Category Archives: Extremophiles

December 20, 2016

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Events

Registration open: Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability – Singapore, 12-15 February 2017

Pregnancy and early life

Sensitive Quantitative Analysis of the Meconium Bacterial Microbiota in Healthy Term Infants Born Vaginally or by Cesarean Section – Ravinder Nagpal – Frontiers in Microbiology

Remodeling of the gut microbiota and structural shifts in Preeclampsia patients in South China – J. Liu – European Journal of Clinical Microbiology & Infectious Diseases

Human respiratory microbiome

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples – Antonina A Votintseva – bioRxiv

Human oral microbiome

Effect of 12-month weekly professional oral hygiene care on the composition of the oral flora in dentate, dependent elderly residents: A prospective study
Maude Wikström – Gerodontology

Human gut microbiome

Roles of the gut in the metabolic syndrome: an overview – L. Fändriks – Journal of Internal Medicine

Review: Microbiome and chronic inflammatory bowel diseases – Jan Wehkamp – Journal of Molecular Medicine

Animal experiments

Resetting microbiota by Lactobacillus reuteri inhibits T reg deficiency–induced autoimmunity via adenosine A2A receptors – Baokun He – Journal of Experimental Medicine

Press: Replacing missing gut bacteria could help treat children with rare autoimmune disease – News Medical

Characterization of meningeal type 2 innate lymphocytes and their response to CNS injury – Sachin P. Gadani – Journal of Experimental Medicine

Press: Team discovers powerful defenders of the brain—with big implications for disease – Medical Xpress

Examination of Mycobacterium avium subspecies paratuberculosis mixed genotype infections in dairy animals using a whole genome sequencing approach – Fraser W. Davidson – PeerJ

Insights into Broilers’ Gut Microbiota Fed with Phosphorus, Calcium, and Phytase Supplemented Diets – Daniel Borda-Molina – Frontiers in Microbiology

Animal microbiome

Fecal microbiota of three bactrian camels (Camelus ferus and Camelus bactrianus) in China by high throughput sequencing of the V3-V4 region of the 16S rRNA gene – Lei Yuan – Journal of Arid Land

Plant, root, and soil microbiome

Metagenomic assembly unravel microbial response to redox fluctuation in acid sulfate soil – Jian-Qiang Su – Soil Biology and Biochemistry

Effect of New Auxin Herbicide Formulations on Control of Herbicide Resistant Weeds and on Microbial Activities in the Rhizosphere – Vijay K. Nandula – American Journal of Plant Sciences

Screening of rhizobacteria from rhizosphere of healthy chili to control bacterial wilt disease and to promote growth and yield of chili – Yulmira Yanti – Biodiversitas

Mycorrhizal colonization of chenopods and its influencing factors in different saline habitats, China – Yinan Zhao – Journal of Arid Land

Water and extremophile microbiome

Degradation of a fluoroquinolone antibiotic in an urbanized stretch of the River Tiber – Anna Barra Caracciolo – Microchemical Journal

Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River – Limin Fan – Scientific Reports

Biological Potential of Chitinolytic Marine Bacteria – Sara Skøtt Paulsen – Marine Drugs
http://www.mdpi.com/1660-3397/14/12/230/htm

Microbial Diversity of Extreme Regions: An Unseen Heritage and Wealth – Saxena AK –
Indian Journal of Plant Genetic Resources

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

A theoretical basis for a nanomolar critical oxygen concentration – E. J. Zakem – Limnology & Oceanography

Bacteria can survive in oxygen-free marine environments – Sumaya Aamir – i4u.com
Simons Foundation Supports Study That Finds Bacteria Can Survive In Oxygen-Free Marine Environments – Philanthropy New York
DNA markers distinguish between harmless, deadly bacteria – Jennifer Chu – Phys.org

Waste and pollution microbiology

Bacterial community structure within an activated sludge reactor added with phenolic compounds – Selene Gómez-Acata – Applied Microbiology and Biotechnology

Microbial ecology

Editorial: Development of microbial ecological theory: stability, plasticity and evolution of microbial ecosystems – Shin Haruta – Frontiers in Microbiology

Microbes in the news

Borborygmus: The Rumble in your Tummy. Video about the microbiome for kids. Eat your veggies, kids. Do it for Borborygmus.

6 Things We Learned About Gut Health And The Microbiome In 2016 – Cayla Dengate – Huffington Post

Research highlight: Rhythm and bacteria – Ashley York – Nature Reviews Microbiology

Baylor investigates antibiotic use, children’s improved autism symptoms – Healio

 

Microbes on the market

How bacteria from your stomach can fight disease. Start-up secures £8m to develop novel therapies – Matt Gooding – Cambridge News

Spin-out seeks to be world leader leveraging microbiome biology’s potential – The PharmaLetter

Sanger Spins Out Microbiotica to Develop Bacteriotherapies – GenEngNews

Science, publishing, and career

Evidence of the Superiority of Female Doctors. New research estimates that if all physicians were female, 32,000 fewer Americans would die every year – James Hamblin – The Atlantic

December 18, 2016

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Virome of the human respiratory tract, vendor effects on mouse gut, soils under beech and spruce, variations in Scottish soils, portable pathogen detection.

Events

Poster submission started: 3rd Annual Translational Microbiome Conference – April 11-13, 2017, Boston, USA

Pregnancy and early life

Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi – Lorenzo Drago – The ISME Journal

Review: Pathogenesis of NEC: Impact of an altered intestinal microbiome – Josef Neu – Seminars in Perinatology

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – British Dental Journal

Human respiratory microbiome

* Review: The Virome of the Human Respiratory Tract – Kristine M. Wylie – Clinics in Chest Medicine

Human vaginal microbiome

Comparison of Culture-dependent and Culture-Independent Molecular Methods for Characterisation of Vaginal Microflora – Shirali Pandya – Journal of Medical Microbiology

Human gut microbiome

Distinct microbiome-neuroimmune signatures correlate with functional abdominal pain in children with autism spectrum disorder – Ruth Ann Luna – CMGH Cellular and Molecular Gastroenterology and Hepatology

Alterations of the gut microbiome in Chinese patients with systemic lupus erythematosus
Zhixing He – Gut Pathogens

Altered Gut Microbiota in Patients With Chronic Pancreatitis is Associated With Gut Barrier Dysfunction and Metabolic Abnormalities – Rupjyoti Talukdar

Dietary Changes Impact the Gut Microbe Composition in Overweight and Obese Men with Prostate Cancer Undergoing Radical Prostatectomy – Andrew D. Frugé – Journal of the Academy of Nutrition and Dietetics

The human intestinal microbiota of constipated-predominant irritable bowel syndrome patients exhibits anti-inflammatory properties – Alain P. Gobert – Scientific Reports

The Interactions Between Gut Microbiota and Lynch Syndrome – Xiao-juan Lu – Clinical Gastroenterology and Hepatology

Review: Enterosalivary nitrate metabolism and the microbiome: intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health – Carl D Koch – Free Radical Biology and Medicine

Review: Community metabolic modeling approaches to understanding the gut microbiome: bridging biochemistry and ecology – Helena Mendes-Soares – Free Radical Biology and Medicine

Review: Microbiota Small RNAs in Inflammatory Bowel Disease – Anca T. Filip – Journal of Gastrointestinal and Liver Diseases

Review: Intestinal Microbiome, Akkermansia muciniphila, and Medicinal Nutrition Therapy – Jeffrey Bland – integrative Medicine

Review: Using the Human Gastrointestinal Microbiome to Personalize Nutrition Advice: Are Registered Dietitian Nutritionists Ready for the Opportunities and Challenges? – Ruth Harvie – Journal of the Academy of Nutrition and Dietetics

Review: Bacterial Biofilms in Colorectal Cancer Initiation and Progression – Shan Li – Trends in Molecular Medicine

Animal experiments

* Vendor Effects on Murine Gut Microbiota Influence Experimental Abdominal Sepsis – Tobias Hilbert – Journal of Surgical Research

The critical role of microbiota within cecal crypts on the regenerative capacity of the intestinal epithelium following surgical stress – Alexander Zaborin – American Journal of Physiology Gastrointestinal and Liver Physiology

Source of supplemental dietary copper, zinc, and manganese affects fecal microbial relative abundance in lactating dairy cows – M.J. Faulkner – Journal of Dairy Science

Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics – Natália C. Gaeta – Journal of Dairy Science

Animal microbiology

Riptortus pedestris and Burkholderia symbiont: an ideal model system for insect–microbe symbiotic associations – Kazutaka Takeshita – Research in Microbiology

Bird: Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota – Lindsay K Newbold – The ISME Journal

Plant, root, and soil microbiome

* Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce – Heiko Nacke – Frontiers in Microbiology

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia – Bruno L. Mello – Scientific Reports

The biogeography of soil archaeal communities on the eastern Tibetan Plateau – Yu Shi – Scientific Reports

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic – Enzong Xiao – Environmental Pollution

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic) – Aleš Eichmeier – PLOS ONE

* Scottish soil: It is elemental: Soil nutrient stoichiometry drives bacterial diversity – Manuel Delgado-Baquerizo – Environmental Microbiology

Microbial soil community analyses for forensic science: Application to a blind test – Sandrine Demanèche – Forensic Science International

Review: Mycorrhiza: The Oldest Association Between Plant and Fungi – Jagnaseni Barman – Resonance

Book Chapter: Bioprospecting Soil Metagenomes for Antibiotics – Chiara Borsetto – Bioprospecting

Water and extremophile microbiome

The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China – Yantian Ma – Archaea

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria – Wajdi Ben Hania – Environmental Microbiology

Book chapter: Bioprospecting Archaea: Focus on Extreme Halophiles – André Antunes – Bioprospecting

Food microbiology

Analysis of the bacterial biodiversity of peaches under refrigerated storage after treatment by high hydrostatic pressure – Maria José Grande Burgos – Food and Bioproducts Processing

Bioreactor, biotechnology, and pollution microbiology

Correlating methane production to microbiota in anaerobic digesters fed synthetic wastewater – K. Venkiteshwaran – Water Research

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes – Georgina Robinson – Scientific Reports

Trace Elements Induce Predominance among Methanogenic Activity in Anaerobic Digestion – Babett Wintsche – Frontiers in Microbiology

Bioinformatics and metagenomics

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes – Mohammadkarim Saeedghalati – arXiv

A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples – Daniel H. Huson – Journal of Biotechnology

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota – Sébastien Raguideau – PLOS Computational Biology

Now published: IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – Genome Biology

Metabolomics

Evaluating metabolic response to light exposure in Lactobacillus species via targeted metabolic profiling – Mengyang Xu – Journal of Microbiological Methods

Review: Phytanic acid consumption and human health, risks, benefits and future trends: A review – P. Roca-Saavedra – Food Chemistry

Viruses and phages

Perspective: Viruses and the origin of microbiome selection and immunity – Steven D Quistad – The ISME Journal

Techniques

* Detection of ESKAPE bacterial pathogens at the point-of-care using isothermal DNA-based assays in a portable, de-gas microfluidic diagnostic assay platform
Lars D. Renner – Applied and Environmental Microbiology

Press: Portable detection system can rapidly identify virulent, multi-drug resistant pathogens in remote areas – News-Medical

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing – Dieter M. Tourlousse – Nucleic Acids Research

Microbes in the news

Gardening Etcetera: Life down under in northern Arizona – Cindy Murray – AZ Daily Sun

CSI: Chem trail: a new way for investigators to narrow down suspect pools using chemical traces found on cellphones – Kelly Kasulis – Boston Globe

China expresses alarm as chilli ‘conspiracy’ heats up Indonesians – South China Morning Post

Adapting and adopting microbiome data into clinical practice – Silvio Pitlik & Omry Koren- BioMed Central

Bacteria that boost insulin-producing cells could yield new diabetes approaches – Arlene Weintraub – Fierce Biotech

Microbes in the market

Research focused on the human microbiome market worth 658 million USD by 2023 – Whatech

AOBiome Launches Phase 2 Clinical Trial Using Novel Bacterial Platform for Treatment of Hypertension – PR Newswire

Live Stock Coverage: What’s Ahead for Seres Therapeutics Inc After Today’s Huge Increase? – Linda Rogers- Frisco Fastball

 

December 14, 2016

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Gaia and her microbiome, a walk in the park, ancient teeth, fillies, bats, ticks, frogs, moss, and high-altitude potatoes.

General microbiome

Gaia and Her Microbiome – John F. Stolz – FEMS Microbiology Ecology

Human oral microbiome

Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth – Nicolás Rascovan – NPJ Biofilms and Microbiome

Influences of pH and iron on the salivary microbiome in individuals with and without caries – Jianye Zhou – Applied and Environmental Microbiology

Human gut microbiome

Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus – Xiaokai Wang – Antonie van Leeuwenhoek

Animal experiments

Intense Exercise and Aerobic Conditioning Associated with Chromium or L-Carnitine Supplementation Modified the Fecal Microbiota of Fillies – Maria Luiza Mendes de Almeida – PLOS ONE

 

Animal microbiome

Mosquitoes: Diversity of Cultivable Midgut Microbiota at Different Stages of the Asian Tiger Mosquito, Aedes albopictus from Tezpur, India – Kamlesh K. Yadav – PLOS ONE

Bats: Microbiome of the sexual scent organ of Leptonycteris yerbabuenae – Osiris Gaona – PeerJ

Ticks: Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California – Nikos Gurfield – PeerJ

Frogs: Environmental fluctuations and host skin bacteria shift survival advantage between frogs and their fungal pathogen – Ana V Longo – ISME Journal

Plant, root, and soil microbiology

Discovery of polyesterases from moss-associated microorganisms – Christina Andrea Müller – Applied and Environmental Microbiology

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil – Honggui Wang – Soil Biology and Biochemistry

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development – Stefan Pfeiffer – FEMS Microbiology Ecology

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures – Senta Heiss-Blanquet – PLOS ONE

Effects of root exudates of woody species on the soil antierodibility in the rhizosphere in a karst region, China – Zhen hong Wang – PeerJ Preprint

Water and extremophile microbiome

Patchiness of Ciliate Communities Sampled at Varying Spatial Scales along the New England Shelf – Jean-David Grattepanche – PLOS ONE

Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China – Yongjuan Chen – Applied Microbiology and Biotechnology

Pristine but metal-rich Río Sucio (Dirty River) is dominated by Gallionella and other iron-sulfur oxidizing microbes – Alejandro Arce-Rodríguez – Extremophiles

Quantification of basal ice microbial cell delivery to the glacier margin – Mario Toubes-Rodrigo – Biogeosciences Discuss

Microbial Diversity of Source and Point-of-Use Water in Rural Haiti – A Pyrosequencing-Based Metagenomic Survey – Nabanita Mukherjee – PLOS ONE

Virus-host infection dynamics of marine single-celled eukaryotes resolved from metatranscriptomics – bioRxiv

Pollution

The Biologists’ Forum: Environmental microbial community analysis methods as applied to bioremediation – Hadassa Shira Guttman – BIOS

Food microbiology

Determination of Fungal Community Diversity in Fresh and Traditional Chinese Fermented Pepper by Pyrosequencing – Lingyan Zhao – FEMS Microbiology Letters

Metagenomics

Using Bacterial Genomes and Essential Genes for the Development of New Antibiotics – Francisco R. Fields – Biochemical Pharmacology

Antibiotic discovery is a walk in the park – Louis-Félix Nothias – PNAS

Metabolomics

Book: Microbial Metabolomics: Applications in Clinical, Environmental, and Industrial Microbiology – Editors: David J. Beale, Konstantinos A. Kouremenos, Enzo A. Palombo – Springer

Microbes in the news

Scientists trap bacteria with optical tractor beam.”The principle underlying this laser beam is similar to the concept to be found in the television series ‘Star Trek,'” said researcher Thomas Huser –  Brooks Hays – UPI

Researchers find bacterial protein that boosts insulin-producing cells in zebrafish – Science Daily

A $5 fix for a nasty parasite: Attachment of Cryptosporidium parvum oocysts to environmental biofilms – EurekAlert

Increasing Product Recalls and Growing Consumer Concerns are Driving the Global Industrial Microbiology Market – Medgadget

 

 

December 8, 2016

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Bacteria in upper GI tract, visceral pain, stromatolites, polluted urban soils.

Pregnancy and early life

Deep sequencing of the 16S ribosomal RNA of the neonatal oral microbiome: a comparison of breast-fed and formula-fed infants – S. S. Al-Shehri – Scientific Reports

Cesarean birth is not associated with early childhood body mass index – L. G. Smithers – Pediatric Obesity

Human skin microbiome

Culture-Based Screening of Aerobic Microbiome in Diabetic Foot Subjects and Developing Non-healing Ulcers – Saba Noor – Frontiers in Microbiology

Human gut microbiome

* The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection – Christian Schulz – Gut

Elderly patients have an altered gut-brain axis regardless of the presence of cirrhosis – Jasmohan S. Bajaj – Scientific Reports

Review: HIV-associated changes in the enteric microbial community: potential role in loss of homeostasis and development of systemic inflammation – Gootenberg, David B – Current Opinion in Infectious Diseases

Review: A Perspective on Brain-Gut Communication: The American Gastroenterology Association and American Psychosomatic Society Joint Symposium on Brain-gut Interactions and the Intestinal Microenvironment – Aroniadis, Olga C. – Psychosomatic Medicine

Review: Mechanisms of Cross-talk between the Diet, the Intestinal Microbiome, and the Undernourished Host – Helene Velly – Gut Microbes

* Review: The Gut Microbiota as a Key Regulator of Visceral Pain – O’ Mahony, Siobhain M – Pain

Crystal ball : Microbiomes, metabolic errors and detection of performance enhancing drug abuse – Environmental Microbiology Reports

Animal and in vitro models

Masked trichothecene and zearalenone mycotoxins withstand digestion and absorption in the upper GI tract but are efficiently hydrolyzed by human gut microbiota in vitro – Silvia W. Gratz – Molecular Nutrition & Food Research

Light/Dark Shifting Promotes Alcohol-Induced Colon Carcinogenesis: Possible Role of Intestinal Inflammatory Milieu and Microbiota – Faraz Bishehsari – International Journal of Molecular Sciences

Colonic luminal microbiota and bacterial metabolite composition in pregnant Huanjiang mini-pigs: effects of food composition at different times of pregnancy – Xiang-feng Kong – Scientific Reports

Animal microbiome

Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria – Olga L. Mayorga – Frontiers in Microbiology

Plant, root, and soil microbiome

Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function – Tanya E. Cheeke – New Phytologist

Diversity of bacteria and archaea in the rhizosphere of bioenergy crop Jatropha curcas – Garima Dubey – 3 Biotech

Clay-to-Carbon Ratio Controls the Effect of Herbicide Application on Soil Bacterial Richness and Diversity in a Loamy Field – H. M. L. I. Herath – Water, Air, & Soil Pollution

* Microorganisms isolated from polluted urban soils highly effectives in degrading recalcitrant pesticides – Liliana Rocío Botero-Botero

Review: The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective – Panagiotis Gkorezis – Frontiers in Microbiology

Review: Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems – Thomas Bell – Proceedings of the Royal Society B

Water and extremophile microbiome

* Participation of algal–bacterial community in the formation of modern stromatolites in Cock Soda Lake, Altai Region – O. S. Samylina – Paleontological Journal

Microbial mediated arsenic biotransformation in wetlands – Si-Yu Zhang – Frontiers of Environmental Science & Engineering

More microbiology

Antibiotic resistance in the wild: an eco-evolutionary perspective – Teppo Hiltunen – Philosophical Transactions of the Royal Society B

Microbes in the news

New polymer £5 notes are three times cleaner and hold less bacteria, scientists have found
Less bacteria sticks to the new polymer notes as it is revealed the old paper notes were among the dirtiest in Europe – Jennifer Hale – The Sun

The Coolest Thing Bio350 Micronauts Learned in Fall 2016 – Mark O. Martin – Microbes Rule Blogspot

Glow-in-the-dark bugs bring art to life: Dr Siouxsie Wiles has teamed up with artists and schoolchildren for this weekend’s SciGlow exhibition at Auckland’s Silo Park – Jamie Morton – NZ Herald

Nearly 2 Million Pounds Of Chicken Recalled For Possible Bacteria – CBS

Magnetic purification of blood ‘pulls out’ the bacteria – Nanowerk

Microbes on the market

uBiome Announces SmartBiomeTM, a Novel Comprehensive Metagenomic Deep Sequencing Research Platform – PR Web

Synlogic CEO downplays ‘yuck factor’ of the microbiome – Big News Network

AGA and The Dannon Company Recognize Microbiome Leader Dr. Gary Wu – BusinessWire

Gut feelings: How the microbiome may affect mental illness and interact with treatment – MedicalXpress

December 6, 2016

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Pooping in space, lichen symbiosis, snow algae on volcanoes, and metagenome-guided peptide and protein identification.

uBiome Blog

* From Lift-Off to Splash-Down: The Scoop on Pooping in Space – Julie Taylor – uBiome

General microbiome

Review: Getting at the “what” and the “how” in symbiosis – Irene L. G. Newton – Environmental Microbiology Reports

The Evolutionary Value of Helpful Microbes: A Response to Shapira – Allen Rodrigo – Trends in Ecology & Evolution

Animal microbiome

DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio – Elena N. Kashinskaya – FEMS Microbiology Ecology

Plant, root, and soil microbiome

* Fungal–algal association patterns in lichen symbiosis linked to macroclimate – Garima Singh – New Phytologist

The missing link in grassland restoration: arbuscular mycorrhizal fungi inoculation increases plant diversity and accelerates succession – Liz Koziol – Journal of Applied Ecology

Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function – Tanya E. Cheeke – New Phytologists

Depth-dependent influence of different land-use systems on bacterial biogeography – Brent J. Seuradge – FEMS Microbiology Ecology

Water and extremophile microbiome

* Primary productivity of snow algae communities on stratovolcanoes of the Pacific Northwest – T. L. Hamilton – Geobiology

Pollution microbiology

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales – Isabel Natalia Sierra-Garcia – Extremophiles

Transformation of hexabromocyclododecane in contaminated soil in association with microbial diversity – Thao Thanh Le – Journal of Hazardous Materials

Proteomics

* A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics -Haixu Tang – PLOS Computational Biology

Microbes in the news

Microbes: Our tiny, crucial allies – David R. Montgomery – The Conversation

Do C-sections alter a baby’s microbiome, hurting later health? – Sharon Begley – STAT news

Let there be light! Compact sterilizing pod uses UV light to kill bacteria – Dyllan Furness – Digital Trends

N.H.’s Oyster Bacteria Threat – Valley News

Doctor’s warning: a cat’s bacteria is worse than its bite. ER doctor says bites ‘almost like getting stabbed with a needle’ and infections can develop quickly — David Burke – CBC

Why Do Our Feet Smell Worse in the Winter? – Stephanie Pappas – Live Science

Science, publishing, and career

12 winners: 11 men, 1 woman. Tech Billionaires Award $25 Million in Breakthrough Prizes to Top Scientists – Robert Hackett -Fortune
$25 Million in Breakthrough Prizes Given in Science and Math -Dennis Overbye – New York Times

 

 

December 3, 2016, part 2

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Recognition of extremophilic archaeal viruses by eukaryotic cells, special issue about the holobiont concept, sleep deprivation, respiratory viruses in infants. So many new papers that I had to spend another couple of hours on the digest today!

General microbiome and ecology

* Themed issue with papers about the holobiont and endosymbionts: Biological Individuality – Biology & Philosphophy

Review: Making a microbiome: the many determinants of host-associated microbial community composition – Karen L Adair – Current Opinion in Microbiology

Pregnancy and early life

* Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants – Insa Korten – mSphere

Does vaginal delivery mitigate or strengthen the intergenerational association of overweight and obesity? Findings from the boston birth cohort – N T Mueller – International Journal of Obesity

The oral cavities of healthy infants harbor high proportions of Streptococcus salivarius strains with phenotypic and genotypic resistance to multiple classes of antibiotics – Thaís H. Palma – Journal of Medical Microbiology

Human respiratory microbiome

Bacterial community collapse: A meta-analysis of the sinonasal microbiota in chronic rhinosinusitis – Brett Wagner Mackenzie – Environmental Microbiology

Review: Viral-Bacterial interactions in the respiratory tract – Carla Bellinghausen – Journal of General Virology

Human skin microbiome

Dysbiotic Bacterial and Fungal Communities Not Restricted to Clinically Affected Skin Sites in Dandruff – Renan C. Soares – Frontiers in Cellular and Infection Microbiology

Gene Function Analysis in the Ubiquitous Human Commensal and Pathogen Malassezia Genus – Giuseppe Ianiri – mBio

Review: Microbial biofilms and the human skin microbiome – Michael Brandwein – NPJ Biofilms and Microbiomes

Human gut microbiome

Clostridium difficile carriage in adult cystic fibrosis (CF); implications for patients with CF and the potential for transmission of nosocomial infection – D.G. Burke – Journal of Cystic Fibrosis

* Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals – Christian Benedict – Molecular Metabolism

Community-Metabolome Correlations of Gut Microbiota from Child-Turcotte-Pugh of A and B Patients – Xiao Wei – Frontiers in Microbiology

Review: Role of gut microbiota in atherosclerosis – Annika Lindskog Jonsson- Nature Reviews Cardiology

Review: The role of diet on gut microbiota composition – S. Bibbò – European Review for Medical and Pharmacological Sciences

Review: Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection – Camilla Tincati – AIDS Research and Therapy

Review: Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes – Elizabeth L. Johnson – Journal of Molecular Medicine

Review: Gut Homeostasis, Microbial Dysbiosis, and Opioids – Fuyuan Wang – Toxicologic Pathology

Animal and in vitro experiments

Sensitive and Simplified Detection of Antibiotic Influence on the Dynamic and Versatile Changes of Fecal Short-Chain Fatty Acids – Xiaoya Zhao – PLOS ONE

* Recognition of extremophilic archaeal viruses by eukaryotic cells: a promising nanoplatform from the third domain of life – Kristine Buch Uldahl – Scientific Reports

Unconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk – Kalaimathi Govindarajan – PLOS ONE

Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs – Anne-Lie Blomström – PLOS ONE

Intraluminal Flagellin Differentially Contributes to Gut Dysbiosis and Systemic Inflammation following Burn Injury – Logan Grimes – PLOS ONE

Early-Life Sugar Consumption Affects the Rat Microbiome Independently of Obesity –
Emily E Noble – Journal of Nutrition

Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Dietary fat and gut microbiota interactions determine diet-induced obesity in mice – Raphaela Kübeck – Molecular Metabolism

Animal microbiome

Deconstructing the Bat Skin Microbiome: Influences of the Host and the Environment –
Christine V. Avena – Frontiers in Microbiology

Plant, root, and soil microbiome

A temporal assessment of nematode community structure and diversity in the rhizosphere of cisgenic Phytophthora infestans-resistant potatoes – Vilma Ortiz – BMC Ecology

Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China – Min Liu – Canadian Journal of Microbiology

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach – Véronique Gourmelon – PLOS ONE

Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain – Min Jung Kwon – Global Change Biology

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China – Zhi-Feng Zhou – Archives of Environmental Contamination and Toxicology

Method: Assessing Bacterial and Fungal Diversity in the Plant Endosphere – Bernd Wemheuer – Methods in Molecular Biology: Metagenomics

Water microbiome

Method: Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies – Dominik Schneider – Methods in Molecular Biology: Metagenomics

Method: Construction and Screening of Marine Metagenomic Large Insert Libraries – Nancy Weiland-Bräuer – Methods in Molecular Biology: Metagenomics

Food microbiology

Microbiological Quality and Variability of Natural Microbiota in Croatian Cheese Maturing in Lambskin Sacks – Jadranka Frece – Food Technology and Biotechnology

Bioinformatics and metagenomics

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing – Hardik I. Parikh – BMC Bioinformatics

Microbes in the news

Podcast (17 min) – Tracking the Daily Rhythms of the Microbiome – Science Friday

ASM delivers “Gift of Knowledge” to Ethiopia with Microbiology Mentoring Program – ASM

Science, publishing, and career
How Trump Could Wage a War on Scientific Expertise. The mechanics of stripping empiricism out of America’s regulatory systems – Ed Yong – The Atlantic

November 30, 2016

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Microbiota-mitochondria crosstalk in Crohn’s Disease, is there a brain microbiome, Akkermansia proteins, Koala retroviruses, New York City park soil microbiomes, gift-giving insects, mud volcanos, 2.5 billion-year-old microbial fossils.

Events

The Gut Institute Microbiome Event in Berkeley, 10/11 December– Gut Institute

General microbiome

Microbial Ecology: Where are we now? – Lisa A. Boughner – Journal of Postdoctoral Research

Human respiratory microbiome

Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients – Ashley D. Smith – PLOS ONE

Human skin microbiome

Towards a bacterial treatment for armpit malodour – Chris Callewaert – Experimental Dermatology

Review: Establishing Tolerance to Commensal Skin Bacteria: Timing Is Everything – Tiffany C. Scharschmidt – Dermatologic Clinics

Human microbes in (nearly) sterile sites

* Lots of extraction controls in this study, but they were not sequenced, and hard to accept there are thriving bacterial communities in our brain: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis – W. G. Branton – Scientific Reports

Human gut microbiome

* Altered intestinal microbiota–host mitochondria crosstalk in new onset Crohn’s disease – Walid Mottawea – Nature Communications

Changes in Intestinal Microbiota Following Combination Therapy with Fecal Microbial Transplantation and Antibiotics for Ulcerative Colitis – Dai Ishikawa – Inflammatory Bowel Diseases

Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism – Federica Gevi – Molecular Autism

Review: Interaction of gut microbiota with bile acid metabolism and its influence on disease states – Christopher Staley – Applied Microbiology and Biotechnology

Animal and in vitro models

* A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice – Hubert Plovier – Nature Medicine

Stable Host Gene Expression in the Gut of Adult Drosophila melanogaster with Different Bacterial Mono-Associations – Carolyn Elya – PLOS ONE

Checks and balances – microbiota shifts in immunosuppressed mice – W. Florian Fricke – Transplantation

Dual-specificity phosphatase 6 deficiency regulates gut microbiome and transcriptome response against diet-induced obesity in mice – Jhen-Wei Ruan – Nature Microbiology

Short Chain Fatty Acids Prevent High-fat-diet-induced Obesity in Mice by Regulating G Protein-coupled Receptors and Gut Microbiota – Yuanyuan Lu – Scientific Reports

Effect of antibiotic pre-treatment and pathogen challenge on the intestinal microbiota in mice – Tadasu Iizumi – Gut Pathogens

Fecal microbiota manipulation prevents dysbiosis and alcohol-induced liver injury in mice – Gladys Ferrere – Journal of Hematology

Impact of red meat consumption on the metabolome of rats – Louise M. A. Jakobsen – Molecular Nutrition & Food Research

11β-hydroxysteroid dehydrogenase-1 deficiency alters the gut microbiome response to western diet – Jethro S Johnson – Journal of Endocrinology

Microbiota induces expression of tumor necrosis factor in postnatal mouse skin – D. V. Yuzhakova – Biochemistry (Moscow)

Animal microbiome

* Phylogenetic diversity of Koala Retrovirus within a Wild Koala Population – K.J. Chappell – Journal of Virology

* Partitioning the effects of mating and nuptial feeding on the microbiome in gift-giving insects – Chad C. Smith – Environmental Microbiology Reports

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2 – Erinn M. Muller – Scientific Reports

Plant, root, and soil microbiome

* Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity – Zachary Charlop-Powers – PNAS

News: Metagenomics Hints at Natural Product Potential of Microbes in New York City Parks – Genome Web
Study: New York City Dirt Rich in Bacteria Related to Medical Treatments – Robert Lee Hotz

* Sulfur-oxidizing bacteria prior to the Great Oxidation Event from the 2.52 Ga Gamohaan Formation of South Africa -Andrew D. Czaja – Geology

Geologist uncovers 2.5 billion-year-old fossils of bacteria that predate the formation of oxygen – Phys.org

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls – Cynthia M. Kallenbach – Nature Communications

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium – Alexander B. Chase – Frontiers in Microbiology

Molecular phylogeny, diversity, community structure, and plant growth promoting properties of fungal endophytes associated with the corms of saffron plant: An insight into the microbiome of Crocus sativus Linn. – Zahoor Ahmed Wani – Fungal Biology

Host and tissue variation overshadow the response of boreal moss-associated fungal communities to increased nitrogen load – Marie L. Davey – Molecular Ecology

Responses of Methanogenic and Methanotrophic Communities to Elevated Atmospheric CO2 and Temperature in a Paddy Field – Yuan Liu – Frontiers in Microbiology

Microbial community structure of surface sediments from a tropical estuarine environment using next generation sequencing – Lidita Khandeparker – Ecological Indicators

Fungal endophytic communities associated to the phyllosphere of grapevine cultivars under different types of management – Carla Marisa Reis Varanda – Fungal Biology

Shifting patterns of microbial N-metabolism across seasons in upland Alaskan tundra soils – Shawna McMahon – Soil Biology and Biochemistry

Disruption of plant-soil-microbial relationships influences plant growth – Daniel P. Keymer – Journal of Ecology

Review: Rhizobial diversity and function in rooibos (Aspalathus linearis) and honeybush (Cyclopia spp.) plants: A review – C. Brink – South African Journal of Botany

Water and extremophile microbiome

Landscape-scale spatial abundance distributions discriminate core from random components of boreal lake bacterioplankton – Juan Pablo Niño-García – Ecology Letters

Diversity and Distribution of Phenol Oxidase Producing Fungi from Soda Lake and Description of Curvularia lonarensis sp. nov. – Rahul Sharma – Frontiers in Microbiology

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports

* Comparative study of Dushanzi and Baiyanggou mud volcano microbial communities in Junggar Basin in Xinjiang, China – Zhiyong Huang – International Research Journal of Public and Environmental Health

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports

Review: Sources of Antibiotics: Hot springs – Girish B. Mahajan – Biochemical Pharmacology

Metagenomics and bioinformatics

Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes – Jonsson Viktor – Journal of Computational Biology

Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains – Weinan Liao – Scientific Reports

Techniques

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community – Miten Jain – Genome Biology

Microbes in the news

The “Internet Of Food,” DNA Testing, And The Quest For The Perfect Diet – Fastcompany

Geologist uncovers 2.5 billion-year-old fossils of bacteria that predate the formation of oxygen – Phys.org

Major finding identifies nitrogen as key driver for gut health – Knowridge

Each animal species hosts a unique microbial community and benefits from it – David Salisbury – Vanderbilt University News

In Brazil, prestigious scientific journal “Nature Communications” focuses on Adventist lifestyle – Felipe Lemos – Adventist

Genes, early environment sculpt the gut microbiome – Science Daily

OpenBiome Now Stores Your Stool In Case of C. difficile Infection – Gastroenterology and Endoscopy News

November 26, 2016

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Human reproductive microbiome

Una destinatio, viae diversae: Does exposure to the vaginal microbiota confer health benefits to the infant, and does lack of exposure confer disease risk? – Kjersti Aagaard – EMBO Reports

Review: Female reproductive tract microbiome in gynecological health and problems – Shyamalina Haldar – Journal of Reproductive Health and Medicine

Animal microbiome

Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria – Violetta Vacchini – Environmental Microbiol Reports

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis – Juliane Wippler – BMC Genomics

Microbial communities of lycaenid butterflies do not correlate with larval diet – Melissa Whitaker – Frontiers in Microbiology

Bees: Report on the microbiota of Melipona quadrifasciata affected by a recurrent disease – Sebastián Díaz – Journal of Invertebrate Pathology

Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants – Aline Sartori Guidolin – Microbial Ecology

Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes – Dennis Versluis – Frontiers in Microbiology

Plant, root, and soil microbiome

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks – Eduardo Pérez-Valera –  Environmental Microbiology

Integrated Proteomics and Metabolomics Suggests Symbiotic Metabolism and Multimodal Regulation in a Fungal-Endobacterial System – Zhou Li – Environmental Microbiology

Water and extremophile microbiome

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient – C. Monard – Scientific Reports

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments – Sizhong Yang – Scientific Reports

Microbial Activity Response to Solar Radiation across Contrasting Environmental Conditions in Salar de Huasco, Northern Chilean Altiplano – Klaudia L. Hernández – Frontiers in Microbiology

Built environment / money microbiome

Dirty Money: A Matter of Bacterial Survival, Adherence, and Toxicity – Frank Vriesekoop – Microorganisms

Metabolomics

Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes – Jeremy L. Motley – Journal of Natural Products

http://pubs.acs.org/doi/full/10.1021/acs.jnatprod.6b00772

Techniques

Note: human contamination in feces samples is usually low (e.g. compared to oral or vaginal samples; not really an issue in my opinion: An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction – Jitendra Kumar – Genomics, Proteomics & Bioinformatics

More microbiology

Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria – Fouad El Baidouri – Nature Ecology & Evolution

Press: Reshaping our ideas of bacterial evolution – Science Daily

Microbes in the news

This paper is not yet available online at Molecular Biology and Evolution, but already some press about it:
A comprehensive tree of prokaryotic life – Science Daily
New insights from the most comprehensive tree of prokaryotic life assembled to date – Phys.org

Bacteria taught to bond carbon and silicon for the first time – Aviva Rutkin – New Scientist

Binge-eating bacteria extract energy from sewage – Science Daily

Video: Good Germs; Bad Germs. Microbes in the kitchen, 14 households, 500 swabs – University of Oxford – YouTube

Bacteria Hysteria

Note: Sponsored by a company specialized in pest control and hygiene products. Primary school bacteria leaves teachers at risk of sickness – TES

November 24, 2016

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Happy Thanksgiving! My inbox was full of exciting new papers, so here is a digest before I start cooking.

Microbiota and epigenetics, predatory bacteria to control infection, bacteria control water levels in leaves, microbial volatile compounds affect plant growth, the invertebrate virome, and natural products as mediators of disease.

Human respiratory microbiome

Evidence of microbiota dysbiosis in chronic rhinosinusitis – Michael Hoggard – International Journal of Allergy & Rhinology

Human gut microbiome

ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins – Emily R. Davenport – BMC Genomics

New treatment options for irritable bowel syndrome with predominant diarrhea – Weber, H. Christian – Current Opinion in Endocrinology, Diabetes and Obesity

Animal models

* Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues – Kimberly A. Krautkramer – Molecular Cell

Press: Changes in the diet affect epigenetics via the microbiota – EurekAlert
Gut’s microbial community shown to influence host gene expression – EurekAlert

* Injections of Predatory Bacteria Work Alongside Host Immune Cells to Treat Shigella Infection in Zebrafish Larvae – Alexandra R. Willis – Current Biology

Harnessing the power of predatory bacteria as a ‘living antibiotic’ – Phys.org

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice – Tze Guan Tan – PNAS

Plant, root, and soil microbiome

+ Bacteria establish an aqueous living space in plants crucial for virulence – Xiu-Fang Xin – Nature

Press: Bacteria Spread Infection in Plants by Manipulating Water Level in Leaves – Howard Hughes Medical Institute

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus – Jonathan W. Leff – New Phytologist

Host species and environmental variation can influence rhizobial community composition
– Holly B. Vuong – Journal of Ecology

* Arabidopsis Responds to Alternaria alternata Volatiles by Triggering Plastid Phosphoglucose Isomerase-Independent Mechanisms – Ángela María Sánchez-López – Plant Physiology
* Volatile compounds emitted by diverse phytopathogenic microorganisms promote plant growth and flowering through cytokinin action – Ángela María Sánchez-López – Plant, Cell & Environment
* Commentary: The methylerythritol 4-phosphate pathway as a metabolic crossroad for microbial and plant volatile organic compounds – Manuel Rodriguez-Concepcion – Plant, Cell & Environment

Press: Compounds produced by phytopathogenic microbes encourage plant growth – EurekAlert

Water and extremophile microbiome

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers – Maggie C. Y. Lau – PNAS

Viruses and phages

* Redefining the invertebrate RNA virosphere – Mang Shi – Nature

World of viruses uncovered. Pioneering study of invertebrates discovers 1,445 viruses including several new families – EurekAlert

Metabolomics

* Review: Natural products as mediators of disease – Neha Garg – Natural Products Reports

Techniques

Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe – Sena Bae – PNAS

Research highlight: Culturomics: illuminating microbial dark matter – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Microbes in the news

Small world: The hot field of the microbiome. Ever since the discovery that bacteria can be good for us, there’s been a race to get into the lab. With Christine Szymanski and Josh Neufeld – Sharon Oosthoek – Maclean’s

Allergies: D-tryptophan explains probiotic characteristics of bacteria – Health Canal

Bacteria-destroying robot could replace antibiotics: Dutch inventer (sic) – Janene Pieters – NLTimes

Molecular chameleons reveal bacterial biofilm – EurekAlert

QIAGEN and CosmosID Launch New Plugin for Metagenomics Analysis – BusinessWire

Milliken recalls carpet cleaning powder on bacteria fears – Reuters

Bik’s non-microbiology Picks

Influence of Pokémon Go on Physical Activity: Study and Implications – Tim Althoff – arXiv

Aspartame may prevent, not promote, weight loss by blocking intestinal enzyme’s activity – EurekAlert

November 23, 2016

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Why You Should Probably Be Glad You’re Not a Brown Bear or an Edible Dormouse – Julie Taylor – uBiome blog

“Thankfully, when you have your own microbiome analyzed by uBiome, you’ll be relieved to know that we won’t be sending round a guy in a helicopter with a tranquilizer gun. All you need to do is lightly swab a piece of used toilet paper.”

Human gut microbiome

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection – Stephan J. Ott – Gastroenterology

Research highlight: Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Review: Candida albicans cell-type switching and functional plasticity in the mammalian host – Suzanne M. Noble – Nature Reviews Microbiology

Review: Gut Bacteria and Hydrogen Sulfide: The New Old Players in Circulatory System Homeostasis – Lenka Tomasova – MDPI Molecules

Microbiology of nearly sterile sites

Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome – Kema Malki – PLOS ONE

Animal experiments

Eye of the Finch: Characterization of the Ocular Microbiome of House Finches in Relation to Mycoplasmal Conjunctivitis – Courtney A. Thomason – Environmental Microbiology

Composition and diversity of mucosa-associated microbiota along the entire length of the pig gastrointestinal tract; dietary influences – Jennifer Kelly – Environmental Microbiology

Heat Stress Affects Facultative Symbiont-Mediated Protection from a Parasitoid Wasp – Eleanor R. Heyworth – PLOS ONE

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium – Sandrine Brugiroux – Nature Microbiology

Assessment of the Fecal Microbiota in Beef Calves – J.S. Weese – Journal of Veterinary Internal Medicine

The role of microbiota in compensatory growth of protein-restricted rats – Yizhi Zhu – Microbial Biotechnology

Animal microbiome

Molecular diversity of bacterial endosymbionts associated with dagger nematodes of the genus Xiphinema (Nematoda: Longidoridae) reveals a high degree of phylogenetic congruence with their host – Juan E. Palomares-Rius – Molecular Ecology

Plant, root, and soil microbiome

Shared and host-specific microbiome diversity and functioning of grapevine and accompanying weed plants – Abdul Samad – Environmental Microbiology

Root isoflavonoids and hairy root transformation influence key bacterial taxa in the soybean rhizosphere – Laura J. White – Environmental Microbiology

Water and extremophile microbiome

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean – Wenxue Wu – Environmental Microbiology

Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō‘ihi Seamount – Jarrod J. Scott – Environmental Microbiology

Probing the evolution, ecology and physiology of marine protists using transcriptomics – David A. Caron – Nature Reviews Microbiology

Food microbiology

High-Throughput Sequencing of Viable Microbial Communities in Raw Pork Subjected to a Fast Cooling Process – Chao Yang – Journal of Food Science

Microbes in the news

Set of 12 microbiology postcards – PREORDER – Microbes and Molecules sciart card set featuring bacteria and fungi, gift for scientist – The Vexed Muddler – Etsy.com

Traces of antibiotic-resistant bacteria have been found in polluted city air. Not good – David Nield – ScienceAlert

Why Sprouts Are Especially Good At Harboring Dangerous Bacteria – Sara G. Miller – LiveScience / Huffington Post

Infectious Diseases Keep Delivering Surprises To The U.S. – Katherine Hobson – NPR

UVA Microbiologist Expands His Research Across the Atlantic – University of Virginia

By Wagging its ‘Tail,’ Bacteria Common in CF Lung Infections May Initiate Immune Reaction – Joana Fernandes – Cystic Fibrosis News Today

‘In five years this will be routine’: Map My Gut start-up offers personalised microbiome advice – Annie-Rose Harrison-Dunn – NutraIngredients

Can bacteria in yogurt calm your anxiety? – Jeff Sossamon – Futurity