacterial exchange in your washing machine.

Events

Throughout the year, Pat offers 4-5 workshops on mothur and programming in R for microbial ecologists. February mothur workshop by Patrick Schloss, February 8-10, Detroit

General microbiome

Review: Tools for the Microbiome: Nano and Beyond – Julie S. Biteen – ACS Nano

Human skin microbiome

Microorganisms inhabiting follicular contents of facial acne are not only Propionibacterium but also Malassezia spp. – Narifumi Akaza – The Journal of Dermatology

Human oral microbiome

Review: Beyond the oral microbiome – Howard F. Jenkinson – Environmental Microbiology

Prevalence of Candida albicans and Candida dubliniensis in caries-free and caries-active children in relation to the oral microbiota—a clinical study – A. Al-Ahmad – Clinical Oral Investigations

Human respiratory microbiome

Looking beyond respiratory cultures: Microbiome-cytokine signatures of bacterial pneumonia and tracheobronchitis in lung transplant recipients – Jyoti Shankar – American Journal of Transplantation

The Lung Immune Response to Bacteria in Chronic Obstructive Pulmonary Disease – Paul T. King – American Journal of Respiratory and Critical Care Medicine

Review: The Microbiome in Cystic Fibrosis – Yvonne J. Huang – Clinics in Chest Medicine

Human gut microbiome

Not a very novel insight: Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing – Ravi Ranjan – Biochemical and Biophysical Research Communications

Review: The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – Alcohol Research Current Reviews

Review: The First Line of Defense: The Effects of Alcohol on Post-Burn Intestinal Barrier, Immune Cells, and Microbiome – Adam M. Hammer

Microbiome models

Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis – David Berry – Frontiers in Microbiology

The Anti-Oxidant Drug Tempol Promotes Functional Metabolic Changes in the Gut Microbiota – Jingwei Cai – Journal of Proteome Research

Effects of the dietary protein level on the microbial composition and metabolomic profile in the hindgut of the pig – Liping Zhou – Anaerobe

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis – Zhengyu Du – Gut Pathogens

Animal microbiome

The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs – Evelyne Mann – Frontiers in Microbiology

Microbial community of Pacific abalone (Haliotis discus hannai) juveniles during a disease outbreak in South China – Liu-yang Shi – Aquaculture Research

The Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, root, and soil microbiomes

Impact of forest management practices on soil bacterial diversity and consequences for soil processes – Federica Colombo – Soil Biology and Biochemistry

Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology – Mushafau Adewale Akinsanya – Genomics Data

Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA – Shijin Wu – Applied Microbiology and Biotechnology

Copper pollution decreases the resistance of soil microbial community to subsequent dry–rewetting disturbance – Jing Li – Journal of Environmental Sciences

Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA – Chao Liang – Soil Biology and Biochemistry

Water and waste microbiome

Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers – Lorenzo Proia – Environmental Pollution

Biogeochemical importance of the bacterial community in uranium waste deposited at Key Lake, Northern Saskatchewan – VF Bondici – Geomicrobiology Journal

Built environment microbiome

Bacterial Exchange in Household Washing Machines – Chris Callewaert- Frontiers in Microbiology

Survival of Antarctic Cryptoendolithic Fungi in Simulated Martian Conditions On Board the International Space Station – Onofri Silvano – Astrobiology

Darkening on lead-based pigments: Microbiological contribution – Tânia Rosado – Color Research & Application

Microbes in the news

Giant Balls of Bacteria Pile Up on Arctic Lake Beds, Ooze Toxin – Emily Benson – EOS

This Squid Could Help Humans Repel Dangerous Flesh-Eating Bacteria – Esther Inglis-Arkell – Gizmodo

Lackner Investigates Whether Brain Changes Affect Gut Microbiome – University of Buffalo

Science, publishing, and career

2015 London Naturejobs Career Expo: Science communication videos – Julie Gould – Nature Blogs
How to deal with the media
How to get a job
How to deal with articles that misrepresent science
Do you need a PhD?

Korean prosecutors seek jail time for professors in massive plagiarism scheme – Mark Zastrow – Retraction Watch

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