Category Archives: Microbes in the News

December 19, 2016

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An oral pathogen with a very long name is linked to rheumatoid arthritis, a deep-sea bone-eating snail, and the excreted microbiota of bats.

Human oral microbiome

* Aggregatibacter actinomycetemcomitans–induced hypercitrullination links periodontal infection to autoimmunity in rheumatoid arthritis – Maximilian F. Konig – Science Translational Medicine

Press: Bacteria That Causes Gum Disease Also Triggers Inflammatory Response In Rheumatoid Arthritis – Saranya Palanisamy – Tech Times

Human vaginal microbiome

The Cervicovaginal Microbiota in Women Notified for Chlamydia trachomatis Infection: A Case-Control Study at the Sexually Transmitted Infection Outpatient Clinic in Amsterdam, The Netherlands – Charlotte van der Veer – Clinical Infectious Diseases

Editorial Commentary: The Cervicovaginal Microbiota and Infection Risk After Exposure to an Exogenous Pathogen – Daniel B. DiGiulio – Clinical Infectious Diseases

Human gut microbiome

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

Animal experiments

Alternative protein sources in the diet modulate microbiota and functionality in the distal intestine of Atlantic salmon (Salmo salar) – Karina Gajardo – Applied and Environmental Microbiology

Animal microbiome

* The Specific and Exclusive Microbiome of the Deep-Sea Bone-Eating Snail, Rubyspira osteovora – H.S. Aronson – FEMS Microbiology Ecology

Origin of Sulfur in Diet Drives Spatial and Temporal Mercury Trends in Seabird Eggs From Pacific Canada 1968–2015 – Kyle H. Elliott – Environmental Science & Technology

Press: Bacteria control levels of dangerous pollutant in seabirds – Phys.org

The excreted microbiota of bats: evidence of niche specialization based on multiple body habitats – Muriel Dietrich – FEMS Microbiology Letters

Western Bats as a Reservoir of Novel Streptomyces Species with Antifungal Activity – Paris S. Hamm – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Bacterial communities affected by experimental disturbances to canopy soils of a temperate rainforest – Cody R. Dangerfield – bioRxiv

Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere – Xing Xing Zhang – Journal of Biogeography

Ectomycorrhizal fungal response to warming is linked to poor host performance at the boreal-temperate ecotone – Christopher W. Fernandez – Global Change Biology

Review: PGPR = plant growth-promoting rhizobacteria: The Contribution of Genome Mining Strategies to the Understanding of Active Principles of PGPR Strains – Julia Paterson – FEMS Microbiology Ecology

Water microbiome

Effects of actinomycete secondary metabolites on sediment microbial communities – Nastassia V. Patin – Applied and Environmental Microbiology

Pollution and waste microbiology

Elucidating carbon sources driving microbial metabolism during oil sands reclamation – Lauren M. Bradford – Journal of Environmental Management

Techniques

Comparison of Collection Methods for Fecal Samples in Microbiome Studies – Emily Vogtmann – American Journal of Epidemiology

Microbes in the news

Refers to meeting abstract: Microbiomes interact with mental health treatment – Tim Sandle – Digital Journal

South Dakota high schools introduce students to health care: students grew bacteria in petri dishes – Jaci Conrad Pearson – Washington Times

New medicine: How the gut breaks the mind – Govind Vijaykumar – Deccan Chronicle

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 17, 2016

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Periodontal pathogens in crack users, the human gut microbiome in health and disease, iron availability during polymicrobial infection, ecology of soil microorganisms, lake diurnal dynamics.

Human oral microbiome

* “Cut that ivory into skinny pieces, then she clean it with her face” (The Weeknd – Starboy lyrics):  RT-PCR quantification of periodontal pathogens in crack users and non-users – M Casarin

The Subgingival Microbiome, Systemic Inflammation and Insulin Resistance: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) – Ryan T. Demmer – Journal of Clinical Periodontology

Human gut microbiome

Prospective Randomized Controlled Study on the Effects of Saccharomyces boulardii CNCM I-745 and Amoxicillin-Clavulanate or the Combination on the Gut Microbiota of Healthy Volunteers – Toufic A Kabbani – Gut Microbes

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota – A. Sloan Devlin – Cell Host & Microbe
Preview: Microbial Modulation of a Uremic Toxin – Sarah M. Skye – Cell Host & Microbe

Host–microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake – Camilla Pedersen – British Journal of Nutrition

Poster abstract: In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example – EM Pferschy-Wenzig – Planta Medica

Poster abstract: Metabolic fate of ellagitannins in human gut microbiota ex vivo cultures – JP Piwowarski – Planta Medica

Commentary: Do diverticula provide a unique niche for microbiota which can lead to activation of the innate immune system? – Robin C Spiller – Gut

* Review: The Human Intestinal Microbiome in Health and Disease – Susan V. Lynch – The New England Journal of Medicine

Animal and in vitro experiments

* Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection – Apollo Stacy – PLOS Pathogens

A genome-wide screen of bacterial mutants that enhance dauer formation in C. elegans – Amit Khanna – Scientific Reports

Research in worms provides a model to study how the microbiome influences disease in humans – Phys.org

Identification and Characterization of Trimethylamine-N-oxide Uptake and Efflux Transporters – Wendy A. Teft – Molecular Pharmaceutics

Hydrolysis of Dicaffeoylquinic Acids from Ilex kudingcha Happens in the Colon by Intestinal Microbiota – Minhao Xie – Journal of Agricultural and Food Chemistry

Bacterial Communities Differ among Drosophila melanogaster Populations and Affect Host Resistance against Parasitoids – Mariia Chaplinska – PLOS ONE

Animal microbiome

Amphibian gut microbiota shifts differentially in community structure but converges on habitat-specific predicted functions – Molly C. Bletz – Nature Communications

The genome of Rhizobiales bacteria in predatory ants reveals urease gene functions but no genes for nitrogen fixation – Minna-Maria Neuvonen – Scientific Reports

Poster abstract: How to fight against the decay- the burying beetle and its gut microbiota – P Heise – Planta Medica

Poster abstract: Latrunculid sponges, their microbial communities and secondary metabolites: connecting conserved bacterial symbionts to pyrroloiminoquinone production – RA Dorrington – Planta Medica

Plant, root, and soil microbiome

* Editorial: Special thematic issue on the ecology of soil microorganisms – Petr Baldrian – FEMS Microbiology Ecology

Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations – J. M. Young – FEMS Microbiology Ecology

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil – Seung-Yoon Oh – PLOS ONE

Variations in Soil Microbial Biomass Carbon and Soil Dissolved Organic Carbon in the Re-Vegetation of Hilly Slopes with Purple Soil – Ning Yang – PLOS ONE

Disentangling the influence of earthworms in sugarcane rhizosphere – Lucas P. P. Braga – Scientific Reports

Poster abstract: 3D-Plant2cells project: Spatial metabolomic, spatial metagenomic, and 3D mass spectrometry imaging, to explore the impact of pesticides on plant metabolome and microbiota – LF Nothias – Planta Medica

Poster abstract: Stromatolite microbial communities as a source of new bioactive secondary metabolites – PM Flatt – Planta Medica

Water and pollution microbiome

* Lake bacterioplankton dynamics over diurnal timescales – Lorena M. Grubisic – Freshwater Biology

Dynamics of Heterocapsa sp. and the associated attached and free-living bacteria under the influence of dispersed and undispersed crude oil – T. Severin – Letters in Applied Microbiology

More microbiology

Microbial Ecology: Where are we now? – Lisa Boughner and Pallavi Singh – PostDoc Journal

Microbes in the news

Video: Meet Prof Gisèle LaPointe: how microbes play a big role in our health and what she finds most exciting about her research – YouTube

Video: The Microbiology of Beer – Microbes After Hours. With Charles Bamforth, University of California, Davis and Rebecca Newman, Dogfish Head Craft Brewery – ASM – YouTube

The ancient viruses of the Arctic – Manchester Metropolitan University

Bacteria, viruses, fungi…oh my! – Jennifer Gonsoulin – ABC3340

7 Benson High School individuals test positive for tuberculosis bacteria – KETV

December 16, 2016

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General microbiome

Forging new links between the microbiome and cancer – Bryn Nelson – Cancer Cytopathology

Pregnancy and early life

Review: Planting the seed: Origins, composition, and postnatal health significance of the fetal gastrointestinal microbiota – Lisa F. Stinson – Critical Reviews in Microbiology

Human respiratory microbiome

Review: The respiratory tract microbiome and lung inflammation: a two-way street – G B Huffnagle – Mucosal Immunology

Human gut microbiome

Influence of potassium-competitive acid blocker on the gut microbiome of Helicobacter pylori-negative healthy individuals – Taketo Otsuka – Gut

High Prevalence of Gut Microbiota Colonization with Broad-Spectrum Cephalosporin Resistant Enterobacteriaceae in a Tunisian Intensive Care Unit – Elaa Maamar – Frontiers in Microbiology

Review: Linking Dietary Patterns with Gut Microbial Composition and Function – Amy M. Sheflin – Gut Microbes

Review: The role of the gastrointestinal tract in the pathogenesis of rheumatic diseases – Francesco Ciccia – Best Practice & Research Clinical Rheumatology

Animal experiments

Alteration in the Gut Microbiota Provokes Susceptibility to Tuberculosis – Nargis Khan – Frontiers in Immunology

Animal microbiome

Faecal virome of red foxes from peri-urban areas – Ivana Lojkić – Comp Immunol Microbiol Infect Dis

The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimps – Jinbo Xiong – Microbial Ecology

Faecal virome of red foxes from peri-urban areas – Comp Immunol Microbiol Infect Dis

Plant, root, and soil microbiome

Vertical stratification of the foliar fungal community in the world’s tallest trees – Joshua G. Harrison – American Journal of Botany

Impact of mowing management on nitrogen mineralization rate and fungal and bacterial communities in a semiarid grassland ecosystem – Jiangye Li – Journal of Soils and Sediments

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil – Lei Wang – Frontiers in Microbiology

Temporal Variations in Diazotrophic Communities and nifH Transcripts Level Across the Agricultural and Fallow Land at Jaipur, Rajasthan, India – Sushma Sharma – Indian Journal of Microbiology

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC) – Rosa Margesin – Microbial Ecology

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils – S. Emilia Hannula – Frontiers in Microbiology

Water and extremophile microbiome

Life in deep subsurface – Grégoire Galès – E2S Web of Conferences

Microbiology of cultural heritage

Microbial Life and Death in a Foxing Stain: a Suggested Mechanism of Photographic Prints Defacement – Maria Carla Sclocchi – Microbial Ecology

Microbiology of death

Artful decomposition: the microbial necrobiome – Kevin Lyons – People, peas and pathogens

Microbes in the news

It takes guts: Lawrence David explains unconventional research on microbiome – Jackie Dillon – Duke Chronicle

Water filters could increase bacteria in Flint water, researchers say – Oona Goodin-Smith – Mlive

How is the gut microbiome established? – Philip Dube – Taconic

Soil Bacteria Could Help Absorb Natural Gas Leaks – Aaron Sidder – EOS

Microbes on the market

The Microbiome Defined and Understood Using A.I. – Nanalyze

Microbiome Therapeutics Market Size To Reach USD 433.5 Million By 2025: Grand View Research, Inc. – SAT PR News

December 15, 2016

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Preannouncement of the second SF Bay Area Microbiome Meetup in January, enteric dysfunction in Malawian children, gastric microbiota in twins, Antarctic fish, soil of a medieval foundry.

Events

Preannouncement: 2nd SF Bay Area Microbiome Meetup – January 31, 2017 – Illumina, San Francisco – SF Biome

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

Human gut microbiome

Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children – M. Isabel Ordiz – Am J Trop Med Hyg

Characterization of Gastric Microbiota in Twins – Quanjiang Dong – Current Microbiology

Faecal Carriage of Gram-Negative Multidrug-Resistant Bacteria among Patients Hospitalized in Two Centres in Ulaanbaatar, Mongolia – Bayaraa Baljin – PLOS ONE

Lifestyle and geographic insights into the distinct gut microbiota in elderly women from two different geographic locations – Ji-Hee Shin – Journal of Physiological Anthropology

Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals – Marco Toscano – Digestive and Liver Disease

Review: The intestinal microbiota in allogeneic hematopoietic cell transplant and graft-versus-host disease – Anna Staffas – Blood

Review: A story of metformin-butyrate synergism to control various pathological conditions as a consequence of gut microbiome modification: Genesis of a wonder drug? –
Kunal Maniar – Pharmacological Research

Animal models

Selective photoantisepsis – David M. Harris – Lasers in Surgery and Medicine

Press: Laser Treatments Shown Effective in Killing Bacteria That Cause Dental Disease – Photonics

Induction of FXR signaling in germ-free mice colonized with a human microbiota – Annika Wahlström – Journal of Lipid Research

Modulation of urinary siderophores by the diet, gut microbiota and inflammation in mice –
Xia Xiao – Journal of Nutritional Biochemistry

Value added by Spirulina platensis in two different diets on growth performance, gut microbiota, and meat quality of Japanese quails – Mohamed S. Yusuf – Veterinary World

Triatomine bugs, their microbiota and Trypanosoma cruzi: asymmetric responses of bacteria to an infected blood meal – Sebastián Díaz – Parasites & Vectors

Dietary Keratan Sulfate from Shark Cartilage Modulates Gut Microbiota and Increases the Abundance of Lactobacillus spp. – Qingsen Shang – Marine Drugs

New insights into the role of the porcine intestinal yeast, Kazachstania slooffiae, in intestinal environment of weaned piglets – Vladimir Urubschurov – FEMS Microbiology Ecology

Animal microbiome

The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis – Wei Song – BioMed Research International

Plant, root, and soil microbiome

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

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression – Jie Hu – mBio

Composition of endophytic fungal community associated with leaves of maize cultivated in south Brazilian field – Vivian J. Szilagyi-Zecchin – Acta Microbiologica et Immunologica Hungarica

Vegetation type and layer depth influence nitrite-dependent methane-oxidizing bacteria in constructed wetland – Mengxi Yang – Archives of Micobiology

Water and extremophile microbiome

Nitrate addition has minimal short-term impacts on Greenland ice sheet supraglacial prokaryotes – Karen A. Cameron – Environmental Microbiology Reports

Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: A comparative analysis – Anwesha Ghosh – Genomics Data

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics – Luciana Principal Antunes – Scientific Reports

Pollution microbiology

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA – Feng Shen – Scientific Reports

Paleomicrobiology to investigate copper resistance in bacteria: Isolation and description of Cupriavidus necator B9 in the soil of a medieval foundry – David C. Gillan – Environmental Microbiology

More microbiology

Stochastic Model for Direction Changes of Swimming Bacteria – Guido Fier – bioRxiv

Microbes in the news

Pitt study links cystic fibrosis lung inflammation to opportunistic bacteria – Lydia Nuzum – BizJournals

December 13, 2016

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Top 25 Microbiology Blog and Website List for Microbiologists – What a great list! But I’m a bit sad that I did not make it. But, lots of other great blogs luckily are listed here. Meantime, I will just carry the “I did not make it” badge.

Jobs

Lecturer in Oral Microbiology – University of Bristol

Human gut microbiome

Gut microbiome in children with enthesitis-related arthritis in a developing country and the effect of probiotic administration – A. Aggarwal – Clinical & Experimental Immunology

Review: Role of the Microbiota in Colorectal Cancer: Updates on Microbial Associations and Therapeutic Implications – Olivia I. Coleman – BioResearch

Paper Hopes To Link Diet, Gut Microbiome And Colorectal Cancer – Science2.0

Animal microbiome

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community  – Nir Friedman – Environmental Microbiology

Potential role of ectoparasites (Zeuxapta seriolae and Caligus lalandei) in the transmission of pathogenic bacteria in yellowtail kingfish Seriola lalandi, inferred from cultivable microbiota and molecular analyses – F A Sepúlveda – Journal of Fish Diseases

Microbe in the news

“Eight minutes of struggling arthropods set to Beethoven’s Moonlight Sonata” – Bacteria Help Pitcher Plants Trap Prey –  Elizabeth Preston – Discover Magazine

Orange ‘ooze’ in Beaver Brook a harmless bacteria, city officials say – Xander Landen – Sentinel Source

Why are we so passionate about the smiling poop emoji? – Samantha Selinger-Morris – ABC

Researcher rethinks lactic acid bacteria – Stevie Kenyon – Daily Cardinal

Video: The Microbiome and Outcomes After Allogeneic Transplant – Robert Jenq – Cancer Network

Digging Deep for New Bacteria – Scientists find a whole ecosystem in fracking water – Eric Betz – Discover

Your head or your gut? – Justin D. Glenn – Labnews

Make-up of equine gut bacteria altered by exercise, study shows – Horse Talk

Bacteria Beef Up New Tree of Life. The new tree of life includes previously unknown species throughout the bacterial branches – Jonathon Keats – Discover

Researchers’ findings offer clue on how to block biofilm shields of bacterial infections – Science Daily

Microbes on the market

 

Biofilm tech wins CTAQ award – Food Quality News

C3J Therapeutics Unveils Development of Two New Product Formulations of Lead Candidate C16G2 for Prevention of Dental Caries – Nasdaq

The Detox Me Action Kit by Silent Spring Institute – IndieGoGo

DNA Biohackers Are Giving The FDA A Headache With Glow-In-The-Dark Booze. A biohacker thought he could sell something cool without consequences. The FDA thought otherwise. – Stephanie M. Lee – Buzzfeed

Product News: Rainin Pos-D™ Pipettes Allow Environmental Microbiology Researchers to Investigate Biodegradation of Oil  – Select Science

December 12, 2016

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Review on human milk microbiome, oral microbiome changes in seasonal athletes, gut microbiome and bipolar disorder.

Jobs

Assistant Professor In Quantitative Ecology or Evolution of Microbes – UCLA – MicroBEnet

Pregnancy and early life

Effect of probiotics in prevention of atopic dermatitis is dependent on the intrinsic microbiota at early infancy – Ekaterina Avershina – Journal of Allergy and Clinical Immunology

* Review: Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk – Michelle K McGuire – Current Opinion in Biotechnology

Human respiratory microbiome

Review: Viral–bacterial co-infections in the respiratory tract – Lauren O Bakaletz – Current Opinion in Microbiology

Human oral microbiome

* I was wondering if testing same group of athletes participating in 2 different sports could not be confounded with seasonal effects of maybe different study loads during the different year. But no access to the paper, so can not see details. Elevated salivary IgA, decreased anxiety, and an altered oral microbiota are associated with active participation on an undergraduate athletic team – Ashley L. Lamb – Physiology & Behavior

Human gut microbiome

* The gut microbiome composition associates with bipolar disorder and illness severity – Simon J. Evans – Journal of Psychiatric Research

Letter of the Editor: A Microbiome Assessment of Medical Marijuana – George Thompson III – Clinical Microbiology and Infection

Review: Archaea: essential inhabitants of the human digestive microbiota – Vanessa Demonfort Nkamga – Human Microbiome Journal

Animal experiments

Application of a dynamic gastrointestinal in vitro model combined with a rat model to predict the digestive fate of barley dietary fibre and evaluate potential impact on hindgut fermentation – Cristina Teixeira – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

Characterization and identification of microbial communities in bovine necrotic vulvovaginitis – N.Y. Shpigel – The Veterinary Journal

Crab: Gut Microbiota and Metabolic Phenotype of Portunus Trituberculatus – Ting-Lan Zeng – Chinese Journal of Analytical Chemistry

Plant, root, and soil microbiome

Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata – Suvendu Das – Journal of Hazardous Materials

Food microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Bioinformatics and metagenomics

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics – Karel Sedlar – Computational and Structural Biotechnology Journal

Microbes in the news

Predatory bacteria used to release bioplastics – Tim Sandle – Digital Journal

The Secret Soviet Virus That Helps Kill Bacteria. Antibiotic resistance is threatening to render antibiotics useless, but scientists may have found their answer in bacteria-eating viruses. – Trace Dominguez – Seeker

Bacteria found in close to two-thirds of NZ supermarket chicken – TV New Zealand

Science, publishing, and career

This would not be my headline choice: Trump says ‘nobody really knows’ if climate change is real – Juliet Eilperin – Washington Post

December 10, 2016

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Airway microbiota of infants with cystic fibrosis, an X-linked IBD risk gene in mice, Colorado flood impact, and metabolic profiling of men eating pasta and bread.

General microbiome

Review: Arguments Reinforcing the Three-Domain View of Diversified Cellular LifeArguments Reinforcing the Three-Domain View of Diversified Cellular Life – Arshan Nasir – Archaea

Opinion: Koch’s Postulates to Metagenome and NextGeneration Sequencing, But what is Next? – Santanu Chattopadhyay – Journal of Gastrointestinal Disorders and Liver Function

Human oral microbiome

Review: Gram-Positive Anaerobes in Periodontal Pathogenesis: New Kids on the Block? – A Mini Review – Journal of Bacteriology & Mycology:

Human respiratory microbiome

* Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis – Theresa A. Laguna – PLOS ONE

The Microbiome and the Pathophysiology of Asthma – Ashley Sullivan – Respiratory Research

Human gut microbiome

Review: Intestinal Immunity and Gut Microbiota in Atherogenesis – Tomoya Yamashita – Journal of Atherosclerosis and Thrombosis

Review: Microbiome, Growth Retardation, and Metabolism: Are they related? – Daniel J. Hoffman – Annals of Human Biology

Animal experiments

Cosmc is an X-linked inflammatory bowel disease risk gene that spatially regulates gut microbiota and contributes to sex-specific risk – Matthew R. Kudelka – PNAS

Depletion of Gut Microbiota Protects against Renal Ischemia-Reperfusion Injury – Diba Emal – Journal of the American Society of Nephrology

Probiotic Roles of Lactobacillus spp. in Swine: Insights from Gut Microbiota – Valerie Diane V. Valeriano – Journal of Applied Microbiology

Gut microbiota from metabolic disease-resistant, macrophage-specific RIP140 knockdown mice improves metabolic phenotype and gastrointestinal integrity – Yi-Wei Lin – Scientific Reports

Antimicrobial growth promoters modulate host responses in mice with a defined intestinal microbiota – Kirsty Brown – Scientific Reports

High Fibre Diet and Acetate Supplementation Change the Gut Microbiota and Prevent the Development of Hypertension and Heart Failure in DOCA-Salt Hypertensive Mice
Francine Z. Marques – Circulation

Plant, root, and soil microbiome

Microbial remediation of aromatics-contaminated soil – Ying Xu – Frontiers of Environmental Science & Engineering

Plant pathogens but not antagonists change in soil fungal communities across a land abandonment gradient in a Mediterranean landscape – L. Bosso – Acta Oecologica

High taxonomic variability despite stable functional structure across microbial communities – Stilianos Louca – Nature Ecology & Evolution

Repeated glyphosate exposure induces shifts in nitrifying communities and metabolism of phenylpropanoids – Marco Allegrini – Soil Biology and Biochemistry

Water microbiology

Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea – Kai Wang – Scientific Reports

Influence of the Po River runoff on the bacterioplankton community along trophic and salinity gradients in the Northern Adriatic Sea – Ilaria Pizzetti – Marine Ecology

Dynamic metabolic exchange governs a marine algal-bacterial interaction – Einat Segev – eLIFE
Research highlight: When a relationship turns ugly – Andrea Du Toit – Nature Reviews Microbiology

Food microbiology and functional foods

Cultivable microbiome of fresh white button mushrooms – Werner Rossouw

A MeSH-based text mining method for identifying novel prebiotics – Shan, Guangy – Medicine

Waste and pollution microbiology

Effect of structural carbohydrates and lignin content on the anaerobic digestion of paper and paper board materials by anaerobic granular sludge – Jorge Gonzalez-Estrella – Biotechnology and Bioengineering

* Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes – Emily Garner – Scientific Reports

Sequential bioleaching of copper from brake pads residues using encapsulated bacteria – François Vermeulen – Minerals Engineering

Feed it some of your old protein gels: Isolation and Characterization of Acrylamidase from Arthrobacter sp. DBV1 and Its Ability to Biodegrade Acrylamide – Dattatray K. Bedade – Applied Biochemistry and Biotechnology

Copper exposure to soil under single and repeated application: Selection for the microbial community tolerance and effects on the dissipation of antibiotics – Bei Liu – Journal of Hazardous Materials

Resistome

A diverse intrinsic antibiotic resistome from a cave bacterium – Andrew C. Pawlowski – Nature Communications

Million-Year-Old ‘Hero Bug’ Emerges From Cave – Michaeleen Doucleff – NPR

Metabolomics

* Metabolic Profiling Reveals Differences in Plasma Concentrations of Arabinose and Xylose after Consumption of Fiber-Rich Pasta and Wheat Bread with Differential Rates of Systemic Appearance of Exogenous Glucose in Healthy Men – Andre J Pantophlet – The Journal of Nutrition

Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways – Kieran James – Scientific Reports

Viruses and phages

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses – Simon Roux – PeerJ

Microbial ecology

Paradoxes in Leaky Microbial Trade – Yoav Kallus – bioRxiv

Microbes in the news

Video: Living together: the symbiosis of host-microbial interactionsVideo: Living together: the symbiosis of host-microbial interactions – Margaret McFall-Ngai – iBiology

Scientist Studies the Infant Resistome to Combat Superbugs – Infection Control Today

Diet, the gut microbiome, and colorectal cancer: are they linked? – EurekAlert

 

Microbes on the market

Medical Game-Changers Beckon. On #1 of the Top 10: Using the Microbiome to Prevent, Diagnose, and Treat Disease –  Casey McDonald

VC-backed Enterome hires Patel as chief medical officer and adds Garceau to board – PE Hub

Second Genome Announces Appointments in Human Resources, Finance to Support Corporate Growth – Yahoo.com

As school gardens spread, so do the teaching moments – Adrian Higgins – Washington Post

Twitter as a Tool for Teaching and Communicating Microbiology: The #microMOOCSEM Initiative – EHU

New evidence shows how bacterium in undercooked chicken causes GBS – EurekAlert

Science, publishing, and career

The Microbiology Effect: A Call for Education Research – Samantha L. Elliott – J. Microbiol. Biol. Educ.
The Necessity of Prerequisite Undergraduate Microbiology Courses for Pre-Allied Health Professionals – Andrea M. Rediske – J. Microbiol. Biol. Educ.
Supporting Microbiology in the Nursing Curriculum – Bethany Adamec – ASM

On the origin of nonequivalent states: how we can talk about preprints – Cameron Neylon – bioRxiv

Why a First Amendment win is good for science – Adam Marcus and Ivan Oransky – STATNews

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 7, 2016

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Microbiota of migratory birds, blue fungus living in snow, migrating from SSU rRNAs to metagenomics.

Jobs

Awesome job at awesome institute: Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Human gut microbiome

Special issue of Trends in Food Science & Technology; several papers have appeared here before but worth checking out: Unravelling the role of the gut microbiome in energy balance and brain development and function: the European project MyNewGut

Review: Homeostasis of the Gut Barrier and Potential Biomarkers – Jerry M Wells – American Journal of Physiology, Gastrointestinal and Liver Physiology

Review: Challenges in simulating the human gut for understanding the role of the microbiota in obesity – M. Aguirre – Beneficial Microbes

Animal models

Integrated Role of Bifidobacterium animalis subsp. lactis Supplementation in Gut Microbiota, Immunity, and Metabolism of Infant Rhesus Monkeys – Xuan He – mSystems

Review: Dissecting the interplay between intestinal microbiota and host immunity in health and disease: Lessons learned from germfree and gnotobiotic animal models – Ulrike Fiebiger – European Journal of Microbiology and Immunology

Animal microbiome

* Changes in gut microbiota of migratory passerines during stopover after crossing an ecological barrier – William B. Lewis – The Auk

Plant, root, and soil microbiome

* Microbial Community Structure and Function of Soil following Ecosystem Conversion from Native Forests to Teak Plantation Forests – Vidya De Gannes – Frontiers in Microbiology

Drought tolerance of bioenergy grass Saccharum spontaneum L. enhanced by arbuscular mycorrhizae – P.P. Mirshad – Rhizosphere

Perspective: Microbiome selection could spur next-generation plant breeding strategies – Murali Gopal – Frontiers in Microbiology

Water and extremophile microbiome

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean – Rene M. Boiteau – PNAS

Phylogenetic diversity of microbial communities of the Posolsk Bank bottom sediments, Lake Baikal – S. M. Chernitsyna – Microbiology

Dampened copepod-mediated trophic cascades in a microzooplankton-dominated microbial food web: A mesocosm study – Bernadette Pree – Limnology and Oceanography

* Antarctomyces pellizariae sp. nov., a new, endemic, blue, snow resident psychrophilic ascomycete fungus from Antarctica – Graciéle C. A. de Menezes – Extremophiles

Temporal variability of bacterial communities in cryoconite on an Alpine glacier – Andrea Franzetti – Environmental Microbiology Reports

Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP) – Michael Morando – Frontiers in Microbiology

Pollution microbiology

Effect of metal concentration on the microbial community in acid mine drainage of a polysulfide ore deposit – V. V. Kadnikov – Microbiology

Metagenomics and bioinformatics (viruses too)

MEGARes: an antimicrobial resistance database for high throughput sequencing – Steven M. Lakin – Nucleic Acids Research

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center – Alice R. Wattam – Nucleic Acids Research

Alignment-free d2* oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences – Nathan A. Ahlgren – Nucleic Acids Research

*  Crystal Ball: Migrating SSU rRNA gene surveys to the metagenomics era – Josh D. Neufeld – Environmental Microbiology Reports

Techniques

DNA extraction from benthic Cyanobacteria: comparative assessment and optimization – V. Gaget – Journal of Applied Microbiology

Microbial ecology

Microbial Community Coalescence for Microbiome Engineering – Matthias C. Rillig – Frontiers in Microbiology

More microbiology

How to Define Pathogenicity, Health, and Disease? – Mauno Vihinen – Human Mutation-Variation, Informatics, and Disease

Crystal Ball: Accessories make the microbe – Lisa Y. Stein – Environmental Microbiology Reports

Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data – Shiori Sagawa – bioRxiv

Microbes in the news

With my former Stanford co-worker Fiona Strouts: New farmers’ market baker knows art, science of bread-making. Stanford fellow brings baking know-how to Portola Valley farmers’ market – Dave Boyce – Mountain View Voice

New Mechanism to Control Human Viral Infections Discovered – Sean Nealon – University of California Riverside

Uterine microbiota play a key role in implantation and pregnancy success in in vitro fertilization – EurekAlert (see digest October 12)

Understanding microbiome impact on pig health – National Hog Farmer

Syphilis is coming back – Juha Wahlstedt – Clinical Laboratory Blogspot