March 19, 2016

A Month in Mammoth. Two sleep researchers braved the subterranean environment of a Kentucky cave to see if they could train their bodies to abandon the cyclical rhythms of the 24-hour day – The Scientist

Night Night, Flipper – Watch underwater footage of a dolphin sleeping in the wild – The Scientist

Scientists Find That Getting Multiple Tattoos Strengthens Your Immune System – Kelly Tatera – Science Explorer

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March 10, 2016

Posted on March 10, 2016 by eliesbik

Signals within microbial communities, feeding the microbiome with milk, gut metagenomes of Japanese subjects, multiethnic cohorts, biogeography of viruses in the sea, and finding transcription start sites.

General human microbiome

Review: Signaling in Host-Associated Microbial Communities – Michael A. Fischbach and Julia A. Segre – Cell

Review: The microbiome systemic diseases connection – T.A. van der Meulen – Oral Diseases

Review: The human microbiota: novel targets for hospital-acquired infections and antibiotic resistance – Melinda M. Pettigrew – Annals of Epidemiology

Pregnancy and birth

The placental microbiome is altered among subjects with spontaneous preterm birth with and without chorioamnionitis – Amanda L. Prince – American Journal of Obstetrics and Gynecology

It’s in the Milk: Feeding the Microbiome to Promote Infant Growth – Stavros Bashiardes – Cell Metabolism

The Microbiome in Necrotizing Enterocolitis: A Case Report in Twins and Minireview –
Suchitra K. Hourigan – Clinical Therapeutics

Comment: Gut microbiome and necrotising enterocolitis: time for intervention? –
Alessio Fasano – The Lancet

Human oral microbiome

Not sure if I agree with the goal of this paper: Natural Antimicrobials and Oral Microorganisms: A Systematic Review on Herbal Interventions for the Eradication of Multispecies Oral Biofilms – Lamprini Karygianni – Frontiers in Microbiology

Human urinary tract microbiome

The Urinary Microbiome Differs Significantly between Patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as between Patients with Different Clinical Phenotypes – Daniel A Shoskes – Urology

Human gut microbiome

The gut microbiome of healthy Japanese and its microbial and functional uniqueness – Suguru Nishijima – DNA Research

Microbiome Heterogeneity Characterizing Intestinal Tissue and Inflammatory Bowel Disease Phenotype – Tyler, Andrea D. – Inflammatory Bowel Diseases

Perspective: Characterisation and therapeutic manipulation of the gut microbiome in inflammatory bowel disease – J. Schulberg – Internal Medicine Journal

FMT Happens: Regulating Fecal Microbiota Therapy in Canada; What You Need to Know – Shahad Salman – World Medical & Health Policy

Review: Characterization of the Gut Microbiome in Epidemiologic Studies: The Multiethnic Cohort Experience – Benjamin C. Fu – Annals of Epidemiology

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Animal models

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes – Chenhong Zhang – ISME Journal

Review: Viruses in Rodent Colonies: Lessons Learned from Murine Noroviruses – Stephanie M. Karst – Annual Review of Virology

Animal microbiome

Study of the Aminoglycoside Subsistence Phenotype of Bacteria Residing in the Gut of Humans and Zoo Animals – Teresita de J. Bello González – Frontiers in Microbiology

Allows the consumption of toxic cabbage: SaxA-mediated isothiocyanate metabolism in phytopathogenic Pectobacteria – Cornelia U. Welte – Applied and Environmental Microbiology

Comparison of Fecal Microbiota of Mongolian and Thoroughbred Horses by High-Throughput Sequencing of the V4 Region of the 16S rRNA Gen (sic) – Yiping Zhao – Asian Australian Journal of Animal Sciences

Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples – Martin W. Nielsen – Veterinary Microbiology

I really feel for horses who are sick of grass. Abstract: Analysis of the large intestinal and faecal microbiota of horses with grass sickness using denaturing gradient gel electrophoresis – D. Nölkes – Journal of Equine Veterinary Science

Plant, root, and soil microbiome

Phyllosphere Fungal Communities Differentiate More Thoroughly than Bacterial Communities Along an Elevation Gradient – Corinne Vacher – Microbial Ecology

A compositional shift in the soil microbiome induced by tetracycline, sulfamonomethoxine and ciprofloxacin entering a plant-soil system – Hui Lin – Environmental Pollution

Water and extremophile microbiome

Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi – József Geml – FEMS Microbiology Ecology

Review: Biogeography of Viruses in the Sea – Cheryl-Emiliane T. Chow – Annual Review of Virology

DGGE: Oil removal and effects of spilled oil on active microbial communities in close to salt‑saturation brines – Yannick Y. Corsellis – Extremophiles

Bioreactors and waste microbiology

Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures – Haifeng Geng – Microbial Ecology

Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters – Arda Gülay – ISME Journal

Bacterial communities in different locations, seasons and segments of a dairy wastewater treatment system consisting of six segments – Kikue Hirota – Journal of Environmental Sciences

Food microbiology

Resistome diversity in cattle and the environment decreases during beef production – Noelle R Noyes – eLIFE

Inactivation of Salmonella on tainted foods: using blue light to disinfect cucumbers and processed meat products – J. Stephen Guffey – Food Science & Nutrition

Bioinformatics and metagenomics

Review: Recovering complete and draft population genomes from metagenome datasets – Naseer Sangwan – Microbiome

Dissecting phylogenetic fuzzy weighting: theory and application in metacommunity phylogenetics – Leandro D. S. Duarte – Methods in Ecology and Evolution

Transcriptomics

A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome – Laurence Ettwiller – BMC Genomics

Fungi

Perspective: The invisible dimension of fungal diversity – David Hibbett – Science

Microbes in the news

At Stanford: Center launched to explore, exploit human microbiome – Bruce Goldman – Stanford Medicine

Columbia Expands Its Microbiome Research – Christopher Williams – Columbia University Medical Center

UT professor develops technique to enhance desirable traits of plants, animals through microbiology – Maluly Martinez Benavides – The Daily Texan

5th World Summit “Gut Microbiota For Health”: Media Information on Top Issues Ready for Download

Gut bacteria make cabbage poison harmless – Radboud University

Scientists developed a robust method for analysis of intestinal bacteria – Science Codex

Nukadoko: rich in beneficial bacteria: Nukadoko is made by fermenting rice bran, a byproduct of milling brown rice, with lactic acid bacteria and yeast. – Natsuko Tamaki – The Japan News

A mouse’s house may ruin experiments. Environmental factors lie behind many irreproducible rodent experiments – Sara Reardon – Nature

Viral infections may affect respiratory microbiome of patients with CF – Healio

Science, publishing, and career

German Defense Minister to keep doctoral degree – plagiarism found on 44% – Debora Weber-Wulff – Copy, Shake, and Paste

Bik’s Picks

How long can you chew on goat meat? Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans – Katherine D. Zink – Nature

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March 9, 2016

Posted on March 9, 2016 by eliesbik

Two papers on altered microbiome in HIV-infected humans and SIV-infected monkeys, ESBL carriage in hospital wards and medical students, fungus infection affects frog song, and protein recycling in the ocean.

Pregnancy and birth

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study – Barbara B Warner – The Lancet

Human gut microbiome

Editorial: The HIV-Associated Enteric Microbiome Has Gone Viral – Brent E. Palmer – Cell Host & Microbe

Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome – Cynthia L. Monaco – Cell Host & Microbe

Comparison of the faecal colonization rates with extended-spectrum beta-lactamase producing enterobacteria among patients in different wards, outpatients and screened medical students – Fatemeh Ebrahimi – Microbiology and Immunology

Animal models

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination – Scott A. Handley – Cell Host & Microbe

Animal microbiome

Enhanced call effort in Japanese tree frogs infected by amphibian chytrid fungus –
Deuknam An – Biology Letters

Plant, root, and soil microbiome

Diversity and bioactivity of bacterial endophyte community of Cupressaceae – J. Soltani – Forest Pathology

Leaf litter decomposition in remote oceanic island streams is driven by microbes and depends on litter quality and environmental conditions – Verónica Ferreira – Freshwater Biology

Network modules and hubs in plant-root fungal biomes – Hirokazu Toju – Journal of the Royal Society Interface

Water and extremophile microbiome

Diverse, uncultivated bacteria and archaea underlying the cycling of dissolved protein in the ocean – William D Orsi – The ISME Journal

Food microbiology

Detection of pathogenic Escherichia coli and microbiological quality of chilled shrimp sold in street markets – Liliana Jose Barbosa – Letters in Applied Microbiology

More microbiology

Antimicrobial activity of extracts from macroalgae Ulva lactuca against clinically-important Staphylococci is impacted by lunar phase of macroalgae harvest – Amy M. Deveau – Letters in Applied Microbiology

Microbes in the news

Bacteria discovered by scientists in London cuts dependence on commercial fertilizers – John Miner – LFPress

Fungus makes tree frogs sing – Nature

Michigan researchers start $9.2M effort to study bacteria – Click on Detroit

“Nightmare Bacteria” Found in Southern California Sewage Treatment Plants – Alexander Haro – The Inertia

Two Starbucks Items Voluntarily Recalled Due to Bacteria, Allergen Risk – Gillian Mohney – ABC News

Science, publishing, and career

Scientific record: Class uncorrected errors as misconduct – Sophien Kamoun – Nature

A Multi-dimensional Investigation of the Effects of Publication Retraction on Scholarly Impact – Xin Shuai – Arxiv

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Somewhere between March 8 and March 9, 2016

Posted on March 9, 2016 by eliesbik

Human symbionts inject to persist, diet and exercise in mice, a 17-year long experiment, and using peanut butter as a vehicle to deliver probiotics in developing countries.

Human skin microbiome

Proteobacteria from the human skin microbiota: Species-level diversity and hypotheses – C. Cosseau – One Health

Human respiratory microbiome

Clinical metagenomics for the management of hospital- and healthcare-acquired pneumonia – Etienne Ruppé – Future Microbiology

Human gut microbiome

Analysis of Gut Microbiota in Coronary Artery Disease Patients: a Possible Link between Gut Microbiota and Coronary Artery Disease – Takuo Emoto – Journal of Atherosclerosis and Thrombosis

PhD Thesis: Indigenous Australians have a distinctive gut microbial profile compared to Caucasian controls and patients with inflammatory bowel disease – Iyngkaran, Guruparan – Melbourne Medical School

Review: Changes in the Intestinal Microbiome and Alcoholic- and Non-alcoholic Liver Diseases—Causes or Effects? – Naga S. Betrapally – Gastroenterology

Review: Microbiome alterations in HIV infection a review – B Williams – Cellular Microbiology

Review: Extensive Intestinal Resection Triggers Behavioral Adaptation, Intestinal Remodeling and Microbiota Transition in Short Bowel Syndrome – Camille Mayeur – MDPI Microorganisms

Microbiome models

Human symbionts inject and neutralize antibacterial toxins to persist in the gut – Aaron G. Wexler – PNAS

The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice – Sara C. Campbell – PLOS ONE

Chronic Psychological Stress Disrupted the Composition of the Murine Colonic Microbiota and Accelerated a Murine Model of Inflammatory Bowel Disease – Yohei Watanabe – PLOS ONE

Flavanol-Enriched Cocoa Powder Alters the Intestinal Microbiota, Tissue and Fluid Metabolite Profiles, and Intestinal Gene Expression in Pigs – Saebyeol Jang – The Journal of Nutrition

Deletion of the Toll-Like Receptor 5 Gene Per Se Does Not Determine the Gut Microbiome Profile That Induces Metabolic Syndrome: Environment Drumpfs Genotype
Wei Zhang – PLOS ONE

Animal microbiome

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance – Bettina Glasl – ISME Journal

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis – Filip Husnik – BioRxiv

No access for me, but I assume this is in birds: Microbial shifts associated with necrotic enteritis – Gunther Antonissen – Avian Pathology

Plant, root, and soil microbiome
Orchids: Differences in mycorrhizal communities between Epipactis palustris, E. helleborine and its presumed sister species E. neerlandica – Hans Jacquemyn – Annals of Botany

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment – Ben Bond-Lamberty – PLOS ONE

Evaluation of a diagnostic microarray for the detection of major bacterial pathogens of potato from tuber samples – Y. Degefu – EPPO Bulletin

Shifts in symbiotic associations in plants capable of forming multiple root symbioses across a long-term soil chronosequence – Felipe E. Albornoz – Ecology and Evolution

Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China – Bingchang Zhang – Journal of Basic Microbiology

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica – Marc W. Van Goethem – FEMS Microbiology Ecology

Bacterial indicator taxa in soils under different long-term agricultural management – N.G. Jiménez-Bueno – Journal of Applied Microbiology

Water and extremophile microbiome

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge – Huiluo Cao – Scientific Reports

Nutrient treatments alter microbial mat colonization in two glacial meltwater streams from the McMurdo Dry Valleys, Antarctica – Tyler J. Kohler – FEMS Microbiology Ecology

Bioreactor microbiology

Gut microbiota-involved mechanisms in enhancing systemic exposure of ginsenosides by coexisting polysaccharides in ginseng decoction – Shan-Shan Zhou – Scientific Reports

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis
Gang Luo – Biotechnology for Biofuels

Waste and pollution microbiology

Temporal dynamics of biotic and abiotic drivers of litter decomposition – Pablo García-Palacios – Ecology Letters

Microbial Community Structures in Petroleum Contaminated Soils at an Oil Field, Hebei, China – Yizhi Sheng – CLEAN – Soil, Air, Water

Effect of microbial community structure on organic removal and biofouling in membrane adsorption bioreactor used in seawater pretreatment – Sanghyun Jeong – Chemical Engineering Journal

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems – Journal of Environmental Sciences – A.O. Babatunde

Functional foods and food microbiology

For applications in developing countries: Influence of probiotics, included in peanut butter, on the fate of selected Salmonella and Listeria strains under simulated gastrointestinal conditions – Y.A.K. Klu – Journal of Applied Microbiology

Bioinformatics and metagenomics

Read networks and k-laminar graphs – Finn Volkel – ArXiv

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment – Jeongsu Oh – PLOS ONE

Protocol: Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments – Luke K. Ursell – Springer Protocols Handbooks

Regression Analysis for Microbiome Compositional Data – Pixu Shi – ArXiv

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences – Chen Shi-Yi – Journal of Computational Biology

Techniques

Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies – James L. O’Donnell – PLOS ONE

More microbiology

Alice’s living croquet theory – Didier Raoult – International Journal of Antimicrobial Agents

Genomic approaches for understanding dengue: insights from the virus, vector, and host – Shuzhen Sim – Genome Biology

Microbes and infection

Multiplex detection and identification of viral, bacterial, and protozoan pathogens in human blood and plasma using a high-density resequencing pathogen microarray platform – Moussa Kourout – Transfusion

Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages – Rachelle Mariano – mSystems

Microbes in the news

Cutting Board Companions – Katherine Dahlhausen – MicroBEnet @PhDKD

Standard practice of giving premature babies antibiotics needs to be rethought, argues new study – Jessica Firger – Newsweek

Bacterial brawls mark life in the gut’s microbiome – Bill Hathaway – Phys.org

How your microbiome can put you at the scene of the crime – Kai Kupferschmidt – Science

Soy protein may diversify gut microbiota more than dairy protein: Study – Stephen Daniells – Nutraingredients
Sleep Deprivation Caused By Jet Lag And Shift Work Could Be Treated Through Your Gut Microbiome – Cayla Dengate – Huffington Post

U-M Students Analyze Their Own Biological Samples to Study How Microbes Affect Human Health – Infection Control Today

#1 is outdated but rest ok: 10 things you need to know about your gut – Naomi Mead – Netdoctor

The Dannon Company Announces Fourth-Annual Winner of Yogurt and Probiotics Fellowship Grant: Micah Eimerbrink – BusinessWire

Science, publishing, and career

Insights into the PeerJ Preprint: “Gender bias in open source” – PeerJ Blog

Bik’s Picks

I Speak Whale: Vast assembly of vocal marine mammals from diverse species on fish spawning ground – Delin Wang – Nature

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March 8, 2016

Posted on March 8, 2016 by eliesbik

A very special edition of Bik’s Picks on this International Women’s Day: Soil decomposition on Mount Kilimanjaro, genome of a Ruminococcus associated with IBS, survival of microbes during the digestion of cheese.

Human oral microbiome

Editorial: Oral Biofilm Architecture at the Microbial Scale – Maria D. Ferrer – Trends in Microbiology

Human reproductive tract microbiome

Cervical Microbiota Associated with Risk of Higher Grade Cervical Intraepithelial Neoplasia in Women Infected with High-Risk Human Papillomaviruses – Chandrika J Piyathilake – Cancer Prevention Research

Human gut microbiome

Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome – Ulla Hynönen – Anaerobe

Opinion: Gut microbiota impact on stroke outcome: Fad or fact? – Katarzyna Winek – J Cereb Blood Flow Metab

Review: Mechanisms linking the gut microbiome and glucose metabolism – Kristina M Utzschneider – J Clin Endocrinol Metab

Review: Gut Microbiome and Kidney Disease in Pediatrics: Does Connection Exist? – Tetyana L. Vasylyeva – Frontiers in Microbiology

Review: The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes – Mariia Taguer – Clinical Pharmacology & Therapeutics

Review: Obesity and Asthma: Microbiome-metabolome Interactions – Stephanie A Shore – American Journal of Respiratory Cell and Molecular Biology

Animal models

Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens – Melody Y. Zeng – Immunity

Plant, root, and soil microbiome

Methodological Guidelines for Accurate Detection of Viruses in Wild Plant Species – Christelle Lacroix – Applied and Environmental Microbiology

Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis – Iris Bertani – Environmental Microbiology

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil-Associated Bacteria – Sachiko Masuda – Microbes and Environments

Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil? – Minna Männistö – Soil Biology and Biochemistry

Temperature sensitivity and enzymatic mechanisms of soil organic matter decomposition along an altitudinal gradient on Mount Kilimanjaro – Еvgenia Blagodatskaya – Scientific Reports

Influence of pesticide seed treatments on rhizosphere fungal and bacterial communities and leaf fungal endophyte communities in maize and soybean – Rachel Nettles – Applied Soil Ecology

Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum – Isabell von Rein – Global Change Biology

Water and extremophile microbiome

Abundance and Biogeography of Picoprasinophyte Ecotypes and Other Phytoplankton in the Eastern North Pacific Ocean – Melinda P. Simmons – Applied and Environmental Microbiology

Metagenomic 16s rrna investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine – Oleksandra Bobrova – Acta Biochimica Polonica

Waste and pollution microbiology

Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing – Alison M. Cupples – Chemical Engineering & Technology

Food microbiology

Survival of lactic acid and propionibacteria in low- and full-fat Dutch-type cheese during human digestion Ex vivo – Aleksandra Martinovic – Letters in Applied Microbiology

Metagenomics and bioinformatics

Review: Targeted metagenomics of active microbial populations with stable-isotope probing -Sara Coyotzi – Current Opinion in Biotechnology

Infection and microbiology

Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach – Saskia Decuypere – PLOS Neglected Tropical Diseases

Microbes in the news

Fibre and protein enhance gut bacteria in children – Malene Sommer Christiansen – Science Nordic

Extreme Microbiome Project Aims to Characterize Microbes Living in Harsh Environments – Monica Heger – Genome Web

UTI bacteria use hooks to hang on inside you when you pee – Clare Wilson – New Scientist

Science, publishing and career

Statistical significance and its part in science downfalls – Hilda Bastian – PLOS Blogs

Microbiology and Nature in Video Games – Alex Alexiev – MicroBEnet

Tricon2016: The Microbiome: Sorting Out the Hype from the Hope – Bonnie Feldman – Storify

Leap day, giant viruses, and gene-editing – Dawn Field – Oxford University Press blog
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March 5, 2016

Posted on March 5, 2016 by eliesbik

Lung microbes in Cystic Fibrosis, microbiota of reindeer, strawberry phyllosphere, and microbes in raindust.

Pregnancy and birth

Dynamics of Gut Microbiota According to the Delivery Mode in Healthy Korean Infants – Eun Lee- Allergy Asthma Immunol Res.

Review: Respiratory Microbiome of New-Born Infants – David J. Gallacher – Frontiers in Pediatrics

Review: Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features – Silvia Arboleya – Annual Review of Food Science and Technology

Review: Maternal microbiome – A pathway to preterm birth – Angela E. Vinturache – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease – Deborah A. Hogan – PLOS ONE

Human oral microbiome

Levels of Candidate Periodontal Pathogens in Subgingival Biofilm – R.R.D.S Oliveira – Journal of Dental Research

Human gut microbiome

Effects of plant stanol ester consumption on fasting plasma oxy(phyto)sterol concentrations as related to fecal microbiota characteristics – Sabine Baumgartner – The Journal of Steroid Biochemistry and Molecular Biology

Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients – Forbes, Jessica D. – Inflammatory Bowel Diseases

Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis – Ohad Manor – Scientific Reports

Research highlight: Growth impairment in undernourished children – Claire Greenhill – Nature Reviews Endocrinology

Review: Elucidating the role of the host genome in shaping microbiome composition – Emily R. Davenport – Gut Microbes

Review: The Microbiome: A Key Regulator of Stress and Neuroinflammation – Kieran Rea – Neurobiology of Stress

Review: The Brain-Gut-Microbiome Axis: What Role Does it Play in Autism Spectrum Disorder? – Ruth Ann Luna – Current Developmental Disorders Reports

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: The human gut microbiome and its dysfunctions through the meta-omics prism – Stanislas Mondot – Annals of the New York Academy of Sciences

Animal models

Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model – Gaorui Bian – Environmental Microbiology

Effects of environmental temperature on the gut microbial communities of tadpoles – Kevin D. Kohl – Environmental Microbiology

Apple-Derived Pectin Modulates Gut Microbiota, Improves Gut Barrier Function, and Attenuates Metabolic Endotoxemia in Rats with Diet-Induced Obesity – Tingting Jiang – MDPI Nutrients

The effects of fecal microbial transplantation on microbiome and immunity in SIV-infected macaques – Tiffany Hensley-McBain – Journal of Virology

Soy Protein Compared with Milk Protein in a Western Diet Increases Gut Microbial Diversity and Reduces Serum Lipids in Golden Syrian Hamsters – Dustie N Butteiger – Journal of Nutrition

Review: The interplay between intestinal bacteria and host metabolism in health and disease: lessons from Drosophila melanogaster – Adam C. N. Wong – Disease Models & Mechanisms

Animal microbiome

New Insights into the Microbiota of the Svalbard Reindeer Rangifer tarandus platyrhynchus – Sylwia Zielińska – Frontiers in Microbiology

Geographically conserved microbiomes of four temperate water tunicates – Patrick L. Cahill – Environmental Microbiology Reports

Twenty five new viruses associated with the Drosophilidae (Diptera) – Claire L Webster – bioRxiv

Plant, root, and soil microbiome

Soil Microbial Community Interactions Under Tillage Systems in Australia – Vivian A. Rincon-Florez – Plant, Soil and Microbes

Variation of Bacterial Community Diversity in Rhizosphere Soil of Sole-Cropped versus Intercropped Wheat Field after Harvest – Zhenping Yang – PLOS ONE

Dispersal of Bacillus subtilis and its effect on strawberry phyllosphere microbiota under open field and protection conditions – Feng Wei – Scientific Reports

Temporally Variable Geographical Distance Effects Contribute to the Assembly of Root-Associated Fungal Communities – Christopher J. Barnes – Frontiers in Microbiology

Elevation gradient of soil bacterial communities in bamboo plantations – Yu-Te Lin – Botanical Studies

Soil microbial functional capacity and diversity in a millet-shrub intercropping system of semi-arid Senegal – S. Diakhaté – Journal of Arid Environments

Bioaugmentation of microbes to restore coastal wetland plants to protect land from coastal erosion – Regina Bledsoe – International Biodeterioration & Biodegradation

Review: Nutrient scavenging activity and antagonistic factors of non-photobiont lichen-associated bacteria: a review – M. Auður Sigurbjörnsdóttir – World Journal of Microbiology and Biotechnology

Water, rain, and extremophile microbiome

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin – Silke Langenheder – Environmental Microbiology Reports

Comparative summer dynamics of surface cyanobacterial communities in two connected lakes from the west of Ireland – N. Touzet – Science of The Total Environment

Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean – Ghida Nouhad Itani – Scientific Reports

Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific – Sarah K. Hu – FEMS Microbiology Ecology

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge – Julie L. Meyer – Scientific Reports

Biodigester microbiology

This one sounded wrong: Microbial diversity in an anaerobic digester with biogeographical proximity to geothermal active region – Rishi Mahajan – Environmental Technology

Food microbiology

Impact of mulches and growing season on indicator bacteria survival during lettuce cultivation – Aixia Xu – International Journal of Food Microbiology

Built environment microbiology

Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center – Aaron J. Prussin II – PLOS ONE

Bioweathering Potential of Cultivable Fungi Associated with Semi-Arid Surface Microhabitats of Mayan Buildings – Benjamín O. Ortega-Morales – Frontiers in Microbiology

Microbiome of death

Review: The Thanatomicrobiome: A Missing Piece of the Microbial Puzzle of Death – Gulnaz T. Javan – Frontiers in Microbiology

Waste and pollution microbiology

Isolation and characterization of yeasts associated with plants growing in heavy-metal- and arsenic-contaminated soils – Juan Ramos-Garza – Canadian Journal of Microbiology

Review: Understanding the development of environmental resistance among microbes: A Review – Jatin Srivastava – CLEAN – Soil, Air, Water

Review: Microbial communities, processes and functions in acid mine drainage ecosystems – Lin-xing Chen – Current Opinion in Biotechnology

Infection microbiology

Absence of Serological Evidence of Rickettsia spp., Bartonella spp., Ehrlichia spp. and Coxiella burnetii Infections in American Samoa – Colleen Lau – Ticks and Tick-borne Diseases

Comparison between a Broad-Range Real-Time and a Broad-Range End-Point PCR Assays for the Detection of Bacterial 16S rRNA in Clinical Samples – Mariam Meddeb – Annals of Clinical & Laboratory Science

Metagenomics and bioinformatics

Capturing the most wanted taxa through cross-sample correlations – Mathieu Almeida – The ISME Journal

MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation
Gabriele Andrea Lugli – FEMS Microbiology Letters

Sequence techniques

Microbial Ecology in the Era of Next Generation Sequencing – Surajit De Mandal – Omics: Next Generation: Sequencing & Applications

Microbial Ecology

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? – Emily B. Graham – Frontiers in Microbiology

Microbes in the news

Would you try to vaginally “seed” your baby’s microbiome after a C-section – Jonathan Eisen – The Tree of Life

Science, publishing, and career

This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter – Andrew David Thaler – Southern Friend Science

The “Creator” paper, Post-pub Peer Review, and Racism Among Scientists – Dr24hours – Complex Roots

UC reclassifies master’s degrees, charges elevated tuition – Nanette Asimov – SF Chronicle

She Wanted to Do Her Research. He Wanted to Talk ‘Feelings.’ – A. Hope Jahren – NY Times

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March 4, 2015

Posted on March 4, 2016 by eliesbik

Long term use of protein pump inhibitors, bovine genetics and microbial methane, fungi for biodegradation, Bayesian fingerprinting.

Human oral microbiome

Impact of smoking on experimental gingivitis. A clinical, microbiological and immunological prospective study – D. C. Peruzzo – Journal of Periodontal Research

Human gut microbiome

A comparison of the gut microbiome between long-term users and non-users of proton pump inhibitors – A. G. Clooney – Alimentary Pharmacology & Therapeutics

Animal microbiome

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance – Rainer Roehe – PLOS Genetics

When Parasites Are Good for Health: Cestode Parasitism Increases Resistance to Arsenic in Brine Shrimps – Marta I. Sánchez – PLOS Pathogens

Plant, root, and soil microbiome

A New Perspective on Sustainable Soil Remediation—Case Study Suggests Novel Fungal Genera Could Facilitate in situ Biodegradation of Hazardous Contaminants – Lauren M. Czaplicki – Remediation Journal

Fungal effects on plant–plant interactions contribute to grassland plant abundances: evidence from the field – Jonathan A. Bennett – Journal of Ecology

Status of microbial diversity in agroforestry systems in Tamil Nadu, India – Srinivasan Radhakrishnan – Journal of Basic Microbiology

Water microbiome

Microfungi Potentially Pathogenic for Humans Reported in Surface Waters Utilized for Recreation – Anna Biedunkiewicz – CLEAN – Soil, Air, Water

Waste and pollution microbiology

Bait and scrape: An approach for assessing biofilm microbial communities on organic media used for gas-phase biofiltration – Jason P. Oliver – Ecological Engineering

Food microbiology

Review: Microbial Safety of Wood in Contact with Food: A Review – Florence Aviat – Comprehensive Reviews in Food Science and Food Safety

Bioinformatics

Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding – Ziheng Yang – BioRxiv

blastjs: a BLAST+ wrapper for Node.js – Martin Page – BMC Research Notes

Microbes in the news

uBiome Investigates Health Implications of Seniors’ Changing Microbiomes, Seeks Participants – Benzinga

Mystery bacteria linked to 18 deaths in Wisconsin – CBS News

Includes Pat Schloss: 78 Fellows Elected to the American Academy of Microbiology – ASM

Science, publishing, and career

A Science Journal Invokes ‘the Creator,’ and Science Pushes Back – Madison Kotack – Wired

PLOS ONE retracting paper that cites “the Creator” – Alison McCook – Retraction Watch

#IAmAResearchParasite – Marcia McNutt – Science

Making a game of science – Elizabeth Pennisi – Science

Yes, Even CRISPR Pioneer Jennifer Doudna Experiences Gender Bias – Lisa Potter and Jon Brooks – KQED

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March 3, 2016

Posted on March 3, 2016 by eliesbik

Gut microbiome of Indian Nicobarese tribe, CDI patients’ stories about life before and after stool transplants, cryptic species in Nematoda, and similar fungi at opposite poles.

Pregnancy and birth

Review: The Developing Microbiome of the Preterm Infant – Mara E. DiBartolomeo – Clinical Therapeutics

Gut colonization by aerobic microorganisms is associated with route and type of nutrition in premature neonates – Ülle Parm – Nutrition Research

Human oral microbiome

Influence of a triclosan toothpaste on periodontopathic bacteria and periodontitis progression in cardiovascular patients: a randomized controlled trial – G. J. Seymour – Journal of Periodontal Research

Human respiratory microbiome

Review: Microbes and asthma: Opportunities for intervention – Hermelijn H. Smits – Journal of Allergy and Clinical Immunology

Understanding Persistent Bacterial Lung Infections: Clinical Implications Informed by the Biology of the Microbiota and Biofilms – Alexa A. Pragman – Clinical Pulmonary Medicine

Human gut microbiome

Elucidating the richness of bacterial groups in the gut of nicobarese tribal community – Perspective on their lifestyle transition – Maile Anwesh – Anaerobe

Resistant potato starches (type 4 RS) exhibit varying effects on laxation with and without phylum level changes in microbiota: A randomised trial in young adults – W.J. Dahl – Journal of Functional Foods

Recommended: Fecal microbiota transplantation for recurrent Clostridium difficile infection: The patient experience – Amy L. Pakyz – American Journal of Infection Control

Analysis of Gut Microbiome Reveals Significant Differences Between Men with Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls – Daniel A. Shoskes – The Journal of Urology

RiMINI – the influence of rifaximin on minimal hepatic encephalopathy (MHE) and on the intestinal microbiome in patients with liver cirrhosis: study protocol for a randomized controlled trial – Christian Schulz – BMC Trials

Editorial: Dysbiosis in fungal microbiota in IBD – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Models of microbiome research

Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

Effect of breast feeding time on physiological, immunological and microbial parameters of weaned piglets in an intensive breeding farm – G.R. García – Veterinary Immunology and Immunopathology

Animal microbiome

Prevalence of potential nitrogen-fixing, green sulfur bacteria in the skeleton of reef-building coral Isopora palifera – Shan-Hua Yang – Limnology and Oceanography

An investigation of the microbiota in uterine flush samples and endometrial biopsies from dairy cows during the first 7 weeks postpartum – Lif Rødtness Vesterby Knudsen – Theriogenology

Coexisting cryptic species of the Litoditis marina complex (Nematoda) show differential resource use and have distinct microbiomes with high intraspecific variability – S Derycke – Molecular Ecology

Hologenome analysis of two marine sponges with different microbiomes – Taewoo Ryu – BMC Genomics

Plant, root, and soil microbiome

Land use change in the Amazon rainforest favors generalist fungi – Rebecca C Mueller – Functional Ecology

Drivers of phosphorus limitation across soil microbial communities – Petr Čapek – Functional Ecology

Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures – Guixiang Zhou – Scientific Reports

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic) – Tao Zhang – Frontiers in Microbiology

Diversity of endophytic fungal and bacterial communities in Ilex paraguariensis grown under field conditions – María Laura Pérez – World Journal of Microbiology and Biotechnology

Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches – Steven D. Leavitt – Scientific Reports

Rhizosphere competence of wild-type and genetically-engineered Pseudomonas brassicacearum is affected by the crop species – Stacey Blouin Bankhead – Phytopathology

Actinorhizal Alder Phytostabilization Alters Microbial Community Dynamics in Gold Mine Waste Rock from Northern Quebec: A Greenhouse Study – Katrina L. Callender – PLOS ONE

Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs – A. Ö. C. Dupont – Environmental Microbiology

Water and extremophile microbiome

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome – Shunyan Cheung – Journal of Plankton Research

Not poles apart: Antarctic soil fungal communities show similarities to those of the distant Arctic – Filipa Cox – Ecology Letters

Food microbiology

Salmonella in Shell Eggs: Mechanisms, Prevention and Detection – Seockmo K – Omics Journal of Nutrition & Food Sciences

Intensive aquaculture selects for increased virulence and interference competition in bacteria – Lotta-Riina Sundberg – Proceedings of the Royal Society B

Application of electrolyzed oxidizing water in production of radish sprouts to reduce natural microbiota – Chunling Zhang – Food Control

Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions, seasonality and their spoilage potential – Nuwan R. Vithanage – International Dairy Journal

Microbiological characteristics of fresh tofu produced in small industrial scale and identification of specific spoiling microorganisms (SSO) – Franca Rossi – LWT – Food Science and Technology

Built Environment and Waste Microbiome

The efficacy of disinfectants in the decontamination of dental unit water lines: an in vitro laboratory study – Mrudula Patel – BDJ Open

Review: Bacterial communities in full-scale wastewater treatment systems – Agnieszka Cydzik-Kwiatkowska – World Journal of Microbiology and Biotechnology

Preferential methanogenic biodegradation of short-chain n-alkanes by microbial communities from two different oil sands tailings ponds – Mohd Faidz Mohamad Shahimin – Science of The Total Environment

Microbes in space

Two older papers that showed up in my PubMed alert today:
Review: The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond – Wilfred F.M. Röling – Astrobiology
Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions – Andrew C. Schuerger – Astrobiology

Phages and viruses

Diversity of phage infection types and associated terminology: the problem with “Lytic or Lysogenic” – Zack Hobbs – FEMS Microbiology Letters

Techniques

Effect of Freezing Conditions on Fecal Bacterial Composition in Pigs – Barbara U. Metzler-Zebeli – MDPI Animals

Microbes in the news

Astronaut Scott Kelly back on earth, Northwestern profs celebrate – Chicago Sun Times

Microbial Manifesto: The Global Push to Understand the Microbiome (Kavli Roundtable) – Alan Brown – Live Science

‘Gut’ bacteria may help put a kink in family obesity cycle – Science Codex

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March 1, 2016

Posted on March 1, 2016 by eliesbik

Colonization of the mouth in babies, biofilm in dinosaur bone, lichen symbiosis, microbial forensics, horse stool transplants, and ViromeScan.

Pregnancy and birth

Probiotic Supplementation and Late-Onset Sepsis in Preterm Infants: A Meta-analysis – Shripada C. Rao – Pediatrics

Early colonization of the oral cavity in 6- and 12-month-old infants by cariogenic and periodontal pathogens: a case-control study – Vlasta Merglova – Folia Microbiologica

Review: Perinatal nutrition: How to Take Care of the gut microbiota? – Izaskun García-Mantrana – Clinical Nutrition Experimental

Human skin microbiome

Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis – Gitte J. M. Christensen – BMC Genomics

Human oral microbiome

Bacterial community shifts during healing of palatal wounds: comparison of two graft harvesting approaches – Suzanne L. Delima – Journal of Clinical Periodontology

Human gut microbiome

Innate Sensing of the Gut Microbiota: Modulation of Inflammatory and Autoimmune Diseases – Aline Ignacio – Frontiers in Immunology

Does the intestinal microbial community of Korean Crohn’s disease patients differ from that of western patients? – Chang Soo Eun – BMC Gastroenterology

Review: Gut Microbiota Modification: Another Piece in the Puzzle of the Benefits of Physical Exercise in Health? – Begoña Cerdá – Frontiers in Physiology

Editorial: The Microbiome in Critical Illness: Firm Conclusions or Bact to Square One?
John D. Lyons – Digestive Diseases and Sciences

Editiorial: Posttraumatic Stress Disorder Does the Gut Microbiome Hold the Key? –
Sophie Leclercq – Canadian Journal of Psychiatry

Animal models of microbiome research

Cognitive Impairment by Antibiotic-Induced Gut Dysbiosis: Analysis of Gut Microbiota-Brain Communication – Esther E. Fröhlich – Brain, Behavior, and Immunity

Epigenome-Microbiome crosstalk: A potential new paradigm influencing neonatal susceptibility to disease – Rene Cortese – Epigenetics

Animal microbiome

Testing the Hypothesis of Biofilm as a Source for Soft Tissue and Cell-Like Structures Preserved in Dinosaur Bone – Mary Higby Schweitzer – PLOS ONE

The holobiont concept: the case of xylophagous termites and cockroaches – Mercedes Berlanga – Symbiosis

Termites: Characterization of the Core and Caste-Specific Microbiota in the Termite, Reticulitermes flavipes – Jacquelynn Benjamino – Frontiers in Microbiology

The sea cucumber microbiome is so hot right now: Individual Apostichopus japonicus fecal microbiome reveals a link with polyhydroxybutyrate producers in host growth gaps – Yohei Yamazaki – Scientific Reports

Gut bacterial communities across tadpole ecomorphs in two diverse tropical anuran faunas – Miguel Vences – The Science of Nature

Review: Equine faecal microbiota transplant: Current knowledge, proposed guidelines and future directions – K. R. Mullen – Equine Veterinary Education

Plant, root, and soil microbiome

Differential Response of Potato Toward Inoculation with Taxonomically Diverse Plant Growth Promoting Rhizobacteria – Tahir Naqqash – Frontiers in Plant Science

Disentangling the relative importance of host tree community, abiotic environment, and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient – Shunsuke Matsuoka – FEMS Microbiology Ecology

Changes of soil microbial community under different degraded gradients of alpine meadow – Yaoming Li – Agriculture, Ecosystems & Environment

Responses of Soil Fungal Populations and Communities to the Thinning of Cryptomeria Japonica Forests – Wan-Rou Lin – Microbes and Environments

Land-Cover Legacy Effects on Arbuscular Mycorrhizal Abundance in Human and Wildlife Dominated Systems in Tropical Savanna – Geofrey E. Soka – Advances in Ecology

Response of Soil Microbial Properties to Long-Term Application of Organic and Inorganic Amendments in a Tropical Soil (Saria, Burkina Faso) – Ndeye Hélène Diallo-Diagne – OJSS

Microspatial variability in community structure and photophysiology of calcified macroalgal microbiomes revealed by coupling of hyperspectral and high-resolution fluorescence imaging – R. G. Perkin – Scientific Reports

Lichen: Understanding Microbial Multi-Species Symbioses – Ines A. Aschenbrenner – Frontiers in Microbiology

Water and extremophile microbiome

Protist metabarcoding and environmental biomonitoring: time for change – J. Pawlowski – European Journal of Protistology

Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure – Deric R. Learman – Frontiers in Microbiology

Book Chapter: Life in the Anoxic Sub-Seafloor Environment: Linking Microbial Metabolism and Mega Reserves of Methane Hydrate – Varsha Honkalas – Advances in Biochemical Engineering/Biotechnology

Waste and pollution microbiology

Potential Impacts of PCBs on Sediment Microbiomes in a Tropical Marine Environment – James S. Klaus – MDPI J. Mar. Sci. Eng.

Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions – Nataliya M. Shchegolkova – Frontiers in Microbiology

Food microbiology

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate – Francesca De Filippis – Scientific Reports

Forensic microbiology

Review: Expansion of Microbial Forensics – Sarah E. Schmedes – Journal of Clinical Microbiology

Bioinformatics, viruses, metagenomics

ViromeScan: a new tool for metagenomic viral community profiling – Simone Rampelli – BMC Genomics

MIMIVIRE is a defence system in mimivirus that confers resistance to virophage – Anthony Levasseur – Nature

More microbiology

Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform – Kazuki Nakamura – Scientific Reports

Expanding the Diet for DIET: Electron Donors Supporting Direct Interspecies Electron Transfer (DIET) in Defined Co-Cultures – Li-Ying Wang – Frontiers in Microbiology

Microbes and infection

Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts – Liang Ma – Nature Communications

Microbes in the news

NASA’s lab rat: What astronaut Scott Kelly’s year in space can teach us – Sharon Begley – STAT news

Video: Bacteria Can Be Your Best Friend, interview with Ned Ruby and Margaret McFall-Ngai – ThinkTech Hawaii

Inside the secret defense systems of giant viruses – Carl Zimmer – STATnews

How Gut Microbiota Impacts HIV Disease. A new understanding of the role gut microbiota plays in HIV disease is beginning to emerge, suggesting potential new strategies to manage the infection – Bob Roehr – Scientific American

The Case of the Missing Microbes – Kevin Bonham – Scientific American

Faecal transplants could be useful in treating diarrhoea in horses – review – Horse Talk

Antibiotic use in preschoolers alters intestinal microbiome, increases disease risk – Healio

Altering the Gut Microbiome with Early Life Exercise – HCP Live

Obstructive sleep apnea raises hypertension risk, a possible link with gut bacteria: Study– Devon Andre – Belmarra Health

Tipping the Balance in Microbiome Standoffs.The Human Microbiome May Dispose Us toward Health or Illness On The Basis Of Tiny Shifts in Microbial Subpopulations – MaryAnn Labant – GenEngNews

Fighting Infections with Viruses, as Antibiotics Fail – NewsMax

HU develops Jerusalem sewage viruses to kill off resistant dental bacteria – Jerusalem Post

Turning bacteria into ‘SWARMBOTS’: Groups of microbes could be engineered to help combat harmful bugs in the gut – Daily Mail

Bacteria or Virus? New Tests May Identify What’s Causing Your Infection – The Wall Street Journal

Science, publishing, and career

I’m quoted here too: Blatt is back: “open debate cornerstone of scientific process” – Leonid Schneider- For Better Science

An introvert goes conferencing – Strategies to cope – Stephen B Heard – Scientist Sees Squirrel

Bik’s Picks

Ever Wonder What a Neanderthal Considered a Delicacy? – Erika Engelhaupt – National Geographic

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Food Microbiology

March 19, 2016

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March 8, 2016

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