Category Archives: Water microbiome

November 22, 2016

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Vaginal Mirobiome in PPROM, Prevotella copri and rheumatoid arthritis, mice transplanted with stool from lean or obese humans, archaea in a pond.

Pregnancy and early life

High Diversity and Variability in the Vaginal Microbiome in Women following Preterm Premature Rupture of Membranes (PPROM): A Prospective Cohort Study – Teenus Paramel Jayaprakash – PLOS ONE

Human oral microbiome

Review: The oral microbiome – an update for oral healthcare professionals – M. Kilian – British Dental Journal

Human gut microbiome

Chronic opioid use is associated with altered gut microbiota and predicts readmissions in patients with cirrhosis – C. Acharya – Alimentary Pharmacology and Therapeutics

In vitro fermentation of B-GOS: Impact on faecal bacterial populations and metabolic activity in autistic and non-autistic children – Roberta Grimaldi – FEMS Microbial Ecology

Evidence for Immune Relevance of Prevotella copri, a Gut Microbe, in Patients with Rheumatoid Arthritis – Annalisa Pianta – Arthitis & Rheumatology

Review: Human gut microbiota: the links with dementia development – Rashad Alkasir – Protein & Cell

Review: Gut hormones and gut microbiota: implications for kidney function and hypertensionGut hormones and gut microbiota: implications for kidney function and hypertension – Baris Afsar – Journal of the American Society of Hypertension

Review: Dysbiosis in the intensive care unit: Microbiome science coming to the bedside – Georgios D Kitsios – Journal of Critical Care

Review: Interactions between gut microbes and host cells control gut barrier and metabolism – P D Cani – International Journal of Obesity Supplements

Review: Life history and eco-evolutionary dynamics in light of the gut microbiota – Emilie Macke – Oikos

Animal experiments

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans – Li Zhang – ISME Journal

Gut bacteria affect our metabolism – Science Daily

Animal microbiome

Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae
– Shantanu P. Shukla – Molecular Ecology

Thesis: Characterization of the juvenile green turtle (Chelonia mydas) microbiome associated with the ontogenic shift from pelagic habitats to inshore resident areas – James T. Price – Purdue University

Tick microbiome and pathogen acquisition altered by host blood meal – Andrea Swei – The ISME Journal

Plant, root, and soil microbiome

Investigation of Endophytic Bacterial Community in Supposedly Axenic Cultures of Pineapple and Orchids with Evidence on Abundant Intracellular Bacteria – Natalia Pimentel Esposito-Polesi – Current Microbiology

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest – Witoon Purahong – Scientific Reports

High-methionine soybean has no adverse effect on functional diversity of rhizosphere microorganisms -J.G. Liang – Plant Soil Environment

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China – Jing Yan Tang – BMC Microbiology
https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-016-0892-3
Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons – Hirokazu Toju – PLOS ONE

Isolation and Identification of Keratinolytic Bacteria that Exhibit Feather-degrading Potentials – F. O. Iruolaje – Journal of Advances in Biology & Biotechnology

Water and extremophile microbiome

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria – Marco Mangiagalli – The FEBS Journal

Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis – Margarita Kambourova – Archaea

Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities – Christine N. Shulse – Microbiology Open

Conference abstract: Defining the boarders of extreme life: The study of microbial communities and their settings gives insights into Mars analogue life within the MASE project – A Perras – 16th International Symposium on Microbial Ecology

Pollution microbiology

Influence of plantation on microbial community in porous concrete treating polluted surface water – Yan Long – International Biodeterioration & Biodegradation

Food microbiology

Study of the bacterial diversity of foods: PCR-DGGE versus LH-PCR – Cristiana Garofalo – International Journal of Food Microbiology

Viruses and phages

Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments – Samuel L Diaz-Munoz – bioRxiv

More microbiology

Uncovering new drugs and targets – Andrea Du Toit – Nature Reviews Microbiology

Microbiota under pressure – Andrea Aguilar – Nature Reviews Nephrology

Microbes in the news

‘Bacteria beaters’ win Longitude Prize Discovery Award – Shan Ross – The Scotsman

Bacteria for bio-toilets by February 15 – The Times of India

Your Office Has a Microbiome, and It Might Make You Sick – Zoe Schlanger – Wired

Tomato plants are more resistant against nematodes when colonized by a fungus – Farming Futures

Scientists use bacteria to map out NZ. A team of scientists growing bacteria in the shape of New Zealand have caught the attention of their colleagues across the globe – News Australia

The cover image is a map of New Zealand drawn with pyoverdine-producing P. aeruginosa cells in an ocean of indigoidine-synthesizing E. coli. – Cell Chemical Biology

Science, publishing, and career

Citizen science: The people behind the data – Mary Goodchild – NERC Planet Earth

November 19, 2016

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Metformin and diabetes, lizards, Brazilian tree phyllosphere, Amazonian dark earth, air pollution in China, microbiomes of ice cream and cannabis.

General microbiome

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History – Andrew W. Brooks – PLOS Biology

Review: A place for host–microbe symbiosis in the comparative physiologist’s toolbox – Kevin D. Kohl – Journal of Experimental Biology

Human skin and wound microbiology

Review: Cooperative Evolutionary Strategy between the Bacteriome and Mycobiome – Mahmoud Ghannoum – mBio

Human gut microbiome

Metformin Is Associated With Higher Relative Abundance of Mucin-Degrading Akkermansia muciniphila and Several Short-Chain Fatty Acid–Producing Microbiota in the Gut – Jacobo de la Cuesta-Zuluaga – Diabetes Care

News: Metformin Alters Gut Microbiota Composition in Diabetes – Doctors Lounge

Review (Blastocystis) : Modulating the Gut Micro-Environment in the Treatment of Intestinal Parasites – Luis Vitetta – Journal of Clinical Medicine

Review: Recent advances in Entamoeba biology: RNA interference, drug discovery, and gut microbiome – Pedro Morgado – F1000 Research

Microbes in blood, urine, and tissue

Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis – Benjamin Lelouvier – Hepatology

Review: The Urinary Tract Microbiome in Health and Disease – Isabel M. Aragón – European Urology Focus

Animal experiments

A High-Fat High-Sucrose Diet Rapidly Alters Muscle Integrity, Inflammation and Gut Microbiota in Male Rats – Kelsey H. Collins – Scientific Reports

Animal microbiome

Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions, and transmission – Kevin D. Kohl – Molecular Ecology

In liver, not in feces: Metagenomic Evaluation of Bacteria from Voles – Katja A. Koskela – Vector-Borne and Zoonotic Diseases

Plant, root, and soil microbiome

Phyllosphere Metaproteomes of Trees from the Brazilian Atlantic Forest Show High Levels of Functional Redundancy – M.R. Lambais – Microbial Ecology

Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil – Leandro Nascimento Lemos – Genomics Data

Metal-resistant rhizobacteria isolates improve Mucuna deeringiana phytoextraction capacity in multi-metal contaminated soils from a gold mining area – Cácio Luiz Boechat – Environmental Science and Pollution Research

Identification of the Core Set of Carbon-Associated Genes in a Bioenergy Grassland Soil
Adina Howe – PLOS ONE

The nutrient preference of plants influences their rhizosphere microbiome – Feng Cai – Applied Soil Ecology

Effect of microbial-based inoculants on nutrient concentrations and early root morphology of corn (Zea mays) – Pamela Calvo – Journal of Plant Nutrition and Soil Science

The impact of winter legume and cereal cover crops on rhizosphere microbial communities of subsequent vegetable crops for contrasting crop decline – L.M. Manici – Biological Control

Impacts of protected colonial birds on soil microbial communities: When protection leads to degradation – María T. Domínguez – Soil Biology and Biochemistry

Water and pollution microbiome

Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera – Megan M. Morris – Frontiers in Microbiology

Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater – Dongping Wang – Microbiology Open

Screening and In Situ Monitoring of Potential Petroleum Hydrocarbon Degraders in Contaminated Surface Water – Bulent Icgen – Clean Soil Air Water

Source tracking using microbial community fingerprints: Method comparison with hydrodynamic modelling – D.T. McCarthy – Water Research

Air microbiology

Airborne particulate matter pollution in urban China: A chemical mixture perspective from sources to impacts – Ling Jin – National Science Review

Review: Monitoring of the airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios – Andrés Núñez – International Microbiology

Review: Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments – Andrés Núñez – International Microbiology

Food and cannabis microbiology

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests – Kevin McKernan – F1000 Research

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak – Andrea Ottesen – BMC Microbiology

Bioinformatics

[PDF] A small-sample multivariate kernel machine test for microbiome association studies – Xiang Zhan – Fred Hutch Research

More microbiology

Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems – Adrian G. Patterson – Molecular Cell

Bacteria communicate to ramp up collective immune response to viral threats – Science Daily

A Molecular Genetic Basis Explaining Altered Bacterial Behavior in Space – Luis Zea – PLOS ONE

Alabama researcher helps solve mystery of runaway bacteria on spaceships – AL.com

Microbes in the news

Podcast: This Week in Microbiology: microbial DNA found on ATM machines in New York City, and how hydraulic fracturing, or fracking, alters microbial ecosystems deep in the Earth – TWIM

One swab from the surface of your smartphone can tell scientists all about your lifestyle
– Karen Turner – Washington Post

This bacteria is getting harder for kids to fight – Mashable

Armpit Bacteria Transplants Could Save Us From Our Stink – Kaleigh Rogers – Motherboard

Worrying traces of resistant bacteria in air – EurekAlert

 

Science, publishing, and career

An Open Letter from and to Female Scientists – Kelly Ramirez – Scientific American
500 Women Scientists: An open letter from women of science

Who Will Advise Trump on Science? – Ed Yong – The Atlantic

 

 

 

November 17, 2016

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Sepsis diagnosis through fecal gases, colonic lesion detection, microbiological map of the horse GI tract, beachgrass invasion, thromobolites.

Pregnancy and early life

Detection of Sepsis in Preterm Infants by Fecal Volatile Organic Compounds Analysis: A Proof of Principle StudyDetection of Sepsis in Preterm Infants by Fecal Volatile Organic Compounds Analysis: A Proof of Principle Study – Berkhout, Daniel J.C. – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model – Nielson T. Baxter – Microbiome

Disturbances of the Perioperative Microbiome Across Multiple Body Sites in Patients Undergoing Pancreaticoduodenectomy – Rogers, Matthew B. – Pancreas

Animal experiments

Lactobacillus salivarius Isolated from Patients with Rheumatoid Arthritis Suppresses Collagen-Induced Arthritis and Increases Treg Frequency in Mice – Liu Xiaofei – Journal of Interferon & Cytokine Research

Animal microbiome

Horse: A Microbiological Map of the Healthy Equine Gastrointestinal Tract – Aaron C. Ericsson – PLOS ONE

Scallop: Characterization of the microbiota associated to Pecten maximus gonads using 454-pyrosequencing – Aide Lasa – International Microbiology

Catfish: Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes – Jacob W. Bledsoe – PLOS ONE

Bacteria discovery offers possible new means of controlling crop pest – Phys.org

Plant, root, and soil microbiome

Combined effects of reduced irrigation and water quality on the soil microbial community of a citrus orchard under semi-arid conditions – F. Bastida – Soil Biology and Biochemistry

Seasonality and partitioning of root allocation to rhizosphere soils in a midlatitude forest – Rose Z. Abramoff – Ecosphere

Beachgrass invasion in coastal dunes is mediated by soil microbes and lack of disturbance dependence – Aaron S. David – Ecosphere

Thirty-one years of rice-rice-green manure rotations shape the rhizosphere microbial community and enrich beneficial bacteria – Xiaoxia Zhang – Soil Biology and Biochemistry

Points of View: Dinner in the dark: Illuminating drivers of soil organic matter decomposition – Annemieke van der Wal – Soil Biology and Biochemistry

Water and extremophile microbiome

Spatial homogeneity of bacterial and archaeal communities in the deep eastern Mediterranean Sea surface sediments – Sabine Keuter – International Microbiology

Thrombolite fabrics and origins: Influences of diverse microbial and metazoan processes on Cambrian thrombolite variability in the Great Basin, California and Nevada – Cara Harwood Theisen – Sedimentology

Three-Dimensional Structure of the Ultra-oligotrophic Marine Bacterium Pelagibacter – Xiaowei Zhao – Applied and Environmental Microbiology

Metagenomics and bioinformatics

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C) – Matthew Z. DeMaere

Proteomics and metabolomics

Discovery of MRSA active antibiotics using primary sequence from the human microbiome – John Chu – Nature Chemical Biology – DOI: 10.1038/nchembio.2207

Researchers discover new antibiotics by sifting through the human microbiome – Phys.org

Sequencing techniques

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification -Josef Wagner – BMC Microbiology

Bacteria in the news

Solving how harmless bacteria become an unwelcome guest – University at Buffalo

MRSA and other superbugs: could you be at risk when flying? – Lisa Salmon – BT

‘Sweet’ solution to kill bacteria in drinking water developed – Economic Times

Prenatal stress alters gut bacteria to cause lifelong problems in offspring – Medical News Today

How Drug-Resistant Bacteria Travel from the Farm to Your Table – Melinda Wenner Moyer – Scientific American

Simple changes to antibiotic treatment of MRSA may help beat the bacteria – Medical Xpress

Gut microbiota may play important role in influencing onset of blinding wet AMD – News Medical

Gut Microbiome May Determine Immunotherapy Response – Liam Davenport – Medscape

Feeling Hangry? The Science Behind Gut Health and Mood – Dana Angelo White – FoodNetwork

Gut bacteria diversity linked to immunotherapy response in melanoma patients – LabNews

Microbes on the market

Modified Bacteria Could Cure a Fatal Genetic Disorder Found in Infants – Futurism

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

November 16, 2016

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Infants with and without colic, supplementing adults with breastmilk sugars, honey bee viruses, and forensic metabolomics of cell phones.

Pregnancy and early life

Comparison of formula-fed infants with and without colic revealed significant differences in total bacteria, Enterobacteriaceae and faecal ammonia – Francesco Savino – Acta Pediatrica

Human gut microbiome

Bacterially-Associated Transcriptional Remodelling in a Distinct Genomic Subtype of Colorectal Cancer Provides a Plausible Molecular Basis for Disease Development – Katie S. Lennard – PLOS ONE

Oral supplementation of healthy adults with 2′-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota – Emma Elison – British Journal of Nutrition

News: Effects of Human Milk Oligosaccharides Supplementation on Adult Gut Microbiota – Hummer Aslam – Medical News Bulletin

Gut microbiota influences pathological angiogenesis in obesity-driven choroidal neovascularization – Elisabeth MMA Andriessen – EMBO Molecular Medicine

Gut flora connects obesity with pathological angiogenesis in the eye – Rebecca Scholz – EMBO Molecular Medicine

Animal microbiome

Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes – Jacob W. Bledsoe – PLOS ONE

Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea – Anna Roik – PLOS ONE

Honey Bee Viruses in Wild Bees: Viral Prevalence, Loads, and Experimental Inoculation – Adam G. Dolezal – PLOS ONE

Plant, root, and soil microbiome

Microbiome engineers: Grazers, browsers, and the phytobiome stampede – Karen A Garrett – BioRxiv

Fine-scale spatial distribution of orchid mycorrhizal fungi in the soil of host-rich grasslands` – Samuele Voyron – New Phytologist

Water and extremophile microbiome

Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations – Marcus S Bray – bioRxiv

Ordination obscures the influence of environment on plankton metacommunity structure – Tad A. Dallas – Limnology and Oceanography Letters

Metabolomics

Lifestyle chemistries from phones for individual profiling – Amina Bouslimani – PNAS

Cellphone Smudges Yield a Trove of Forensic Data. Researchers say molecules and microbes left on phone, keys, credit cards can linger for months – Wall Street Journal
Chemical traces on your phone reveal your lifestyle, scientists say – The Guardian
Cellphone crud could help I.D. crime victims – Gary Robbins – San Diego Union Tribune
The Grime on Your Smartphone Can Reveal Your Secrets – Christopher Wanjek – Live Science

Effects of Liver Resection on Hepatic Short-Chain Fatty Acid Metabolism in Humans – Evelien P. J. G. Neis – PLOS ONE

Microbes in the news

Biologists give bacteria thermostat controls – Whitney Clavin – Phys.org

Yes, your beer pong cup is teeming with bacteria – Alexandra Ossola – Popular Science

Scientists discover important link between immune system, gut bacteria and glucose metabolism – News Medical

Immune system uses gut bacteria to control glucose metabolism – Oregon State

Bacteria turn trees into pollution-eating machines – Anthony King – Horizon

From the 2016 European Society for Medical Oncology (ESMO) Congress: The Future of Cancer Drugs: RNA Therapies, Bacteria, and Viruses – Kate M. O’Rourke – Medscape

Bile duct bacteria pose cancer risk – Biotech in Asia

November 15, 2016

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Microbial profiling in the classroom, viral abundance in seawater membrane vesicles, two Akkermansia in vitro studies, the phyllospere of Phoenix’ urban forest, the (im)possibility to reconstruct plasmids, high confidence protein annotations.

General microbiome

Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont – Lynn Chiu – PhilSci Archive

Microbial Community-Level Physiological Profiling as an Inquiry Laboratory Exercise – Pamela A. Marshall – The American Biology Teacher

Human oral microbiome

Bacterial communities associated with apical periodontitis and dental implant failure – Simon Dingsdag – Microbial Ecology in Health and Disease

Human respiratory microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff –  Current Opinion in Pulmonary Medicine

Human gut microbiome

Oral application of Escherichia coli bacteriophage: safety tests in healthy and diarrheal children from Bangladesh – Shafiqul Alam Sarker – Environmental Microbiology

The SURMetaGIT study: Design and rationale for a prospective pan-omics examination of the gastrointestinal response to Roux-en-Y gastric bypass surgery – Priscila Sala – Journal of International Medical Research

Review: The Human Microbiome and I-Cubed: A Modern Medical Paradigm – David S. Younger – World Journal of Neuroscience

Animal and in vitro models

In vitro colonisation of the distal colon by Akkermansia muciniphila is largely mucin and pH dependent – F. Van Herreweghen – Beneficial Microbes

Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism – Renee L. Greer – Nature Communications

Animal microbiome

Black rhinoceros (Diceros bicornis) and domestic horse (Equus caballus) hindgut microflora demonstrate similar fermentation responses to grape seed extract supplementation in vitro – N. F. Huntley – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Zhongmin Dai – Scientific Reports

Thesis: The Phyllosphere of Phoenix’s Urban Forest: Insights from a Publicly-Funded Microbial Environment – Benjamin C. MacNeille – Arizona State University

Diversity of phylloplane microflora in certain tea cultivars of Assam, North-East India – Amarjyoti Tanti – European Journal of Biological Research

Review: Do genetically modified plants affect adversely on soil microbial communities?
– Zheng-jun Guan – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health – Chang Soo Lee – Frontiers in Microbiology

Functional diversity of microbial communities in pristine aquifers inferred by PLFA – and sequencing – based approaches – Valerie F. Schwab – Biogeosciences

Trade-off between taxon diversity and functional diversity in European lake ecosystems – Lars Grossmann – Molecular Ecology

Glycerol enhances fungal germination at the water-activity limit for life – Andrew Stevenson – Environmental Microbiology

Bacterial and archeal community composition in hot springs from Indo-Burma region, North-east India – Amrita Kumari Panda – AMB Express

Phages and viruses

Next-generation sequencing and norovirus – Matthew Cotten & Marion Koopmans – Future Virology

Membrane vesicles in sea water: heterogeneous DNA content and implications for viral abundance estimates – Steven J Biller – ISME Journal

Metagenomics and bioinformatics

On the (im)possibility to reconstruct plasmids from whole genome short-read sequencing data – Sergio Arredondo-Alonso – bioRxiv

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Optimal prediction of the number of unseen species – Alon Orlitsky – PNAS

Constraint-based stoichiometric modelling from single organisms to microbial communities
– Willi Gottstein – Journal of the Royal Society Interface

Metabolomics, culturomics, proteomics

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns – Emma Timmins-Schiffman – The ISME Journal

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols – Max Crüsemann – Journal of Natural Products

Probiotics

Review: Probiotics and Subclinical Psychological Symptoms in Healthy Participants: A Systematic Review and Meta-Analysis – Jennifer McKean – The Journal of Alternative and Complementary Medicine

Microbes in the news

Good News at Fred Hutch: Evolutionary biologists Drs. Harmit Malik and Jesse Bloom win American Society for Microbiology awards – Fred Hutch

NTU don once downed a dish of live bacteria, for science’s sake – Straits Times

MCR-1 resistance gene could make its way into bacteria and superbugs in Australia – NT News
Biofilm battle is key to antibiotic war – University of Queensland

‘Probiotics’ on salad greens could make them safer, healthier – The University of Queensland

Monique Keiran: Laziness and hubris making us sick – Times Colonist

From the American Heart Association annual meeting: Could C-Section Birth Raise Child’s Risk of Obesity? – Dennis Thompson – Pantagraph

November 14, 2016

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Infant gut microbiota, oral microbiota of farmworkers with pesticide exposure, critically ill patients, probiotics and Alzheimer’s, Sutterella is a commensal.

Events

Cheese Cultures & Microbiology Class, December 2, 2016, Petaluma – California Artisan Cheese Guild – Eventbrite

Pregnancy and early life

A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol – Julia Simioni – BMC Pediatrics

Establishment and development of the intestinal microbiota of preterm infants in a Lebanese tertiary hospital – Tarek Itania – Anaerobe

Human oral microbiome

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology

News: Study finds link between pesticide exposure and microbiome changes – Brooks Hays – UPI
Pesticide exposures can cause changes in oral microbiome – ASM

Molecular detection of bacteria associated to caries activity in dentinal lesions – Beatriz Gonçalves Neves – Clinical Oral Investigations

Review: Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review – Miguel Padial-Molina – J Oral Maxillofac Res

Human skin microbiome

A Precision Microbiome Approach Using Sucrose for Selective Augmentation of Staphylococcus epidermidis Fermentation against Propionibacterium acnes – Yanhan Wang – Int J Mol Sci

A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes – Maria Allhorn – Scientific Reports

Skin bacteria could protect against disease – Science Daily

Human vaginal microbiome

Escherichia coli and Enterococcus faecalis are able to incorporate and enhance a pre-formed Gardnerella vaginalis biofilm – Joana Castro – Pathogens and Disease

Human gut microbiome

Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study – Jacqueline M. Lankelma – Intensive Care Medicine

Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. – Kaisa Hiippala – Frontiers in Microbiology

Review: Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC) – Jochen Mattner – Int J Mol Sci

Animal microbiome

Review: Microbiota-host interplay at the gut epithelial level, health and nutrition – Jean-Paul Lallès – Journal of Animal Science and Biotechnology

Plant, root, and soil microbiome

Root bacterial endophytes alter plant phenotype, but not physiology – Jeremiah A. Henning – Peer J

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria – Pious Thomas – Microbial Ecology

Water microbiome

Unraveling the microbial community of a cold groundwater catchment system – Burga Braun – Water Research

Built environment microbiome

Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations – Min Gao – Environmental Pollution

Metabolomics

Review: Emerging roles of xenobiotic detoxification enzymes in metabolic diseases – Michael C. Petriello – Reviews on Environmental Health

Probiotics

Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind, and controlled trial – Elmira Akbari -Frontiers in Aging Neuroscience

News: Probiotics improve cognition in Alzheimer’s patients – Medical Xpress

More microbiology

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence – Yok Hian Chionh – Nature Communications

Cracking the code for dormant bacteria. Newly discovered genetic code controls bacterial survival during infections – Anne Trafton – MIT News Office

Microbes in the news

Monitoring in Real Time the Formation and Removal of Biofilms From Clinically Relevant Pathogens – PR Web

From the American College of Rheumatology Annual Scientific Meeting: Gut bacteria may be a trigger for antiphospholipid syndrome – EurekAlert

Three University of Maryland students are sending bacteria samples into space – Rachel Kuipers – the Diamondback

University of Texas at Dallas named “Milestones in Microbiology” – Joanna Urban – ASM

Bethany professor Matthew Swearingen receives research grant – Weirton Daily Times

Scientists try bacteria to halt invasive cheatgrass overwhelming the West – Keith Ridler – LA Times

November 12, 2016

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Two papers on the detection of diseases by metabolomics of breaths or fecal gases, responses of soil bacteria to solar radiation and soil warming, genotyping of probiotics.

General microbiome

Special Issue on ‘Microbe–host interactions’ – Sven Hammerschmidt – FEBS Letters

Pregnancy and early life

Serum cathelicidin, nasopharyngeal microbiota, and disease severity among infants hospitalized with bronchiolitis – Kohei Hasegawa – Journal of Allergy and Clinical Immunology

Human respiratory microbiome

Feasibility of Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics: A Pilot Study – Xiaoling Zang – Journal of Proteome Research

Features of the bronchial bacterial microbiome associated with atopy, asthma and responsiveness to inhaled corticosteroid treatment – Juliana Durack – Journal of Allergy and Clinical Immunology

Human vaginal microbiome

“Murdochiella vaginalis” sp. nov., a new bacterial species cultivated from the vaginal flora of a woman with bacterial vaginosis – Khoudia Diop – Human Microbiome Journal

Human esophagus and stomach microbiome

Editorial: The microbiome as a potential biomarker for oesophageal adenocarcinoma – Julian A Abrams – The Lancet Gastroenterology & Hepatology

A non-endoscopic device to sample the oesophageal microbiota: a case-control study – Daffolyn R Fels Elliott – The Lancet Gastroenterology & Hepatology

Human gut microbiome

Irritable bowel syndrome and active inflammatory bowel disease diagnosed by faecal gas analysis – R. B. M. Aggio – Alimentary Pharmacology and Therapeutics

Review: Formation of propionate and butyrate by the human colonic microbiota – Petra Louis

Review: The Gut Microbiota : The Gateway to Improved Metabolism – Kristina B. Martinez – Gastroenterology Clinics of North America

Review: Regulation of the gut microbiome by inflammasomes – Grace Y. Chen – Free Radical Biology and Medicine

Review: The role of the microbiome in kidney stone formation – Mansi Mehta – International Journal of Surgery

Animal models

Giardia alters commensal microbial diversity throughout the murine gut – Nanelle R Barash – bioRxiv

Animal microbiome

Virus detection using metagenomic sequencing of swine nasal and rectal swabs – Ben M. Hause – J Swine Health Prod

Plant, root, and soil microbiome

Bacterial active community cycling in response to solar radiation and their influence on nutrient changes in a high altitude wetland – Veronica Molina – Frontiers in Microbiology

Land-use change under different climatic conditions: Consequences for organic matter and microbial communities in Siberian steppe soils – Norbert Bischoff – Agriculture, Ecosystems & Environment

Identifying the microbial taxa which consistently respond to soil warming across time and space – Angela M. Oliverio – Global Change Biology

The drivers underlying biogeographical patterns of bacterial communities in soils under sugarcane cultivation – Ademir Durrer – Applied Soil Ecology

Editorial: A small soil bacterium dominates – Ursula Hofer – Nature Reviews Microbiology

Editorial/Review: The Role of Microbial Communities in Tropical Ecosystems – Silvia Pajares – Frontiers in Microbiology

Water microbiome

Cyanobacteria in lakes on Yungui Plateau, China are assembled via niche processes driven by water physicochemical property, lake morphology and watershed land-use – Jingqiu Liao – Scientific Reports

Implications of Ecological Niche Differentiation in Marine Bacteria for Microbial Management in Aquaculture to Prevent Bacterial Disease – Tom Defoirdt – PLOS Pathogens

Bacterial composition, abundance and diversity in fish polyculture and mussel–fish integrated cultured ponds in China – Xiafei Zheng – Aquaculture Research

Food microbiome

Diversity study of microbial community in bacon using metagenomic analysis – Langbo Yi – Journal of Food Safety

Probiotics

Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases – Wesley Morovic – Frontiers in Microbiology

Review: Weight gain by gut microbiota manipulation in productive animals – Emmanouil Angelakis – Microbial Pathogenesis

Viruses and phages

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs – Yi Zheng – Virology

Metabolomics

Book Chapter: A Mathematical Perspective on Microbial Processes in Earth’s Biogeochemical Cycles – Christof Meile – Mathematical Paradigms of Climate Science
Bioinformatics and metagenomics

EMDUnifrac: Exact linear time computation of the Unifrac metric and identification of differentially abundant organisms – Jason McClelland – bioRxiv

Genomic and metagenomic technologies to explore the antibiotic resistance mobilome – José L. Martínez – Annals of the New York Academy of Sciences

More microbiology

The planktonic relationship between fluid-like electrodes and bacteria: wiring in motion
– Sara Tejedor Sanz – ChemSusChem

Experimental study and Random Forest prediction model of microbiome cell surface hydrophobicity – Yong Liu – Expert Systems with Applications

Microbes in the news

uBiome CEO Dr. Jessica Richman to Deliver Opening Keynote at American Medical Informatics Association Symposium – PR web

The impact of the rhizosphere microbiota on root system development and tolerance to environmental constraints in cereals – International Center for Biosaline Agriculture

Miami wants to introduce MORE mosquitoes to fight Zika: Officials considers bringing in bacteria-infected insects to stop spread of virus – Daily Mail

Bruker Moving Into PCR-Based Testing to Expand Clinical Microbiology, MALDI Biotyper Offerings – Genome Web

 

 

November 10, 2016

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Fanconi anemia, Clostridium subcluster decreased in UC, ectomycorrhizas in oak forests, cryoconite hole anaerobes.

Human oral microbiome

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia – C.P. Furquim – Journal of Dental Research

Human gut microbiome

A Single Species of Clostridium Subcluster XIVa Decreased in Ulcerative Colitis Patients – Kozue Takeshita – Inflammatory Bowel Diseases

Composition of gut microbiota in infants in China and global comparison – Ya-Shu Kuang – Scientific Reports

Changes in duodenal tissue-associated microbiota following hookworm infection and consecutive gluten challenges in humans with coeliac disease – Paul Giacomin – Scientific Reports

Making sense of the cause of Crohn’s – a new look at an old disease – Anthony W. Segal – F1000 Research

Metaanalysis: The Emerging Role of the Gut Microbiome in Adult Patients With Multiple Sclerosis – Pamela K. Newland – Journal of Neuroscience Nursing

Review: Escherichia coli Nissle 1917 in Ulcerative Colitis Treatment: Systematic Review and Meta-analysis – Giuseppe Losurdo – Journal of Gastrointestinal and Liver Diseases

Human blood and tissue microbiology

Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections – Vibeke Børsholt Rudkjøbing – BMC Infectious Diseases

Review: Mechanisms of Bacterial Colonization of Implants and Host Response – Christof Wagner – Advances in Experimental Medicine and Biology

Animal models

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease – Ainsley M. Robinson – Inflammatory Bowel Diseases

Microbiota induces tonic CCL2 systemic levels that control pDC trafficking in steady state – M Swiecki – Mucosal Immunology

Siderophore-based immunization strategy to inhibit growth of enteric pathogens – Martina Sassone-Corsia – PNAS

Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice – Shaoqian Zhao – Journal of Molecular Endocrinology

The highly variable microbiota associated to intestinal mucosa correlates with growth and hypoxia resistance of sea bass, Dicentrarchus labrax, submitted to different nutritional histories – François-Joël Gatesoupe – BMC Microbiology

Plant, root, and soil microbiome

Plant growth patterns in a tripartite strip relay intercrop are shaped by asymmetric aboveground competition – Chengdong Huang – Field Crops Research

First detection of Endogone ectomycorrhizas in natural oak forests – Kohei Yamamoto – Mycorrhiza

[PFD] Grape berry bacterial inhibition by different copper fungicides – Guilherme Martins – BIO Web of Conferences

Sensitive responders among bacterial and fungal microbiome to pyrogenic organic matter (biochar) addition differed greatly between rhizosphere and bulk soils – Z Dai – Scientific Reports

Water and extremophile microbiome

Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome – Marek K. Zdanowski – Microbial Ecology

Food microbiology

Sensory, microbiological and physico-chemical characterization of Klila, a traditional cheese made in the south-west of Algeria – Benamara R. N. – African Journal of MIcrobiology Research

Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced? – Bokai Zhu – Environment International

Built environment microbiology

Microbiological evaluation of drinking water available in schools in Cruz das Almas, Brazil – Marcos Vinicius Silva de Andrade – African Journal of MIcrobiology Research

Bioinformatics and metagenomics

Book chapter: DecontaMiner: A Pipeline for the Detection and Analysis of Contaminating Sequences in Human NGS Sequencing Data – Ilaria Granata – Dynamics of Mathematical Models in Biology

More microbiology

Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs – Kenneth Shatzkes – mBio

Predatory bacteria offer potential solution to drug resistance problem – Phys.org
Predatory Bacteria Can Cannibalize Drug-Resistant Bugs – Seeker

Bik’s non-microbiology Picks

Beyond Our Borders? Public Resistance to Global Genomic Data Sharing – Mary A. Majumder – PLOS Biology

Origins of Biodiversity – Michael J. Benton – PLOS Biology

Microbes in the news

Researchers exploring new platform for detecting pathogenic bacteria using bacteriophages – News Medical

Novel vaccines block iron scavenging by bacteria. Agents starve bacteria by raising antibodies to capture the small molecules the microbes release to harvest iron – Stu Borman – Chemical & Engineering News

What’s lurking in the water in Shedd Aquarium – Lisa Bertagnoli – Chicago Business

New biophotonic light sensor can detect Legionella bacteria in minutes – News Medical

Scrubs And Superbug Transmission In ICUs: What We Still Don’t Know Can Kill You – Judy Stone – Forbes
Dangerous bacteria could hitch a ride on nurses’ scrubs – Rachel Sereix – Duke Chronicle

Microbes and the market

Clinical Microbiology Market Expected to Reach $6.72 billion by 2022 – Medgadget

Science, publishing, and career

Rosalind’s Ghost: Biology, Collaboration, and the Female – Caroline Wagner – PLOS Biology

Differences in Collaboration Patterns across Discipline, Career Stage, and Gender – Xiao Han T. Zeng – PLOS Biology

November 8, 2016

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I’m sick at home but my inbox is exploding with new papers, so I scraped myself together for a new Microbiome Digest.

Precision medicine and the microbiome, salivary microbiome of Tsimane mothers and infants, food emulsifiers promote colon cancer in mice, microplastics in urban rivers, and a hypothetical silver Nobel prize for Jeffrey Gordon.

Events

SF Bay Area Microbiome meetup – a new LinkedIn group for people in the San Francisco area interested in all things microbiome!

Society of Nutrition Education and Behavior (SNEB) Webinar – Probiotics: Understanding The Microbiome And The Role Of Probiotics In Long Term Health – Wednesday, December 7 at 12:00 p.m. EST

This one is about me: Stanford Microbiome Pioneer Elisabeth Bik Becomes New Science Editor at uBiome – uBiome

General microbiome

Introducing the Microbiome into Precision Medicine – Thomas M. Kuntz, Jack A. Gilbert – Trends in Pharmacological Sciences

Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche – Sarah M. Kopac – Frontiers in Microbiology

Opinion: Do antibodies select a healthy microbiota? – Jason L. Kubinak & June L. Round – Nature Reviews Immunology

Editorial: Complexity at the sub-genus level – Andrea Du Toit – Nature Reviews Microbiology

Human oral microbiome

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication – Cliff S. Han – PeerJ

A Pilot Study to Evaluate the Oral Microbiome and Dental Health in Primary Open-Angle Glaucoma – Polla, Daniel – Journal of Glaucoma

Sputum microbiology predicts health status in COPD – DCW Braeken – International Journal of Chronic Obstructive Pulmonary Disease

Human respiratory microbiome

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases – Samuel M. Gonçalves – Virulence

Human vaginal microbiome

Effects of pelvic organ prolapse ring pessary therapy on intravaginal microbial flora – Kazuaki Yoshimura – International Urogynecology Journal

Review: Why do lactobacilli dominate the human vaginal microbiota? – SS Witkin – BJOG

Human gastric microbiome

Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status – Llorca, Laura – The Pediatric Infectious Disease Journal

Human gut microbiome

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome – Hailiang Xie – Cell Systems

Culture of previously uncultured members of the human gut microbiota by culturomics – Jean-Christophe Lagier – Nature Microbiology

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota – Francesco Miragoli – FEMS Microbiology Ecology

Animal models

Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota
– Matthew B Biggs – The ISME Journal

Gut microbiota induce IGF-1 and promote bone formation and growth – Jing Yan – PNAS

Dietary emulsifier-induced low-grade inflammation promotes colon carcinogenesis – Emilie Viennois – Cancer Research

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth – Upsornsawan Itthitaetrakool – PLOS ONE

Sex-specific modulation of the gut microbiome and behavior in Siberian hamsters – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Animal microbiome

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates – Julie C. McInnes – Methods in Ecology and Evolution

High-throughput sequencing highlights the significant influence of seasonal housing and teat preparation on the raw milk microbiota – Conor J Doyle – Applied and Environmental Microbiology

Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves – Wei Li – Archives of Microbiology

Repeated sampling of white syndrome-affected corals reveals distinct microbiome at disease lesion fronts – F. Joseph Pollock – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest – Cheng Gao – New Phytologist

AMF, phylogeny, and succession: specificity of response to mycorrhizal fungi increases for late-successional plants – Liz Koziol – Ecosphere

Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils – William A. Argiroff – Microbial Ecology

Effect of disturbance by oil pollution on the diversity and activity of bacterial communities in biological soil crusts from the Sultanate of Oman – Raeid M.M. Abed – Applied Soil Ecology

Book chapter: Root-Microbe Interactions in Response to Soil Conditions – Anil Somenahally – Global Soil Security

Water and extremophile microbiome

Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages – Amanda R. McCormick – Ecosphere

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii – Jason B. Sylvan – Geochimica et Cosmochimica Acta

Bacterial metacommunity organization in a highly-connected aquatic system – Silke Langenheder – FEMS Microbial Ecology

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland – Malin Bomberg – Biogeosciences

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia
– Shipeng Lu – Environmental Microbiology Reports

Review: Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook – Kela P. Weber – Water

Bioinformatics and metagenomics

Alternative for PiCRUST: Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes – Shoko Iwai – PLOS ONE

Measurement of bacterial replication rates in microbial communities – Christopher T Brown – Nature Biotechnology

Microbes in the news

If there was a Nobel silver medal, I’d award it to Jeffrey Gordon and our gut microbes – Tim Spector – The Conversation

The Microbiome Hits #1 for 2017: Cleveland Clinic’s announcement of the Top 10 Medical Innovations came at the conclusion of the 2016 Medical Innovation Summit.

Gut Instincts: The Link Between Diet, the Gut Microbiota and the Brain – Kiana West – Imperial College London

Q&A with Stanford statistics Professor Susan Holmes: Statistics in the era of big data – Stanford News

Conference report: Gut microbes linked to immunotherapy response in melanoma patients – EurekAlert

Gut bacteria ‘may help drugs fight cancer’ – James Gallagher – BBC

Assistant professor Joanna Slusky recognized for work with antibiotic-resistant bacteria – The University Daily Kansan

Three Soundcloud episodes by the Yale Journal of Biology and Medicine on the microbiome, to accompany their September issue:

  1. Microbiome: Episode I: history of the field, current techniques used in microbiome research, and how the microbiome influences our health
  2. Microbiome: Episode IIMicrobiome: Episode II: Dr. Martin Kriegel discusses articles published in our issue, – Yale Journal of Biology and Medicine
  3. Microbiome: Episode III: Dr. Camille Konopnicki, talks about current on going research on the microbiome here at Yale and how microbiome research is evolving and changing.

Companies Bet on Designer Bacteria as New Way to Treat Disease – MIT Technology Review

About Bethany Rader: Researcher studying squid-human bacteria connection – Tim Crosby – The Southern Illinoisan

Horrible title, but nice student work: Students create Frankenstein’s monster of bacteria to detect toxic chemicals – New Atlas

 

November 7, 2015

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Colon cancer tumor location and Fusobacterium nucleatum abundance, eczema in infants, fungi in Crohn’s disease, pH 4 in Yellowstone.

Pregnancy and early life

Altered Gut Microbiota Composition Associated with Eczema in Infants – Huajun Zheng – PLOS ONE

Predominant Lactobacillus species types of vaginal microbiota in pregnant Korean women: quantification of the five Lactobacillus species and two anaerobes – Jeong Hyun Kim – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis – An Hotterbeekx – Scientific Reports

Human gut microbiome

Fungal Microbiota Profile in Newly-diagnosed Treatment-naïve Children with Crohn disease – Mohammad El Mouzan – Journal of Crohn’s and Colitis

Analysis of the Duodenal Microbiome in Autistic Individuals: Association with Carbohydrate Digestion – Kushak, Rafail I. – Journal of Pediatric Gastroenterology and Nutrition

Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location – Kosuke Mima – Clinical and Translational Gastroenterology

Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkinsonism & Related Disorders

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota  – Francesco Miragoli – FEMS Microbiology Ecology

Title is confusing; “No change in mucosal gut Mycobiome” would have been more clear. No Change in the Mucosal Gut Microbiome is Associated With Celiac Disease-Specific Microbiome Alteration in Adult Patients – Valeria D’Argenio – American Journal of Gastroenterology

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: Role of vitamin D on gut microbiota in cystic fibrosis – Mansi Kanhere – The Journal of Steroid Biochemistry and Molecular Biology

Review: Nutrition and the Gut Microbiome in the Elderly – Nuria Salazar – Gut Microbes

Addendum: Support for the Microgenderome Invites Enquiry into Sex Differences – Amy Wallis – Gut Microbes

Animal models

Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model – R. Alan Harris – Scientific Reports

Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Animal microbiome

Identifying bacterial predictors of honey bee health – Giles E. Budge – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Over-winter dynamics of soil bacterial denitrifiers and nitrite ammonifiers influenced by crop residues with different carbon to nitrogen ratios – Enrico Tatti – Applied Soil Ecology

Bacterial and fungal community structure and diversity in a mining region under long-term metal exposure revealed by metagenomics sequencing – Ramya Narendrula-Kotha – Ecological Genetics and Genomics

Conversion of grassland to arable decreases microbial diversity and alters community composition – Katherine E. French – Applied Soil Ecology

Water and extremophile microbiome

Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains – Guang Li Yan – Scientific Reports

Microbial community analysis of pH 4 thermal springs in Yellowstone National Park – Xiaoben Jiang – Extremophiles

Food microbiology

Microbiota of high-pressure-processed Serrano ham investigated by culture-dependent and culture-independent methods – N. Martínez-Onandia – International Journal of Food Microbiology

Applicability of commercial phage-based products against Listeria monocytogenes for improvement of food safety in Spanish dry-cured ham and food contact surfaces – Diana Gutiérrez – Food Control

Pollution and waste microbiology

Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production – Nachiket P. Marathe – PLOS ONE

Microbes in the news

Costa Rican ants might have the secret to better antibiotics – L. Arias – TicoTimes

Waterfowl Worry: Recurring disease kills loons, other birds – Washington Times

STEM Gets Marvelous for a Local Student – how the microbes on the scalp could impact the hair growth – NCTV17.com

Best-selling cleanser recalled over dangerous levels of bacteria. Liz Earle’s ‘Cleanse & Polish Hot Cloth Cleanser’ found to contain potentially dangerous bacteria – Ben Kentish – Interdependent

Microbes and the market

APC Microbiome Institute: Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Financial Times