Category Archives: Phages and viruses

March 12, 2017

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The first day of daylight saving time in the USA and if your Sunday morning started in a (relative) darkness just read about the viruses in the oceanic basement.  Then find out why yogurt can help your mood.  More interesting papers about the gut-brain connection, a microbiota-centric view of diseases of the upper gastrointestinal tract, microbiome and Type 1 & 2 diabetes, and a new method of detecting bacteria during root canal treatments.

General microbiome

Review: Calling All Hosts: Bacterial Communication In Situ – Jessica L. Cleary – Chem

Gut-Brain connection

The Association Between Temperament and Microbiota in Healthy Individuals: A Pilot Study  – Kim H – Psychosomatic medicine

Gut-brain actions underlying comorbid anxiety and depression associated with inflammatory bowel disease –  Aine Abautret-Daly -Acta Neuropsychiatrica

Human gut microbiome

A microbiota-centric view of diseases of the upper gastrointestinal tract – Gerardo Nardone- Gastroenterology & Hepatology

Review: Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine – Jens Nielsen – Cell Metabolism

Intestinal Microbiota in Type 2 Diabetes and Chronic Kidney Disease – A. Sabatino – Current Diabetes Reports

The intestinal proteome of diabetic and control children is enriched with different microbial and host proteins  – Elsa Pinto – Microbiology

Therapeutic efficacy of oral immunization with a non-genetically modified Lactococcus lactis-based vaccine CUE-GEM induces local immunity against Helicobacter pylori infection – Wei Liu – Applied Microbiology & Biotech

Water and extremophile microbiome

Viruses in the Oceanic Basement – OD Nigro -MBio

Models

A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium -Yuli Wang – Biomaterials

Built environment

Review: Microbiome involved in microbial electrochemical systems (MESs): Rijuta G Saratale- Chemosphere

Microbes in the news

Probiotic found in yogurt can reverse depression symptoms, Researchers at the University of Virginia School of Medicine finds

New method of detecting bacteria during root canal treatments 

March 4th, 2017

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Events and jobs

Head, Microbiome Discovery Research – Johnson & Johnson

Multi-site human microbiome

Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients – Jessica R. Galloway-Peña – Genome Medicine

Human gut microbiome

Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use – K. Korpela – Microbiome

Animal experiments

Metaproteogenomics reveals taxonomic and functional changes between cecal and fecal microbiota in mouse – Alessandro Tanca – Frontiers in Microbiology

Animal microbiome

Cultivable gut bacteria provide a pathway for adaptation of Chrysolina herbacea to Mentha aquatica volatiles – Graziano Pizzolante – BMC Plant Biology

Gut bacteria oversee the special relationship between the green mint leaf beetle and watermint – BMC Series Blog

Effects of tussah immunoreactive substances on growth, immunity, disease resistance against Vibrio splendidus and gut microbiota profile of Apostichopus japonicus – Shuhui Ma – Fish & Shellfish Immunology

Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses – Holly H. Ganz – mSystems

The microbiome of the ant-built home: the microbial communities of a tropical arboreal ant and its nest – Jane Lucas – Ecosphere

*Perspective: Gut microbiome transmission in lizards – Timothy J. Colston – Molecular Ecology

Plant, root, and soil microbiome

Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality – Fernando D. Alfaro – Journal of Ecology

Water and extremophile microbiome

Volcanic ash supports a diverse bacterial community in a marine mesocosm – V. Witt – Geobiology

Methylamine as a Nitrogen Source for Microorganisms from a Coastal Marine Environment – Martin Taubert – Environmental Microbiology

Built environment

Response of microbial community structure to pre-acclimation strategies in microbial fuel cells for domestic wastewater treatment – Younghyun Park – Bioresource Technology

Food microbiology

Viable microbial loads on citrus carpoplane during packhouse processing and survival of foodborne pathogens in reconstituted postharvest fungicides – A. Gomba – Journal of Food Safety

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage – Lysiane Duniere – BMC Microbiology

Probiotics / prebiotics

Microbiome dynamic modulation through functional diets based on pre- and probiotics (mannan-oligosaccharides and Saccharomyces cerevisiae) in juvenile rainbow trout (Oncorhynchus mykiss) – Ana Teresa Gonçalves – Journal of Applied Microbiology

Exploration of the effect of probiotics supplementation on intestinal microbiota of food allergic mice – Bo Yang – American Journal of Translational Research

Phages and viruses

Human norovirus binding to select bacteria representative of the human gut microbiota – Erin A. Almand – PLoS ONE

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Bioinformatics

REPARATION: Ribosome Profiling Assisted (Re-)Annotation of Bacterial
genomes – Elvis Ndah – BioRxiv

Normalization and microbial differential abundance strategies depend upon data characteristics – Sophie Weiss – Microbiome

How conserved are the conserved 16S-rRNA regions? – Marcel Martinez-Porchas – PeerJ

Microbes in the news

Gut bacteria affect intestines and brain in IBS patients – Medical News Today

Intestinal Bacteria Alter Gut and Brain Function – Neuroscience News

Why Are People Sending Poop Through the Mail? For Their Health – GQ Magazine

Microbes on the market

Next-gen microbiome drugs are now on sale, should you buy them? – New Scientist

 

February 25, 2017

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Insight into the role of gut microbiome lipid metabolites in central nervous system diseases. A role of invasive plants in altering the soil microbiome. Evidence that microbiome alterations in Crohn’s disease are not genetically based.

Events and jobs

Post-Doctoral Research Associate in immunology, microbiology, virology, and/or biochemistry – MRIGlobal, Gaithersburg, Maryland, USA

Research Scientist – Department of Microbiology – University of Illinois at Urbana-Champaign, USA

Part-Time Microbiology Instructor – Foothill-De Anza Community College District, California, USA

First Stage Researcher with background in environmental microbiology – Faculty of Biology, University of Warsaw, Poland

General microbiome

Altered antibiotic tolerance in anaerobic digesters acclimated to triclosan or triclocarban – Daniel E. Carey – Chemosphere

Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases and Other Escherichia coli Isolated from Food of Animal Origin and Human Intestinal Isolates – Krizman M – Journal of Food Protection

Human oral microbiome

Prospective, randomised, controlled study evaluating early modification of oral microbiota following admission to the intensive care unit and oral hygiene with chlorhexidine – Felipe Francisco Tuon – Journal of Global Antimicrobial Resistance

The potential effect of oral microbiota in the prediction of mucositis during radiotherapy for nasopharyngeal carcinoma -Xiao-Xia Zhu – EBioMedicine

Human urinary microbiome

*Special Issue Preface: Preface to the human microbiome in urologic health and disease – Daniel A. Shoskes – Annals of Translational Medicine

*Review: The mycobiome of the human urinary tract: potential roles for fungi in urology – A. Lenore Ackerman – Annals of Translational Medicine

Human vaginal microbiome

Longitudinal analysis of vaginal microbiota in women with recurrent vulvovaginal candidiasis – Ma X – Journal of Southern Medical University (Nan Fang Yi Ke Da Xue Xue Bao)

Human gut microbiome

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLOS

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z.D Jiang – Alimentary Pharmacology and Therapeutics

Gut-brain axis: Role of lipids in the regulation of inflammation, pain and CNS diseases – Russo R – Current Medicinal Chemistry

What roles do colon stem cells and gap junctions play in the left and right location of origin of colorectal cancers? – James E. Trosko – Journal of Cell Communication and Signaling

Contributions of the Interaction between Dietary Protein and Gut Microbiota to Intestinal Health – Ma N – Current Protein and Peptide Science

*Review: Dietary Fiber Gap and Host Gut Microbiota – Han M – Protein Peptide Letters

Structural Modulation of Gut Microbiota during Alleviation of Antibiotic-Associated Diarrhea with Herbal Formula – Weijie Lv – International Journal of Biological Macromolecules

Association of diverse bacterial communities in human bile samples with biliary tract disorders: a survey using culture and polymerase chain reaction-denaturing gradient gel electrophoresis methods – E. Tajeddin – European Journal of Clinical Microbiology & Infectious Disease

Immunomodulatory Effects of Lactobacillus plantarumLp62 on Intestinal Epithelial and Mononuclear Cells – Thalis Ferreira dos Santos – BioMed Research International

How to modulate gut microbiota: diet, pre-probiotics or antibiotics? – Ponziani FR – Minerva Gastroenterologica E Dietologica

* Review: AISF position paper on nonalcoholic fatty liver disease (NAFLD): Updates and future directions – Italian Association for the Study of the Liver (AISF), Lonardo A – Digestive and Liver Disease

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study -Harry Sokol – Digestive and Liver Disease

 Multi-site human microbiome

Porphyromonas gingivalis lipopolysaccharide induces pro-inflammatory adipokine secretion and oxidative stress by regulating Toll-like receptor-mediated signaling pathways and redox enzymes in adipocytes – Fanny Le Sage – Molecular and Cellular Endocrinology

Animal experiments

Impact of TIGECYCLINE versus other antibiotics on the fecal metabolome and on colonization resistance to CLOSTRIDIUM DIFFICILE in mice – Robin L.P. Jump – Pathological Immunology

Animal microbiome

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird – Jakub Kreisinger – Frontiers in Microbology

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts – Gitta Szabó – The ISME Journal

New roles in hemicellulosic sugar fermentation for the uncultivated Bacteroidetes family BS11 – Lindsey M Solden – The ISME Journal

Changes in rumen microbiota composition and in situ degradation kinetics during the dry period and early lactation as affected by rate of increase of concentrate allowance – K. Dieho – Journal of Dairy Science

Plant, root, and soil microbiome

Response of rhizosphere soil microbial to Deyeuxia angustifolia encroaching in two different vegetation communities in alpine tundra – Lin Li – Scientific Reports

Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants – Sevda Haghi Kia – The ISME Journal

Comparative fibre-degrading capacity in foals at immediate and late post-weaning periods – C. Faubladier – Cambridge Core

The effect of the source of microorganisms on adaptation of hydrolytic consortia dedicated to anaerobic digestion of maize silage – Krzysztof Poszytek – Anaerobe

Water and extremophile microbiome

Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau – Haozhi Long – Environmental Monitoring and Assessment

Direct single-cell biomass estimates for marine bacteria via Archimedes’ principle – Nathan Cermak – The ISME Journal

Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts – Rachel Ashley Levin – The ISME Journal

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton – Ryan W Paerl – The ISME Journal

Elevated temperature increases carbon and nitrogen fluxes between phytoplankton and heterotrophic bacteria through physical attachment – Nestor Arandia-Gorostidi – The ISME Journal

Warming and nutrient enrichment in combination increase stochasticity and beta diversity of bacterioplankton assemblages across freshwater mesocosms – Lijuan Ren – The ISME Journal

Integration of Metagenomic and Stable Carbon Isotope Evidence Reveals the Extent and Mechanisms of Carbon Dioxide Fixation in High-Temperature Microbial Communities – Ryan de Montmollin Jennings – Frontiers in Microbiology

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes – Md Sainur Samad – Frontiers in Microbiology

Predominance of Viable Spore-Forming Piezophilic Bacteria in High-Pressure Enrichment Cultures from ~1.5 to 2.4 km-Deep Coal-Bearing Sediments below the Ocean Floor – Jiasong Fang – Frontiers in Microbiology

Metagenomics and resistome

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection – Li-Guan Li – The ISME

Metabolomics

Assessment of the bimodality in the distribution of bacterial genome sizes – Hyun S Gweon – The ISME Journal

Genome of ‘Ca. Desulfovibrio trichonymphae’, an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut – Hirokazu Kuwahara – The ISME Journal

A family of interaction-adjusted indices of community similarity – Thomas Sebastian Benedikt Schmidt – The ISME Journal

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates – Po-Hsiang Wang – The ISME Journal

Phylogenetic relationships among Staphylococcus aureus isolated from clinical samples in Mashhad, Iran – Farzad Khadem – Journal of Infection and Public Health

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk-disease complex – Abraham Morales-Cruz – Molecular Plant Pathology

More microbes

Redox potential as a master variable controlling pathways of metal reduction by Geobacter sulfurreducens – Caleb E Levar – The ISME Journal

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability – Erin F E Lennon – The ISME Journal

Enhanced microbial electrosynthesis by using defined co-cultures – Jörg S Deutzmann – The ISME Journal

Temperature is a key factor in Micromonas–virus interactions – David Demory – The ISME Journal

Evolutionary convergence in experimental Pseudomonas populations – Peter A Lind – The ISME Journal

Microbes in the news

Are There Health Benefits To Exposing Our Immune Systems To Bacteria? – Forbes
Nutrition: Trust your gut instincts — whole grains are good for you – Los Angeles Daily News

There could be a surprising link between how people respond to a new cancer treatment and their microbiome – Lydia Ramsey – Business Insider

February 23, 2017

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Today’s selection includes an interesting review on how bacteria keep their time. Long term ceftriaxon sodium usage alters gut microbiota and immune system. Clostridium perfringens toxin genes in the gut microbiota of autistic children. Taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. Enjoy!

General microbiome

Distinct signatures of dental plaque metabolic byproducts dictated by periodontal inflammatory status. – Akito Sakanaka – Scientific Reports

*Review: Timing the day: what makes bacterial clocks tick? – Carl Hirschie Johnson – Nature Reviews Microbiology

Human urinary microbiome

Review: The female urinary microbiota, urinary health and common urinary disorders. – Linda Brubaker – Annals of Translational Medicine

Review: Questions and challenges associated with studying the microbiome of the urinary tract – Yige Bao – Annals of Translational Medicine

Review: The association between bacteria and urinary stones. – Andrew L. Schwaderer – Annals of Translational Medicine

Human nearly-sterile sites 

The Conserved Phylogeny of Blood Microbiome – Malay Bhattacharyya – Molecular Phylogenetics and Evolution

Human gut microbiome

Review: The gut microbiome in human neurological disease: A review. – Helen Tremlett – Annals of Neurology

Review: Gut microbiome-based medical methodologies for early-stage disease prevention – Jing-Zhang Wang – Microbial Pathogenesis

Review: Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome. – Hans C. Arora – Annals of Translational Medicine

*Long-term use of ceftriaxone sodium induced changes in gut microbiota and immune system. – Yanjie Guo – Scientific Reports

Note Elies Bik: This study was not performed in humans but in a horrible rat model that can only be qualified as torture. This does not test for depression but for extreme stress. Should not have performed. Proceed with extreme caution. Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics. – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Specific inulin-type fructan fibers protect against autoimmune diabetes by modulating gut immunity, barrier function and microbiota homeostasis. – Kang Chen – Molecular Nutrition and Food Research

Gut microbiota and oxalate homeostasis. – Marguerite Hatch – Annals of Translational Medicine

Tryptophan: A gut microbiota-derived metabolites regulating inflammation. – Lucie Etienne-Mesmin –  World Journal of Gastrointestestinal Pharmacology

*Detection of Clostridium perfringens toxin genes in the gut microbiota of autistic children. – Sydney M. Finegold – Anaerobe

Animal experiments

Butyrate restores HFD induced adaptations in brain function and metabolism in mid-adult obese mice – Ilse A. C. Arnoldussen – International Journal of Obesity

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile. – Lucie Etienne-Mesmin – Gut

Animal microbiome

Individual Signatures Define Canine Skin Microbiota Composition and Variability. – Anna Cuscó – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens‬‬. – Ines Aline Aschenbrenner – Molecular Ecology

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change. – Lin Li – Ecology and Evolution

Water and extremophile microbiome

*Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic. – Etienne Yergeau – Scientific Reports

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils. – Adrienne Narrowe – Environmental Microbiology

Food microbiology

Enhanced Control of Listeria monocytogenes by Enterococcus faecium KE82, a Multiple Enterocin–Producing Strain, in Different Milk Environments. – Elpinki Vandera – Journal of food protection

Probiotics / prebiotics

Review: Probiotics for prevention of urinary stones. – John C. Lieske – Annals of Translational Medicine

Review: Review of the mechanisms of probiotic actions in the prevention of colorectal cancer. – Sandra A. dos Reis – Nutrition Research

Phages and viruses

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses – Lisa Zeigler Allen – mSystems

Microbes in the news 

The Future Of Skin Care: Lotions That Feed Our Microbiome

Collapse of Aztec society linked to catastrophic salmonella outbreak

Smart’ bacteria remodel their genes to infect our intestines

Smallest CRISPR So Far Comes from Food Poisoning Bacteria

Anitha’s non-microbiology picks 

An epigenetics gold rush: new controls for gene expression

Scientists discover 7 ‘Earthlike’ planets orbiting a nearby star

February 22, 2017

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Here’s your daily routine. Autoregressive and non-autoregressive regimes in the human gut microbiome. The interaction between diet, microbiota and personalized nutrition. More topics to think about: reproducibility in the microbiome studies, intellectual property in the microbiome industry, and heavy rain brings fatal bugs to northern Californian dogs.

Events and jobs

The 3rd Annual Translational Microbiome Conference – April 11-13, 2017 – Boston, MA

Microbiology Laboratory Technician – ALS Life Sciences – Ireland

Field Sales Manager, Microbiology, Molecular Biology, Chemistry – Cromwell and Clark – UK

General microbiology

Vancomycin displays time-dependent eradication of mature Staphylococcus aureus biofilms – Virginia Post – Journal of Orthopaedic Research

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment – James E. Gomez – eLife

Press: Genetic mutations that drive antibiotic resistance in bacteria – Science Daily

Global Proteomic Analyses of Macrophage Response to Mycobacterium tuberculosis Infection – Valerie Poirier – BioRxiv

Human gut microbiome

*Two dynamic regimes in the human gut microbiome – Sean M. Gibbons – PLoS Computational Biology

Human intestinal microbiota: Role in development and functioning of the nervous system – O. V. Averina and V. N. Danilenko – Microbiology

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Review: The Influence of the Microbiome on Early-Life Severe Viral Lower Respiratory Infections and Asthma—Food for Thought? – Jason P. Lynch – Frontiers in Immunology

Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection – fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy – Z. D. Jiang – Alimentary Pharmacology and Therapeutics

Review: “We are what our bacteria eat”: The role of bacteria in personalizing nutrition therapy in gastrointestinal conditions – Ruth Harvie – Journal of Gastroenterology and Hepatology

The distinct features of microbial ‘dysbiosis’ of Crohn’s disease do not occur to the same extent in their unaffected, genetically-linked kindred – Umer Zeeshan Ijaz – PLoS One

Animal experiments

Not peer reviewed: Molecular assessment of the fecal microbiota in healthy cats and dogs before and during supplementation with fructooligosaccharides (FOS) and inulin using high-throughput 454-pyrosequencing – Jose F Garcia-Mazcorro – PeerJ

Mouse: The influence of rosuvastatin upon the gastrointestinal microbiota and host gene expression profiles – James A. Nolan – American Journal of Physiology – Gastrointestinal and Liver Physiology

High-cholesterol diet does not alter gut microbiota composition in mice – Lidiya G. Dimova – Nutrition & Metabolism

The effect of gut microbiome on tolerance to morphine mediated antinociception in mice – Minho Kang – Scientific Reports

Mouse: Ambient Ultrafine Particle Ingestion Alters Gut Microbiota in Association with Increased Atherogenic Lipid Metabolites – Rongsong Li – Scientific Reports

Editorial: Sources of variation: Animal microbiota – Alexandra A. Mushegian – Science Signaling

The effects of amoxicillin treatment of newborn piglets on the prevalence of hernias and abscesses, growth and ampicillin resistance of intestinal coliform bacteria in weaned pigs – Jinhyeon Yun – PLoS One

Animal microbiome

Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilised by these intracellular bacteria – Alyce Taylor-Brown – Environmental Microbiology

Corals: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach – Edward G Smith – The ISME Journal

Prevalence of AmpC- and Extended-Spectrum β-Lactamase-Harbouring Enterobacteriaceae in Faecal Flora of a Healthy Domestic Canine Population – D. A. Mathys – Zoonoses and Public Health

Different antibiotic growth promoters induce specific changes in the cecal microbiota membership of broiler chicken – Marcio C. Costa – PLoS One

Plant, root and soil microbiome

A Plant Bacterial Pathogen Manipulates Its Insect Vector’s Energy Metabolism – Nabil Killiny – Applied and Environmental Microbiology

Effective control of root-knot nematode disease with Pseudomonad rhizobacteria filtrate – Ishwar Prakash Sharma and A.K. Sharma – Rhizosphere

Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow region – E. N. Kaparullina – Microbiology

Epiphytic microorganisms degrading aromatic hydrocarbons from the phyllosphere of urban woody plants – O. I. Sazonova – Microbiology

Book chapter: Improving Soil Fertility and Soil Functioning in Cover Cropped Agroecosystems with Symbiotic Microbes – Yang Zhou – Agro-Environmental Sustainability

Book chapter: Role of Phosphate-Solubilising Microorganisms in Sustainable Agricultural Development – Rajesh Kumar and Beenu Shastri – Agro-Environmental Sustainability

Influence of rhinoceros beetle (Trypoxylus dichotomus septentrionalis) larvae and temperature on the soil bacterial community composition under laboratory conditions – Jinu Eo – Soil Biology and Biochemistry

Water and extremophile microbiome

Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India – A. Sharma – Microbiology

Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment – Dong Xu – AMB Express

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens – Jessica Chopyk – Microbiome

The interaction between the proliferating macroalga Asparagopsis taxiformis and the coral Astroides calycularis induces changes in microbiome and metabolomic fingerprints – Stéphane Greff – Scientific Reports

Bioinformatics

MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data – Christopher Noune and Caroline Hauxwell – Biology

Techniques

DNA Barcoding for Fractured Reservoir Analysis – An Initial Investigation – Yuran Zhang – PROCEEDINGS, 42nd Workshop on Geothermal Reservoir Engineering

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR – Claudio Foschi – PLoS One

Microbes in space

The Effect of High-Dose Ionizing Radiation on the Isolated Photobiont of the Astrobiological Model Lichen Circinaria gyrosa – Joachim Meeßen – Astrobiology

Phages and viruses

Non-classical phase diagram for virus bacterial coevolution mediated by clustered regularly interspaced short palindromic repeats – Pu Han and Michael W. Deem – Journal of the Royal Society Interface

Microbes in the news

Probiotics: IP Perspectives on the Microbiome – Jing Liu and Daniel Yarbrough – JDSupra

Targeting Gut Bacteria May Be The Key To Preventing Alzheimer’s – Carolyn Gregoire – The Huffington Post

Space Bacteria Draws Focus of Researchers – Robert Lee Hotz – Wall Street Journal (subscription required)

Irish experts key to battling bacteria – Niall Murray – Irish Examiner

Heavy Rains Bring Dog-Killing Bacteria to Northern California – Tex Dwokin – Care2

February 10, 2017

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Today’s digest features fascinating  research articles on the potential of glycomacropeptide in modulating human gut microbiota of elderly, identifying IBD-like microbiome in at-risk healthy relatives of IBD patients with no clinical signs of inflammation,  long-term climate change affects soil microbial communities and  a reviews on the potential role of transglutaminases in autoimmunity.

General microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

The microbiome of the octocoral Lobophytum pauciflorum: minor differences between sexes and resilience to short-term stress – Wiebke Wessels – FEMS Microbiol Ecology

Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas – Hannah Wang- Genome Medicine

Microbiota composition of simultaneously colonized mice housed under either a gnotobiotic isolator or individually ventilated cage regime – Randi Lundberg – Scientific Reports

Microbial strain-level population structure and genetic diversity from metagenomes – Duy Tin Truong – Genome Research

*Review: Transglutaminases in Dysbiosis As Potential Environmental Drivers of Autoimmunity – Aaron Lerner- Frontiers in Microbiology

Pregnancy and early life

Perspective: The maternal microbiome: Cause or consequence of obesity risk in the next generation? – Jacob E. Friedman – Obesity

Review: Charting the Maternal and Infant Microbiome: What Is the Role of Diabetes and Obesity in Pregnancy? – Sirtaj Singh – Current Diabetes Reports

Human skin microbiome

Skin Microbiome in Small- and Large-plaque Parapsoriasis – Alexander Salava – Acta Dermato-Venereologica

Human gut microbiome

*Glycomacropeptide sustains microbiota diversity and promotes specific taxa in an artificial colon model of elderly gut microbiota – Alexandra Ntemiri – Journal of Agricultural and Food Chemistry

A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – Cellular and Molecular Gastroenterology and Hepatology

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLOS ONE

Review: Gut microbiota modulation and anti-inflammatory properties of dietary polyphenols in IBD: new and consolidated perspectives.  – Angelo Santino – Current Pharmaceutical Design

Animal experiments 

Changes in Microbiota in Rumen Digesta and Feces Due to a Grain-Based Subacute Ruminal Acidosis (SARA) Challenge – Jan C. Plaizier – Microbial Ecology

A maternal Western diet during gestation and lactation modifies offspring’s microbiota activity, blood lipid levels, cognitive responses, and hippocampal neurogenesis in Yucatan pigs – David Val-Laillet – FASEB Journal

Animal microbiome 

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries) – Wenxi Qian – Canadian Journal of Microbiology

Plant, root, and soil microbiome

Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones – Manoj Kumar – Frontiers in Microbiology

*Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Specificity of root microbiomes in native-grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization – Rakesh Santhanam – Molecular Ecology

Water and extremophile microbiome 

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

Phages and viruses

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB – Colin Buttimer – Frontiers in Microbiology

Techniques

Successive DNA extractions improve characterization of soil microbial communities – Mauricio R. Dimitrov – PeerJ

Microbes in the news

Bacteria fed synthetic iron-containing molecules turn into electrical generators

Method to identify bacteria in blood samples works in hours instead of days

Characterizing Cervical Cancer by HPV Strain, Mutations, and Molecular Features

Phage In The Time Of Cholera

An Innovative New Cancer Therapy Hijacks Bacteria to Fight Tumors

Microbes on the market

Chan Zuckerberg Biohub funds first crop of 47 investigators

Anitha’s non-microbiology picks 

Could this pollinating drone replace butterflies and bees?

The physics of why valve amps sound better

Circuits survive on Venus, electronics powered by stomach acid

February 8, 2017

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A dense Digest today, a lot of reviews on the human gut microbiome, a plethora of papers on plant, soil and water microbiomes, and an alarmingly high rate of multi-drug resistant bacteria from human fecal samples in China

Jobs

Teaching and Learning Fellow in Microbiome Data Analysis – University of British Columbia

Microbiology Quality Technician II – CR Bard

Postdoctoral Research Assistant on the Social Dimensions of the Microbiome – University of Oxford

General microbiology

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes – Luke R. Thompson – Environmental Microbiology

Effect of antibiotics on bacterial populations: a multi-hierachical selection process – José Luis Martínez – F1000 Research

Plant growth promoting potential and phylogenetic characteristics of a lichenized nitrogen fixing bacterium, Enterobacter cloacae – Chidanandamurthy Thippeswamy Swamy – Journal of Basic Microbiology

*High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families – Lan-Lan Zhong – bioRxiv

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States – Yi Chen – PLoS One

Human skin microbiome

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

Beyond Cell Division: the Ecological Roles of Autolysins in Oral Biofilm Communities – Nyssa Cullin – Current Oral Health Reports

Human lung microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients – Michael J. Cox – PLoS One

Human gut microbiome

Review: Intestinal Microbiota: Facts and Fiction – M Kverka – Digestive Diseases

Review: Evolutionary and ecological forces that shape the bacterial communities of the human gut – J S Messer – Mucosal Immunology

Review: Dietary Fiber and Prebiotics and the Gastrointestinal Microbiota – Hannah D. Holscher – Gut Microbes

Review: The Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host – Qi Hui Sam – International Journal of Molecular Sciences

Review: The Gut Microbiome in Irritable Bowel Syndrome and Other Functional Bowel Disorders – Yehuda Ringel – Gastroenterology Clinics of North America

Many more human gut microbiome reviews available from the March Issue of the Gastroenterology Clinics of North America

Human gut-microbiome-brain axis

Editorial: Tightening the Case for Gut Microbiota in Autism-Spectrum Disorder – Jonathan Braun – CMGH Cellular and Molecular Gastroenterology and Hepatology

Review: The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan – Gastroenterology Clinics of North America

Metabolomics

Review: Mixing omics: combining genetics and metabolomics to study rheumatic diseases – Cristina Menni – Nature Reviews Rheumatology

Review: Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome – Robert S. Jansen – Trends in Pharmacological Sciences

Rats Urinary Metabolome Reveals for the Potential Role of Functional Foods and Exercise in Obesity Management – Mohammed Farag – Food and Function

Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata) – Ruben Gil-Solsona – PeerJ

Animal experiments

Mouse: Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions – Bei Gao – Environmental Health Perspectives

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet – Hyunmin Koo – Journal of Microbiological Methods

Commentary: Zebrafish screens for new colitis treatments – a bottom-up approach – Jou A. Lee – The FEBS Journal

Mouse: Resistant starch can improve insulin sensitivity independently of the gut microbiota – Laure B. Bindels – Microbiome

Animal microbiome

Invited review: Large-scale indirect measurements for enteric methane emissions in dairy cattle: A review of proxies and their potential for use in management and breeding decisions – E. Negussie – Journal of Dairy Science

Variation of the microbiota and metabolome along the canine gastrointestinal tract – Julia B. Honneffer – Metabolomics

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses – Dagne Duguma – mSphere

Review: Progress in fish gastrointestinal microbiota research – An R. Wang – Reviews in Aquaculture

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics – Pinghua Li – Scientific Reports

Plant, root and soil microbiome

Fungi from Brazilian Savannah and Atlantic rainforest show high antibacterial and antifungal activity – Paula de Paula Menezes Barbosa – Biocatalysis and Agricultural Biotechnology

Impact of Elevated CO2 and/or Temperature on the AM Fungal Diversity in Groundnut Rhizosphere under Open Top Chamber facility – HN Asha – International Journal of Current Microbiology and Applied Sciences

Seed-coating fenugreek with Burkholderia rhizobacteria enhances yield in field trials and can combat Fusarium wilt – Harish Kuma – Rhizosphere

Changes at the Rhizosphere Microbiota of the Sunflower–Orobanche cumana Wallr Pathosystem – TH Hristev – International Journal of Current Microbiology and Applied Sciences

Review: Phosphate Solubilizing Microbes: An Overview – KP Ingle – International Journal of Current Microbiology and Applied Sciences

Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome – Vanessa Nessner Kavamura – Genome Announcements

Effects of Garlic/Cucumber Relay Intercropping on Soil Enzyme Activities and the Microbial Environment in Continuous Cropping – Lantian Du – HortScience

Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system – Cristina Becerra-Castro – Antonie van Leeuwenhoek

Soil microbial community responses to long-term land use intensification in subtropical grazing lands – Sutie Xu – Geoderma

The impact of salinity on the microbial response to drying and rewetting in soil – Kristin M. Rath

The influence of different concentrations of bio-organic fertilizer on cucumber Fusarium wilt and soil microflora alterations – Nan Huang – PLoS One

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype – Jakson Leite – Frontiers in Plant Science

Microbial Interactions in the Phyllosphere Increase Plant Performance under Herbivore Biotic Stress – Muhammad Saleem – Frontiers in Microbiology

Water and extremophile microbiome

Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal Power Plant – Yasuhiro Fujino – Genome Announcements

Marine Microbes as a Potential Source of Cellulolytic Enzymes – N. Trivedi – Chapter 2 of Advances in Food and Nutrition Research, Vol. 79

Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. – Ivan Pogrebnyakov – PLoS One

Coupled Effects of Electrical Stimulation and Antibiotics on Microbial Community in Three-Dimensional Biofilm-Electrode Reactors – Hai-Liang Song – Water, Air, & Soil Pollution

Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas – Wilson H. Johnson – BMC Microbiology

Effects of chemical cleaning on RO membrane inorganic, organic and microbial foulant removal in a full-scale plant for municipal wastewater reclamation – Tong Yu – Water Research

Microbial nitrification, denitrification and respiration in the leached cinnamon soil of the upper basin of Miyun Reservoir – Wen Xu – Scientific Reports

Microbes in space

The Effects of HZE Particles, γ and X-ray Radiation on the Survival and Genetic Integrity of Halobacterium salinarum NRC-1, Halococcus hamelinensis, and Halococcus morrhuae – Leuko Stefan – Astrobiology

Survival, DNA Integrity, and Ultrastructural Damage in Antarctic Cryptoendolithic Eukaryotic Microorganisms Exposed to Ionizing Radiation – Pacelli Claudia – Astrobiology

Phages and viruses

Genomic sequence of ‘Candidatus Liberibacter solanacearum’ haplotype C and its comparison with haplotype A and B genomes – Jinhui Wang – PLoS One

Technology

Microbial Typing by Machine Learned DNA Melt Signatures – Nadya Andini – Scientific Reports

Bioinformatics

From Culture to High-Throughput Sequencing and Beyond: A Layperson’s Guide to the “Omics” and Diagnostic Potential of the Microbiome – Paul W. O’Toole – Gastroenterology Clinics of North America

Microbes in the news

2017 sneak peek: What the new year holds for science – Elizabeth Gibney – Nature

Is It the “Terrible Twos”? Or Is It a Disrupted Gut Microbiome? – Chris Kresser

Microbes on the market

Human Microbiome Market : Global Market Snapshot by 2020 – Persistence Market Research

January 25, 2017

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Joint opinion on measures by the EU to reduce antimicrobial agents in animal husbandry, diet changes the gut microbiome of dogs, and synthetic chemicals might drive global climate change.

Jobs

PhD Position: THE ROLE OF THE GUT MICROBIOME IN LIVER DISEASE: DEVELOPMENT Of BIOINFORMATIC APPROACHES TO IDENTIFY, CHARACTERISE AND ANALYSE THE GUT VIROME – KU Leuven

Postdoctoral Research Scientist, Microbiology, School of Natural Sciences, NUI Galway

Microbiology Supervisor – Clinical Pathology Laboratories, Inc

General microbiology and policy

Artificial bacteria: A semisynthetic organism engineered for the stable expansion of the genetic alphabet – Yorke Zhang – PNAS

Policy opinions: EMA and EFSA Joint Scientific Opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA) – CVMP and BIOHAZ – EFSA Journal

Acid-suppression medications and bacterial gastroenteritis: a population-based cohort study – Wei Li – british journal of clinical pharmacology

Animal experiments

Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions – Qinghong Li – mBio

Water and extremophile microbiome

Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality – Elvina Lee – PLoS One

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing – Mathis Hjort Hjelmsø – PLoS One

Phages and viruses

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems – Luis Jose Rene Arredondo-Hernandez – PLoS One

The Complete Genome Sequence of a Second Distinct Betabaculovirus from the True Armyworm, Mythimna unipuncta – Robert L. Harrison – PLoS One

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand – Achiraya Siriphap – PLoS One

Bioinformatics

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective – Not Only Size Matters! – John Vollmers – PLoS One

Microbes in the news

Study: Babies’ Microbiomes Indifferent to Mode of Delivery – Kerry Grens – The Scientist

About FishTaco: Microbiome as complex as previously thought – Julian Harris – PHG Foundation

Auckland’s water shock: Bacteria levels ‘dangerously high’ – NZ Herald

For healthier buildings, just add bacteria? – Ed Yong – Ted

Xin’s non-microbiology pick

Synthetic chemicals as agents of global change – Emily S Bernhardt – Frontiers in Ecology and the Environment

January 22, 2017

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Events and Jobs

PhD scholarship in Molecular Microbiology– University of Copenhagen-Last Date: February 8, 2017

Quality Control Associate-Microbiology–US-CA-Del Mar

General Microbiome

Impacts of chemical gradients on microbial community structure-Jianwei Chen-The ISME Journal

Human Skin

Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis-Yijing Yu-Journal of Proteomics

Human Respiratory Microbiome

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma–Marcos Pérez-Losada-PLOS One

Adherence of Pseudomonas aeruginosa to cystic fibrosis buccal epithelial cells–Meike Lingner-ERJ

Human Vaginal Microbiome

The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk-Lindsay M. Kindinger-Microbiome

Human Gut Microbiome

Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition-Keerati Wanchai-The American Journal of the Medical Sciences

Review-Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis-Hai Ning Liu-Digestive and Liver Disease

Animal Microbiome

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)-Wenxi Qian-Canadian Journal of Microbiology

The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum–Stephen M. Beverley-mBio

The normal vaginal and uterine bacterial microbiome in giant pandas (Ailuropoda melanoleuca)-Xin Yang-Microbiological Research

Pathogen-mediated manipulation of arthropod microbiota to promote infection–Nabil M. Abraham-PNAS

The gastrointestinal tract of farmed mink (Neovison vison) maintains a diverse mucosa-associated microbiota following a 3-day fasting period-Martin I. Bahl-Microbiology Open

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons–Elizabeth A. Miller-BMC Microbiome

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest-Martin Hartmann-Molecular Ecology

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice-Jingna Liu-Scientific Reports

Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe-Ning Ling-Geoderma

Mineralization of “non-metabolizable” glucose analogues in soil: potential chemosensory mimics of glucose-Kyle Mason-Jones-Journal of Plant Nutrition and Soil Science

Deciphering composition and function of the root microbiome of a legume plant-Kyle Hartman-BMC Microbiome

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass-Colin A. Jackson-Journal of Applied Microbiology

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil–Lateef B. Salam-Environmental Science and Pollution Research

Biocontrol effects of Brevibacillus laterosporus AMCC100017 on potato common scab and its impact on rhizosphere bacterial communities-Shengfu Chen-Biological Control

Co-inoculation with Enterobacter and Rhizobacteria on Yield and Nutrient Uptake by Wheat (Triticum aestivum L.) in the Alluvial Soil Under Indo-Gangetic Plain of India-Ashok Kumar-Journal of Plant Growth Regulation

 Ornamental flowers in new light: Artificial lighting shapes the microbial phyllosphere community structure of greenhouse grown sunflowers (Helianthus annuus L.)–Beatrix W. Alsanius–Scientia Horticulturae

Extremophiles

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats-Meinhard Simon-ISME

Review: Marine Bacterioplankton Seasonal Succession Dynamics-Carina Bunse-Trends in Microbiology

Review: Stress response physiology of thermophiles–Preeti Ranawat-Archives of Microbiology

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights-Emanuele Bosi-BMC Genomics

Sulfur compound oxidation and carbon co-assimilation in the haloalkaliphilic sulfur oxidizers Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum-Wee Kiong Ang-Research in Microbiology

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman–Kaitlin R. Rempfert-Extreme Microbiology

Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system-Qian Dong-Aquatic Microbiology

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China-Jingqiu Liao-Limnology and Oceanography

Unraveling the microbial processes of black band disease in corals through integrated genomics-Yui Sato-Scientific Reports

Preliminary Phylogenetic Analysis of Thermophilic Bacteria Producing Protease isolated from Kuantan Malaysia -Essam A. Makky-JBSR

Identification of a novel fatty acid in the cell membrane of Chryseobacterium frigidisoli PB4T isolated from an East Antarctic glacier forefield-Kai Mangelsdorf-Organic Geochemistry

Phosphorus removal by marine bacterium enhanced with iron in the presence of silicon–Yanru Wang-Journal of Chemical Technology and Biotechnology

 Built Environment Microbiology

Developing Evidence-based Tools for Designing and Evaluating Hospital Inpatient Rooms–Xiaobo Quan-Journal of Interior Design

Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study-J T Salin-Environmental Research

Techniques

Review:  Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism-Robert J. Wallace-Genetics Selection Evolution

Balance Trees Reveal Microbial Niche Differentiation–James T. Morton-Ecological and Evolutionary Science

Virus

Review: Virus–host interactions and their roles in coral reef health and disease–Rebecca Vega Thurber-Nature Reviews Microbiology

Virome of US bovine calf serum-Mohammadreza Sadeghi-Biologicals

More Microbes

Bacillus zeae sp. nov. isolated from the rhizosphere of Zea mays– Peter Kämpfer-International Journal of Systematic and Evolutionary Microbiology

Microbes in News

Capnophilic Enterobacteriaceae-JM. Sahuquillo Arce-Diagnostic Microbiology and Infectious Disease

January 15, 2017

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Microbes in Idiopathic Pulmonary Fibrosis, review on the female urinary microbiota, koalas with “wet bottom”, virus metagenomics of the Namib desert, biosignatures in fossils.

Jobs

Microbiome Research Associate Job – Merck Research Laboratories – Cambridge, MA – Science Careers

Human urinary tract microbiome

* Review: The female urinary microbiota, urinary health and common urinary disorders – Linda Brubaker – Annals of Translational Medicine

Human respiratory microbiome

* Host-Microbial Interactions in Idiopathic Pulmonary Fibrosis – Philip L Molyneaux – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The human gut microbiome as source of innovation for health: which physiological and therapeutic outcomes could we expect?: Human gut mibrobiome [SIC] as source of innovation for health – Joël Doré – Thérapie

In French: Microbiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Le microbiote intestinal comme source d’innovation pour la santé – Joël Doré – Thérapie

Review: Seafood allergen-induced hypersensitivity at the microbiota-mucosal site: implications for prospective probiotic use in allergic response regulation – Linglin Fu – Critical Reviews in Food Science and Nutrition

Review: Impact Of Human Aging And Modern Lifestyle On Microbiota – Maria Gabriela Valle Gottlieb – Critical Reviews in Food Science and Nutrition

Review: Effects of environmental pollutants on gut microbiota – Yuanxiang Jin – Environmental Pollution

Animal experiments

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

Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome – Francesco Rubino – The ISME Journal

Wolbachia Affects Reproduction and Population Dynamics of the Coffee Berry Borer (Hypothenemus hampei): Implications for Biological Control – Yobana A. Mariño – MDPI Insects

Neoagarotetraose protects mice against intense exercise induced fatigue damage by modulating gut microbial composition and function – Na Zhang – Molecular Nutrition & Food Research

Housing Systems Influence Gut Microbiota Composition of Sows but Not of Their Piglets – Tereza Kubasova – PLOS ONE

Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil (Anthonomus grandis) – Emiliano Ben Guerrero – Frontiers in Microbiology

Animal microbiome

* Variation in the microbiome of the urogenital tract of koalas (Phascolarctos cinereus) with and without “wet bottom” – Alistair Raymond Legione – bioRxiv

Plant, root, and soil microbiome

* Fossils: Carbonaceous biosignatures of diverse chemotrophic microbial communities from chert nodules of the Ediacaran Doushantuo Formation – Yuangao Qu – Precambrian Research

Plant, soil and microbial controls on grassland diversity restoration: A long-term, multi-site mesocosm experiment – Ellen L. Fry – Journal of Applied Ecology

Pyrosequencing reveals bacterial communities and enzyme activities differences after application of novel chiral insecticide Paichongding in aerobic soils – Jie Chen – Applied Soil Ecology

Cedar and bamboo plantations alter structure and diversity of the soil bacterial community from a hardwood forest in subtropical mountain – Yu-Te Lin – Applied Soil Ecology

The differentiation of soil bacterial communities along a precipitation and temperature gradient in the eastern Inner Mongolia steppe – Minjie Yao – CATENA

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands – Julia Kyaschenko – The ISME Journal

Association between Grape Yeast Communities and the Vineyard Ecosystems – João Drumonde-Neves – PLOS ONE

Water microbiome

High growth potential and activity of 0.2 µm filterable bacteria habitually present in coastal seawater – Yumiko Obayashi – Biogeosciences Discuss

Chronic exposure effects of silver nanoparticles on stream microbial decomposer communities and ecosystem functions – Ahmed Tlili – Environmental Science & Technology

Waste and pollution microbiology

Global profiling of metabolite and lipid soluble microbial products in anaerobic wastewater reactor supernatant using UPLC/MSe – Phornpimon Tipthara – Journal of Proteome Research

Food microbiology

Rapid concentration detection and differentiation of bacteria in skimmed milk using surface enhanced Raman scattering mapping on 4-mercaptophenylboronic acid functionalized silver dendrites – Panxue Wang – Analytical and Bioanalytical Chemistry

Metagenomics and bioinformatics / Viruses and phages

Robust inference of genetic exchange communities from microbial genomes using TF-IDF – Yingnan Cong – Frontiers in Microbiology

* Virome assembly and annotation: a surprise in the Namib Desert – Uljana Hesse – Frontiers in Microbiology

* Metaviromes of Extracellular Soil Viruses along a Namib Desert Aridity Gradient – Olivier Zablocki – Genome Announcements

Metagenome Sequencing of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin – Célio Dias Santos-Júnior – Genome Announcements

Restoring the Duality between Principal Components of a Distance Matrix and Linear Combinations of Predictors, with Application to Studies of the Microbiome – Glen A. Satten – PLOS ONE

New approach for studying mobile genes using metagenomic analysis – Kazuyuki Ishihara – Oral Diseases

Archaea

New insights into marine group III Euryarchaeota, from dark to light – Jose M Haro-Moreno – The ISME Journal

Techniques

MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling – Kristin Burnum-Johnson – Analyst

An explanation of the Nagoya Protocol and Access and Benefit Sharing, and its implication for microbiology – David Smith – Microbiology

Microbes in the news

You’re probably showering way too often – Rafi Letzter – Business Insider

Viruses May Be Responsible For Life As We Know It – Ryan F. Mandelbaum – Gizmodo

Boost your intake of resistant starch to help your gut thrive – Leslie Beck – The Globe and Mail

We now know bacteria can communicate electrically, and we should be worried
They’re organised – David Nield – Science Alert

Proceed with caution: Autism Causes Update: The Gut-Brain Connection And How A Common Probiotic May Ease Symptoms – Lizette Borreli – Medical Daily

Study provides fundamental insights into functioning of microbiota and human-gut flora symbiosis – News Medical

Microbes on the market

Bristol-Myers Squibb and Enterome Announce Immuno-Oncology Collaboration Focused on Microbiome-Derived Biomarkers, Drug Targets and Bioactive Molecules – SAT Press Releases

Bik’s non-microbiology picks

The Physics of Everyday Life. Why popcorn pops and ducks don’t freeze when swimming in icy water. John Gribbin reviews “Storm in a Teacup” by Helen Czerski – Wall Street Journal