Category Archives: Waste and pollution

December 20, 2016

Posted on by

Events

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

Pregnancy and early life

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

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

Human respiratory microbiome

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

Human oral microbiome

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

Human gut microbiome

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

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

Animal experiments

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

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

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

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

Waste and pollution microbiology

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

Microbial ecology

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

Microbes in the news

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

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

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

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

 

Microbes on the market

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

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

Sanger Spins Out Microbiotica to Develop Bacteriotherapies – GenEngNews

Science, publishing, and career

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

December 19, 2016

Posted on by

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

Posted on by

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

Posted on by

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 15, 2016

Posted on by

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 14, 2016

Posted on by

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

General microbiome

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

Human oral microbiome

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

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

Human gut microbiome

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

Animal experiments

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

 

Animal microbiome

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

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

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

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

Plant, root, and soil microbiology

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

Pollution

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

Food microbiology

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

Metagenomics

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

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

Metabolomics

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

Microbes in the news

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

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

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

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

 

 

December 7, 2016

Posted on by

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

December 6, 2016

Posted on by

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

uBiome Blog

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

General microbiome

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

Pollution microbiology

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

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

Proteomics

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

Microbes in the news

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

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

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

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

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

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

Science, publishing, and career

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

 

 

December 5, 2016

Posted on by

Contraceptives and the vaginal microbiome, Ralstonia and CF outcome, Alzheimer’s, helminths in cats, the Mississippi River.

General microbiome and ecology

Review: Disentangling Interactions in the Microbiome: A Network Perspective – Mehdi Layeghifard – Trends in Microbiology

Book Chapter: Chapter 4 – The Human Microbiome – Jacquelyn S. Meisel – Genomic and Precision Medicine (Third Edition): Foundations, Translation, and Implementation – Chp

Pregnancy and early life

Maternal health and the placental microbiome – Elise Pelzer – Placenta

Human vaginal microbiome

* Effects of Combined Oral Contraceptives, Depot Medroxyprogesterone Acetate, and the Levonorgestrel-releasing Intrauterine System on the Vaginal Microbiome – J. Paul Brooks – Contraception

Review: Lactobacillus iners: Friend or Foe? – Mariya I. Petrova – Trends in Microbiology

Human skin microbiome

The protective effect of microbiota on S. aureus skin colonization depends on the integrity of the epithelial barrier – Marc Burian – Journal of Investigative Dermatology

Human respiratory microbiome

* Ralstonia mannitolilytica in cystic fibrosis: A new predictor of worse outcomes – I. Coman – Respiratory Medicine Case Reports

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing – Claire L. McMurray – Microbiome

Human oral microbiome (also: gut / viruses)

Transmission of viruses via our microbiomes – Melissa Ly – Microbiome

Review: Endodontic Microbiology and Pathobiology : Current State of Knowledge – Ashraf F. Fouad – Dental Clinics of North America

Human gut microbiome

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies – Euan Watt – Microbiome

Review: Crohn’s disease – Joana Torres – The Lancet

Review: The Microbiome in Neurogastroenterology – Geoffrey A. Preidis – Pediatric Neurogastroenterology

Review: The endocrine vitamin D system in the gut – Antonio Barbáchano – Molecular and Cellular Endocrinology

Microbes at nearly sterile sites

* Gram-negative bacterial molecules associate with Alzheimer disease pathology – Xinhua Zhan – Neurology

Press: Gram-negative bacteria may influence Alzheimer’s disease pathology – ScienceDaily

Animal and in vitro models

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota – A. Sloan Devlin – Cell Host & Microbe

Animal microbiome

* Helminth infections and gut microbiota – a feline perspective – Ana M. Duarte – Parasites & Vectors

Review: Defining the Core Microbiome in Corals’ Microbial Soup – Alejandra Hernandez-Agreda – Trends in Microbiology

Plant, root, and soil microbiome

Bacterial consortia inoculation mitigates the water shortage and salt stress in an avocado (Persea americana Mill.) nursery – Patricio J. Barra – Applied Soil Ecology

Heavy Metal Pollution Structures Soil Bacterial Community Dynamics in SW Spain Polluted Salt Marshes – Jennifer Mesa – Water, Air, & Soil Pollution

The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding – Eveline Adam – Plant and Soil

Tolerance of the forest soil microbiome to increasing mercury concentrations – Aline Frossard – Soil Biology and Biochemistry

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

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought – A. Mark Ibekwe – Science of the Total Environment

Cross-compatibility evaluation of plant growth promoting rhizobacteria of coconut and cocoa on yield and rhizosphere properties of vegetable crops – T.H Khadeejath Rajeela – Biocatalysis and Agricultural Biotechnology

Effect of rhizobacterial consortia from undisturbed arid- and agro-ecosystems on wheat growth under differing conditions – N.G. Inostroza – Letters in Applied Microbiology

Differences among Soil-Inhabiting Microbial Communities in Poa annua Turf throughout the Growing Season – Lisa A. Beirn – Corp Science

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake – Pu Shen – PLOS ONE

Water and extremophile microbiome

* Microbial regime changes and indicators of eutrophication on the Mississippi River identified via a human-powered 2900 km transect – Michael W Henson – bioRxiv

Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River – L. Vezzulli – Microbial Ecology

Identity, ecology and ecophysiology of planktic green algae dominating in ice‑covered lakes on James Ross Island (northeastern Antarctic Peninsula) – Linda Nedbalová

Built environment microbiome

Analysis of dark crusts on the church of Nossa Senhora do Carmo in Rio de Janeiro, Brazil, using chemical, microscope and metabarcoding microbial identification techniques – Christine Gaylarde – International Biodeterioration & Biodegradation

Impact of wastewater treatment plant discharge on the contamination of river biofilms by pharmaceuticals and antibiotic resistance – Elodie Aubertheau – Science of the Total Environment

More microbiology

Human to human transmission of arthropod-borne pathogens – Byron E Martina – Current Opinion in Virology

Techniques

Methodological flaws introduce strong bias into molecular analysis of microbial populations – Niclas Krakat – Journal of Applied Microbiology

Microbes in the news

uBiome Awards Microbiome Impact Grant to Explore Effects of Heavy Drinking and Smoking on Oral Microbiome – PR Web

Missing Link in Malaria Evolution Discovered in Historical Specimens – Ben Andrew Henry – The Scientist

Book review: The Human Microbiome Handbook, Jason Tetro, Emma Allen-Vercoe (Eds.). DEStech Publications (March 2016)– Laura M. Cox – Anaerobe

Our ideas about bacteria evolution are wrong – scientists make new discovery – Sandra Hajda – Inquisitr

Bacteria Hysteria

Soap company uses bacteria-coated billboards to prove how dirty your stuff is – Mashable

November 30, 2016

Posted on by

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

Events

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

General microbiome

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

Human respiratory microbiome

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

Human skin microbiome

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

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

Human microbes in (nearly) sterile sites

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

Human gut microbiome

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

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

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

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

Animal and in vitro models

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

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

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

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

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

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

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

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

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

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

Animal microbiome

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

Metagenomics and bioinformatics

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

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

Techniques

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

Microbes in the news

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

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

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

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

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

Genes, early environment sculpt the gut microbiome – Science Daily

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