April 12, 2017

Posted on April 12, 2017 by xinhuang7

A pretty broad Digest today, with a promising phylogenetic marker for fungal community studies, a new issue of the Journal of Microbiological Methods, and several news pieces, including one about brain stimulating for weight loss.

Jobs

Microbiology Technician – Lonza America Inc

BMS Microbiology – South West England

General microbiology

*A new promising phylogenetic marker to study the diversity of fungal communities: the GLYCOSIDE HYDROLASE 63 gene – L. Pérez-Izquierdo – Molecular Ecology Resources

pH-Controlled Cerium Oxide Nanoparticle Inhibition of Both Gram-Positive and Gram-Negative Bacteria Growth – Ece Alpaslan – Scientific Reports

Human oral microbiome

The probiotics in dentistry: a narrative review – A.M. Pujia – European Review for Medical and Pharmacological Sciences

Human ear microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

PrePrint: Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome – Jessica V. Ribado – bioRxiv

Corrigendum: Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific Reports

Seven versus 10 days antibiotic therapy for culture-proven neonatal sepsis: A randomised controlled trial – Smriti Rohatgi – Journal of Paediatrics and Child Health

Animal experiments

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice – Xiaoyu Gao – Applied Microbiology and Biotechnology

Bioactive Molecule from Streptomyces sp Mitigates MDR Klebsiella pneumoniae in Zebrafish Infection Model – Lalitha Cheepurupalli – Frontiers in Microbiology

Animal microbiome

Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing – Mao Li – Scientific Reports

Plant, root and soil microbiome

Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen (Acidovorax citrulli) with Rhizosphere Associated Bacteria – Mahesh Adhikari – The Plant Pathology Journal

Book Chapter: Ecological Restoration Techniques for Management of Degraded, Mined-Out Areas and the Role Played by Rhizospheric Microbial Communities – Prashant Pant & Pratibha Pant – Green Technologies and Environmental Sustainability

Abstract: Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales – Hendershot JN – Ecology

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere – Sadaf Kalam – Journal of Basic Microbiology

Water and extremophile microbiome

Abstract: Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon – P. Behera – Science of the Total Environment

PDF: The Effects of Soil Environmental Factors on the Colonization of Marine Biocontrol Bacteria – Zenghai Bao – Journal of Residuals Science & Technology

Book chapter: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad & Juan M. Gonzalez – Microbial Applications Vol.1

Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance – Weixiong Lin – Ecotoxicology and Environmental Safety

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Microbes in space

Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions – Giorgio Casaburi – Scientific Reports

Phages and viruses

iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus – Songbai Yang – Scientific Reports

Technology

Release of a new issue of the Journal of Microbiological Methods, with various technical articles of potential interest.

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models – Chao Ye – Scientific Reports

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding – Panu Somervuo – Methods in Ecology and Evolution

Microbes in the news

DIRTY PINTS One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly – Sara Kamouni – The Sun

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge – Eleni Rousos – ABC News

*Magnetic brain stimulation causes weight loss – Tim Sandle – Digital Journal

5 Ways to Ruin Wine Before It’s Even Bottled – Laura Burgess – Vine Pair

A public health failure – Otago Daily Times

Study to develop faster detection of antibiotic resistance – Scoop

Microbes on the market

Superbugs receive a dual drug attack – Kate Dearling – The Badger Online

Breast Milk Helps In The Growth Of Microbes Beneficial To Human Colon, Best For Babies Too – Jezreel Smith – The Science Times

March 27, 2017

Posted on March 27, 2017 by Itumeleng

Exploring life within the biofilm and how free-living microbes thrive, and focus on life history patterns of symbionts. Finally, big dairy (Parmalat- South Africa) was found guilty of repeatedly hiding serious infections (Salmonella and Listeria,)from their consumers.

General microbiome

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions.

Wang D. ISME Journal

Symbiont Acquisition and Replacement as a Source of Ecological Innovation.

Sudakaran S. Trends in Microbiology

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants.

Jiao S. Environmental Pollution

March 15, 2017

Posted on March 15, 2017 by edwardmessick

Today’s digest is full of environmental, soil/plant/root, and water related studies among a few gut microbiome studies and some opinion pieces.

Events and jobs

Event: Gut Feeling – How bacteria influence our wellbeing – EMBL-EBI – 21-May-2017

Event: Meeting of the Microbiome Minds – Colorado State University

General microbiome

Opinion: The study of microbiota needs both microbiologists and medical doctors – Didier Raoult – CMI

Pregnancy and early life

Review: Distinct Roles of Cervical Epithelia and Stroma in Pregnancy and Parturition – Shanmugasundaram Nallasamy – Seminars in Reproductive Medicine (Thieme)

The shape of the microbiome in early life – Erika von Mutius – Nature Medicine

Multi-site human microbiome

Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment – Jeanette M. Carlson – J. Vis. Exp.

Human respiratory microbiome

Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa – Laurence Pages-Monteiro – PLOS One

Human skin microbiome

Review: Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome – Mohammed Ashrafi – Future Microbiology

Human vaginal microbiome

Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, an Sexually Transmitted Diseases – Felicia M. Lewis – Obstetrics & Gynecology

Women view key sexual behaviours as the trigger for the onset and recurrence of bacterial vaginosis – Jade E. Bilardi – PLOS One

Human oral microbiome

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study – Sebastien Boutin – Frontiers in Microbiology

Human gut microbiome

*The altered gut microbiota in adults with cystic fibrosis – D.G. Burke – BMC Microbiology

Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate-reducing bacteria: a randomised crossover study – Lee Kellingray – Molecular Nutrition & Food Research

Gastric Acid Suppression Is Associated with an Increased Risk of Adverse Outcomes in Inflammatory Bowel Disease – Shah R – Digestion

NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth – Liang Chen – Nature Immunology

Gut microbiome diversity and high fibre intake are related to lower long term weight gain – Menni C – International Journal of Obesity

We are not alone: a case for the human microbiome in extra intestinal diseases – S. Shivaji – Gut Pathogens

The intestinal microenvironment in sepsis – Katherine T Fay – BBA – Molecular Basis of Disease

The Gut Microbiome and Its Role in Cardiovascular Diseases – W. H. Wilson Tang – Circulation

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion – Wei Sun – Bioresource Technology

Dietary Broccoli Alters Rat Cecal Microbiota to Improve Glucoraphanin Hydrolysis to Bioactive Isothiocyanates – Xiaoji Liu – Nutrients

Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens – Eduardo Crisol-Martinez – PeerJ

Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice – Paul M. Ryan – Microbiome

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome – Daniel Aguirre de Cárcer – PLOS One

Animal microbiome (for animals in the wild)

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time – Sheila Torres – PeerJ

Fine Flounder (Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens – Carolina Ramirez – Frontiers in Microbiology

Use of signature-tagged mutagenesis to identify genes associated with colonization of sheep by E. coli O157:H7 – Nancy A. Cornick – Veterinary Microbiology

The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens – Gerard M. Murray – PLOS One

Plant, root, and soil microbiome

Analysis of microbiota involved in the aged natural fermentation of indigo – Takahiro Okamoto – World Journal of Microbiology and Biotechnology

Microbial solvent formation revisited by comparative genome analysis – Anja Poehlein – Biotechnology for Biofuels

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities – Wepking, C – Proceedings of the Royal Society B-Biological Science

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms – Tobias Weil – Microbiome

Characterization of microbial communities during start-up of integrated fixed-film activated sludge (IFAS) systems for the treatment of oil sands process-affected water (OSPW) – Chunkai Huang – Biochemical Engineering Journal

Effects of experimental addition of nitrogen and phosphorus on microbial and metazoan communities in a peatbog – Tomasz Mieczan – European Journal of Protistology

The potential of native species as bioenergy crops on trace-element contaminated Mediterranean lands – Dominquez MT – Sci Total Environment

Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar – Jaiswal AK – Scientific Reports

Growth and 137Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain – Salem Djedidi – Journal of Environmental Radioactivity

Antibiotic mixture effects on growth of the leaf-shredding stream detritivore Gammarus fossarum – Mirco Bundschuh – Ecotoxicology

Microbial community changes during different empty bed residence times and operational fluctuations in an air diffusion reactor for odor abatement – Elisa Rodriguez – Science of the Total Environment

Response of indigenously developed bacterial consortia in progressive degradation of polyvinyl chloride – Mohammad S Anwar – Protoplasma

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Conference: Effects of simulated deep-sea mining impacts on microbial communities and functions in the DISCOL experimental area – Vonnahme, T – EU FP7 MIDAS final meeting,

Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities – Wei Xing – Journal of Environmental Sciences

PrePrint: Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive 2 presence of metal resistance genes – Ankita Kothari – bioRxiv

Climate, soil and plant functional types as drivers of global fine-root trait variation – Gregoire T. Freschet – Journal of Ecology

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function – Konstantin Gavazov – Science of the Total Environment

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes – Emily B. Graham – Environmental Microbiology

Review: Microbiome involved in microbial electrochemical systems (MESs): A review – Saratale RG – Chemosphere

Chapter Four – Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings – Xinli An – Environmental Science and Pollution Research

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis – Niranjan Nitin Parulekar – PLOS One

Food microbiology

Editorial: Inner Workings: Fermented foods offer up a versatile microbial model system – Alla Katsnelson – PNAS

Probiotics / prebiotics

News article: IBS cure? Probiotics could REDUCE irritable bowel syndrome symptoms AND stress – Olivia Lerche – express.co.uk

Bioinformatics

Applied Metagenomics for Biofuel Development and Environmental Sustainability – Antonio Djalma Nunes Ferraz Junior – Advances of Basic Science for Second Generation Bioethanol from Sugarcane

DEMOGRAPHICS INDUCE EXTINCTION OF DISEASE IN AN SIS MODEL BASED ON CONDITIONAL MARKOV CHAIN – XIAOFENG LUO – Journal of Biological Systems

Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters – Yu Shang – PLOS One

Techniques

Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods – Beibei Wang – Science of The Total Environment

*How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity – Camille Truong – New Phytologist

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research – Shaocun Zhang – Frontiers in Cellular and Infection Microbiology

Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

Ed’s non-microbiology picks (news articles)

First Time Ever: Gene Therapy Reverses Sickle Cell Disease

Earth’s oceans are warming 13% faster than thought, and accelerating

MIT researchers create new form of matter

Gene therapy treats muscle-wasting disease in dogs

World’s oldest plant fossil discovered by student pushes evolution of complex life back 400 million years

March 6, 2017

Posted on March 6, 2017 by Itumeleng

Interesting articles on the how the interactions between bacteria and fungi influence N cycling in soils. Also, fecal sample collection methods influence microbial community structure.

General microbiome

The National Biome Initiative: An Allergy Perspective. Furuta GT. Journal of Allergy and Clinical Immunology

The Microbiome in Allergic Disease: Current Understanding and Future Opportunities – 2017 PRACTALL Document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. Huang YJ. Journal of Allergy and Clinical Immunology

Oral and nasal microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Marino PJ. Journal of Critical Care

Oral and nasal microbiota in Parkinson’s disease. Pereira PA. Parkinsonism and Related Disorders

Gut microbiome

The effect of omeprazole treatment on the gut microflora and neutrophil function. Kostrzewska M. Clinics and Research in Hepatology and Gastroenterology

Water and extremophile microbiome

Bacterial interactions and implications for oil biodegradation process in mangrove sediments. Grativol AD. Marine Pollution Bulletin

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem. Wang Y. Applied and Environmental Microbiology

Probiotics

Probiotic treatment reduces depressive-like behaviour in rats independently of diet. Abildgaard A. Psychoneuroendocrinology

Techniques

Comparison of fecal collection methods for microbiota studies in Bangladesh. Vogtmann E. Applied and Environmental Microbiology

Plant, root, and soil microbiome

How interacting fungal species and mineral nitrogen inputs affect transfer of nitrogen from litter via arbuscular mycorrhizal mycelium. He Y. Environmental Science and Pollution Research

Salmonella Senftenberg adaptation to linalool and its association with antibiotic resistance and environmental persistence. Hollander K. Applied and Environmental Microbiology

Fungal and bacterial contributions to nitrogen cycling in cheatgrass-invaded and uninvaded native sagebrush soils of the western USA. DeCrappeo NM. Plant and Soil

Native soil organic matter as a decisive factor to determine the arbuscular mycorrhizal fungal community structure in contaminated soils. Montiel-Rozas. Biology and Fertility of Soils

March 5, 2017

Posted on March 5, 2017 by galit_ms

Here are few interesting articles for your Sunday morning edition. Canadian bacteria-like fossils may be the oldest evidence of life yet. Black carbon, one of the main components of air pollution, is reported to drastically change the development of bacterial biofilms and key aspects of bacterial colonization and survival. A novel organ culture system described for the mouse intestine shows that the nervous system influences the microbiome/immune system crosstalk. And the power of alternative assays for discovery: Deep sequencing of cell-free DNA from a large patient cohort revealed previously unknown and highly prevalent microbial and viral diversity in humans.

Human vaginal microbiome

The global health impact of vaginal dysbiosis – Janneke H.H.M. van de Wijgert – Research in Microbiology

Human gut microbiome

An Intestinal Organ Culture System Uncovers a Role for the Nervous System in Microbe-Immune Crosstalk – Nissan Yissachar – Cell

Animal microbiome

Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows, Part II: Purulent vaginal discharge versus healthy cows – M.L.S. Bicalho – The journal of Dairy Science

Plant, root, and soil microbiome

Review: Soil-Plant-Microbe Interactions in Stressed Agriculture Management– Shobhit Raj Vimal – Pedosphere

Water and extremophile microbiome

Evidence for early life in Earth’s oldest hydrothermal vent precipitates – Matthew S. Dodd – Nature

Microbes in the news

Study Shows Link Between Microbiome in the Gut and Parkinson’s – University of Alabama at Birmingham

A Japanese study performed by sequencing the gut microbiota of 367 healthy individuals ranging from newborn to 104 years old shows microbiome changes with age

UN issues list of 12 most worrying bacteria

Microbes on the market

Rebiotix Inc. has its lead product for C. diff. treatment granted Fast Track, Orphan Drug, and Breakthrough Therapy status by the FDA.

February 20, 2017

Posted on February 20, 2017 by TinaS

This Monday we have some quite interesting news about microbes! Microbes found inside giant crystals in caves in Chihuahua, Mexico, may have survived there for tens of thousands of years, while meadows of underwater seagrass plants might lower levels of harmful bacteria in nearby ocean waters making the whole ecosystem — from corals to fish to humans — healthier. Enjoy your reading..

Pregnancy and early life

Adenoid bacterial colonization in a paediatric population – João Subtil – European Archives of Oto-Rhino-Laryngology

Human gut microbiome

Review: NLRP6: A Multifaceted Innate Immune Sensor – Maayan Levy – Trends in Immunology

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota – Doris Vandeputte – Gut

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial – Sudarshan Paramsothy – The Lancet

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier – Bouke N. Salden – Clinical Nutrition

Diet-induced obesity, gut microbiota and bone, including alveolar bone loss – Sathima Eaimworawuthikul – Archives of Oral Biology

Animal experiments

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S. Thompson – Frontiers in Behavioral Neuroscience

Plant, root, and soil microbiome

Plant community and nitrogen deposition as drivers of α- and β-prokaryotic diversity in reconstructed oil-sands soils and natural boreal forest soils – Jacynthe Masse – Applied and Environmental Microbiology

Plant-microbial association in petroleum and gas exploration sites in the state of Assam, north-east India—significance for bioremediation – Hemen Sarma – Environmental Science and Pollution Research

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

Water and extremophile microbiome

Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates – Joleah B. Lamb – Science

Phages and viruses

Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function – Sheila Roitman – bioRxiv

Techniques

Effects of gelling agent and extracellular signaling molecules on the culturability of marine bacteria – Anita Mac Rygaard – Applied and Environmental Microbiology

A tool named Iris for versatile high-throughput phenotyping in microorganisms – George Kritikos – Nature Microbiology

Microbes in the news

Microbes survived inside giant cave crystals for up to 50,000 years – Science News

Three-way dance between herbivores, plants and microbes unveiled – Phys.org

Synthetic antibiotic developed by Sask. researchers to combat drug-resistant bacteria – CBC News

Salmonella ‘can kill cancer’: How bacteria that cause food poisoning could be used to attack tumour cells – Colin Fernandez for Daily Mail, UK

Brazilian peppertree packs power to knock out antibiotic-resistant bacteria – Science Daily

Bacteria Hysteria

Drug-resistant deadly bacteria more widespread than previously thought, study finds – News Medical

January 18, 2017

Posted on January 18, 2017 by Itumeleng

Biogeographical patterns and assembly processes of bacterial on glaciers. And, a critical review of interactions between central nervous system and microbiota during health and neurological disease.

● Hospital microbiome

Microbiota-targeted therapies on the intensive care unit. Haak, BW . Current opinions in Critical Care

● Human microbiome and nervous system

Review: Interactions between the microbiota, immune and nervous systems in health and disease. Thomas C Fung.Nature Neuroscience

● Human gut microbiome

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Patrascu O. Scientific Report

Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. Moelling, K. Bacteriophage

● Animal experiments

Pepsin egg white hydrolysate modulates gut microbiota in Zucker obese rats. Requena T. Food & Function

Effect of early antibiotic administration on cecal bacterial communities and their metabolic profiles in pigs fed diets with different protein levels. Zhang C. Anaerobe

● Animal microbiome

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau. Wei YQ. Anaerobe

Gut microbiota isolated from the European pond turtle (Emys orbicularis) and its antimicrobial resistance. Ruzauskas M. Polish Journal of Veterinary Sciences

● Plant, root, and soil microbiome

Restoration using Azolla imbricata increases nitrogen functional bacterial groups and genes in soil. Xiao-Ming Lu. Applied Microbiology and Biotechnology

Ectomycorrhizal fungal diversity associated with endemic Tristaniopsis spp. (Myrtaceae) in ultramafic and volcano-sedimentary soils in New Caledonia. Waseem M. Mycorrhiza

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.Ambrosini, R.Microbial Ecology

● Water and extremophile microbiome

Bacterial community structure and prevalence of Pusillimonas-like bacteria in aged landfill leachate. Remmas, N. Environmental Science and Pollution Research

January 16, 2017

Posted on January 16, 2017 by TinaS

Environmental pollutants have become an increasingly common health hazard. The possible effects of environmental pollutants on gut microbiota and their subsequent effects on health is discussed in highlighted review.

Pregnancy and early life

Antibiotics in Pregnancy Increase Children’s Risk of Otitis Media and Ventilation Tubes – Tine Marie Pedersen – The journal of Pediatrics

Human skin microbiome

Insights into the mast cell–microbiome connection in the skin – Alon Y. Hershko – Journal of Allergy and Clinical Immunology

Microbiota fingerprints lose individually identifying features over time – David Wilkins – Microbiome

Human vaginal microbiome

Association between preterm labor and genitourinary tract infections caused by Trichomonas vaginalis, Mycoplasma hominis, Gram-negative bacilli, and coryneforms – Alaa El-Dien M.S. Hosny – Journal of the Chinese Medical Association

The Vaginal Microbiota and Urinary Tract Infection – Ann E. Stapleton – Microbiol Spectrum

Human nearly-sterile sites

Metabolic profiles of exudates from chronic leg ulcerations – Adam Junka – Journal of Pharmaceutical and Biomedical Analysis

Human oral microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier – Nicolas Dutzan – Immunity

Salivary Gluten Degradation and Oral Microbial Profiles in Health and Celiac Disease – Na Tian – Applied and Environmental Microbiology

Human gut microbiome

Expert review: Management of Clostridium difficile Infection in Inflammatory Bowel Disease: Expert Review from the Clinical Practice Updates Committee of the AGA Institute – Sahil Khanna – Clinical Gastroenterology and Hepatology

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

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Review: The role of the gut microbiota in sepsis – Bastiaan W Haak – The Lancet Gastroenterology & Hepatology

Gut microbiota interactions with the immunomodulatory role of vitamin D in normal individuals – Renata V. Luthold – Metabolism

“Angelakisella massiliensis” gen. nov., sp. nov., a new bacterial species isolated from human ileum – Morgane Mailhe – New Microbes and New Infections

Helicobacter pylori–related metabolic syndrome as predictor of progression to esophageal carcinoma in a subpopulation-based Barrett’s esophagus cohort – Jannis Kountouras – Gastrointestinal Endoscopy

Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans – Sandrayee Brahma – Journal of Functional Foods

Absence of intestinal microbiota increases ß-cyclodextrin stimulated reverse cholesterol transport – Rima H. Mistry – Molecular Nutrition & Food Research

European consensus conference on faecal microbiota transplantation in clinical practice – Giovanni Cammarota – Gut
Animal experiments

Gd-DTPA-induced dynamic metabonomic changes in rat biofluids – Chuanling Wan – Magnetic Resonance Imaging

Increasing dietary nitrate has no effect on cancellous bone loss or fecal microbiome in ovariectomized rats – Melissa N. Conley – Molecular Nutrition & Food Research

Animal microbiome

Improved growth rate and disease resistance in olive flounder, Paralichthys olivaceus, by probiotic Lactococcus lactis WFLU12 isolated from wild marine fish – Thanh Luan Nguyen – Aquaculture

Plant, root, and soil microbiome

The effects of tree species and substrate on carbon sequestration and chemical and biological properties in reforested post-mining soils – Agnieszka Józefowska – Geoderma

Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil – Jichen Wang – Applied Soil Ecology

Water and extremophile microbiome

Effects of the halophilic fungi Cladosporium sphaerospermum, Wallemia sebi, Aureobasidium pullulans and Aspergillus nidulans on halite formed on sandstone surface – Maisa M.A. Mansour – International Biodeterioration & Biodegradation

Epiphytic Planctomycetes communities associated with three main groups of macroalgae – Joana Bondoso – FEMS Microbiology Ecology

Floc formation reduces the pH stress experienced by microorganisms living in alkaline environments -C.J. Charles – Applied and Environmental Microbiology

Capturing compositional variation in denitrifying communities: A multiple primer approach that includes autotrophic denitrifying Epsilonproteobacteria – S.A. Murdock – Applied and Environmental Microbiology

Waste and pollution microbiology

Review: Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation – Sevcan Aydin – Fungal Biology Reviews

Built environment

Biological invasion in the indoor environment: the spread of Eurotium halophilicum on library materials – Andrea Polo – International Biodeterioration & Biodegradation

Review: Integrated management of the risks of stored grain spoilage by seedborne fungi and contamination by storage mould mycotoxins – An update – Francis Fleurat-Lessard – Journal of Stored Products Research

Food microbiology

Impact of environmental conditions and process modifications on microbial diversity, fermentation efficiency and chemical profile during the fermentation of mezcal in Oaxaca – Manuel R. Kirchmayr – LWT – Food Science and Technology

Anti-aging and redox state regulation effects of A-type proanthocyanidins-rich cranberry concentrate and its comparison with grape seed extract in mice – Jingjing Jiao – Journal of Functional Foods

Probiotics / prebiotics

Probiotic mixture improves fatty liver disease by virtue of its action on lipid profiles, leptin, and inflammatory biomarkers – Hessah Mohammed Al-muzafar – BMC Complementary and Alternative Medicine

January 15, 2017

Posted on January 15, 2017 by eliesbik

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

Jobs

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

Human urinary tract microbiome

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

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

Animal experiments

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

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

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

Water microbiome

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

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

Waste and pollution microbiology

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

Food microbiology

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

Metagenomics and bioinformatics / Viruses and phages

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

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

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

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

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

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

Archaea

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

Techniques

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

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

Microbes in the news

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

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

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

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

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

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

Microbes on the market

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

Bik’s non-microbiology picks

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

January 14, 2017

Posted on January 15, 2017 by eliesbik

So it is technically already January 15 most countries, but I have been busy today preparing to transfer Microbiome Digest to an eager group of 20 new contributors. It takes a lot of time to hopefully be able to safe some time – if that makes sense.

My inbox is still full of new alerts, but here is what I have been able to “digest” so far. It’s already a lot!

General human microbiome

Navigating social and ethical challenges of biobanking for human microbiome research –
Kim H. Chuong – BMC Medical Ethics

Editorial: Influence of the microbiota on host physiology – moving beyond the gut
– Kim E. Barrett – The Journal of Physiology

Pregnancy and early life

* Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid – Diogo Antonio Tschoeke – BMC Medical Genomics

Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota – Jasmine C. C. Davis – Scientific Reports

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates – Matthew R Olm – Genome Research

The Microbiome and Complement Activation A Mechanistic Model for Preterm Birth – Alexis B. Dunn – Biological Research for Nursing

Review: Asthma and the microbiome: defining the critical window in early life – Leah T. Stiemsma – Allergy, Asthma & Clinical Immunology

Human gut microbiome

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage – Manuela G. Neuman – Experimental and Molecular Pathology

Serum Trimethylamine N-oxide, Carnitine, Choline and Betaine in Relation to Colorectal Cancer Risk in the Alpha Tocopherol and Beta Carotene Study – Kristin A. Guertin – Cancer Epidemiology, Biomarkers & Prevention

Laboratory Testing of Donors and Stool for Fecal Microbiota Transplantation for Recurrent C. difficile Infection – Michael H. Woodwort – Journal of Clinical Microbiology

Editorial: Gut microbiota: implications for sports and exercise medicine – Owen Cronin – British Journal of Sports Medicine

Review/Addendum: Pathogen control at the intestinal mucosa – H2O2 to the rescue
Ulla G. Knaus – Gut Microbes

Editorial: Tune into the rhythm of your bugs – Purna Kashyap – Science Translational Medicine

Preview: Are Gut Microbes Responsible for Post-dieting Weight Rebound? – Julien Chilloux – Cell Metabolism

Review: Involvement of Reduced Microbial Diversity in Inflammatory Bowel Disease – Dawei Gong – Gastroenterology Research and Practice

Year in Review: Gut microbiota in 2016: A banner year for gut microbiota research – Wendy S. Garrett – Nature Reviews Gastroenterology & Hepatology

Review: Gut microbiota disturbance during helminth infection: can it affect cognition and behaviour of children? – Vanina Guernier – BMC Infectious Diseases

Review: An expanding stage for commensal microbes in host immune regulation – Yan Shi – Cellular & Molecular Immunology

Perspective: Decoding host–microbiota communication in the gut – now we’re flying!
– Stephen J. Keely – The Journal of Physiology

Just based on the abstract, this appears a wild hypothesis potentially ignoring economic status, fiber consumption etc: Latitude as a co-driver of human gut microbial diversity? – Emma Dikongué – Ideas that Push the Boundaries

Book: Gut Microbiome and Behavior, Volume 131 – John F. Cryan, Gerard Clarke – Elsevier

Animal experiments

Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice – Jaques Belik – Scientific Reports

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Year in review: Microbiome in 2016: T follicular helper cells and the gut microbiome in arthritis – Veena Taneja – Nature Reviews Rheumatology

Animal microbiome

* Bacterial Communities Associated with Houseflies (Musca domestica L.) Sampled within and between Farms – Simon Bahrndorff – PLOS ONE

Microbiome variation in corals with distinct depth distribution ranges across a shallow–mesophotic gradient (15–85 m) – Bettina Glasl – Coral Reefs

Symbiont-induced odorant binding proteins mediate insect host hematopoiesis – Joshua B Benoit – eLIFE

Drivers of variation in species impacts for a multi-host fungal disease of bats –
Kate E. Langwig – Philosophical Transactions of the Royal Society B

Sponges: Evaluating the core microbiota in complex communities: A systematic investigation – Carmen Astudillo-Garcia – Environmental Microbiology

Plant, root, and soil microbiome

Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland – Haggai Wasserstrom – Scientific Reports

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Water microbiome

Built environment microbiome

Microbial diversity in different compartments of an aquaponics system – Zala Schmautz – Archives of Microbiology

Food microbiology

The influence of thiamine and riboflavin on various spoilage microorganisms commonly found in beer – Barry Hucker – The Journal of The Institue of Brewing

Waste and pollution microbiology

Microbial flora analysis for the degradation of beta-cypermethrin – Zhang Qi – Environmental Science and Pollution Research

Fungi (also see Animal Microbiome)

Medical mycology and fungal immunology: new research perspectives addressing a major world health challenge – Neil A. R. Gow – Philosophical Transactions of the Royal Society B

Proteomics and metabolomics

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota – Aitor Blanco-Míguez – Database

Perspective: Progress in the biology and analysis of short chain fatty acids – Roel J. Vonk – The Journal of Physiology

Bioinformatics and biostatistics

Using Machine Learning to Identify Major Shifts in Human Gut Microbiome Protein Family Abundance in Disease – Mehrdad Yazdani – IEEE

Press: Teaching Computers to Recognize Sick Guts: Machine-Learning and the Microbiome – Tiffany Fox – Calit2

Microscale Insight into Microbial Seed Banks – Kenneth J. Locey – Frontiers in Microbiology

* EMPeror: Bringing the Dynamic Microbiome to Life with Animations – Yoshiki Vázquez-Baeza – Cell Host & Microbe

Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities – Gongchao Jing – Scientific Reports

Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices – Hua X. – Human Heredity

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets – Xilin Xu – Biophysics Reports

Techniques

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

Editorial: Microbial Nanoscopy: Breakthroughs, Challenges, and Opportunities – Yves F. Dufrêne – ACS Nano

More microbes

* Asgard archaea illuminate the origin of eukaryotic cellular complexity – Katarzyna Zaremba-Niedzwiedzka – Nature

* Species-Independent Attraction to Biofilms through Electrical Signaling – Jacqueline Humphries – Cell

Bacteria Send Electrical Pulses as Recruitment Ads – Ed Yong – The Atlantic
Researchers discover bacteria can communicate electrically, like neurons – Andrew Tarantola – Engadget
Bacteria recruit other species with long-range electrical signals – Science Daily

A bacterial global regulator forms a prion – Andy H. Yuan – Science

Prion-like protein spotted in bacteria for the first time
Until now, prions were only seen in the cells of eukaryotic organisms such as plants and animals – Charles Q. Choi – Nature

A periplasmic polymer curves Vibrio cholerae and promotes pathogenesis – Thomas M. Bartlett – Cell

Cholera bacteria infect more effectively with a simple twist of shape – Science Daily

Assembly of a nucleus-like structure during viral replication in bacteria – Vorrapon Chaikeeratisak – Science

Microbes in the news

Man’s best friend, bacteria’s worst enemy: dog sniffs out superbug in Canadian hospital – Ashifa Kassam – The Guardian

This article is not as bad as the title suggests but with photoshopped images:
Revealed: The millions of stomach-churning bacteria lurking in YOUR hair, skin, lungs, gut and mouth – and why – Mary Kekatos – Daily Mail

Video: Career profiles: Program Director at National Science Foundation Matthew Kane – American Society for Microbiology

A clear picture of bacteria: A new study has frozen bacteria extremely fast to gain a true-to-nature image of the internal and external structure – Science Daily

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Microbiome Digest – Bik's Picks

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

Category Archives: Waste and pollution

April 12, 2017

March 27, 2017

March 15, 2017

March 6, 2017

March 5, 2017

Pregnancy and early life

Multi-site human microbiome

Human respiratory microbiome

Human vaginal microbiome

Human gut microbiome

Animal microbiome

Plant, root, and soil microbiome

Water and extremophile microbiome

Microbes in the news

Microbes on the market

February 20, 2017

January 18, 2017

January 16, 2017

January 15, 2017

January 14, 2017