Category Archives: Food Microbiology

January 24, 2016

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Antibiotic therapy in preterm labor, shrimp microbial dynamics, volcanic desert on Mount Fuji, coffee processing, and Antarctic permafrost limits microbial life.

Pregnancy and birth

Antibiotic Therapy Increases the Risk of Preterm Birth in Preterm Labor without Intra-Amniotic Microbes, but may Prolong the Gestation Period in Preterm Labor with Microbes, Evaluated by Rapid and High-Sensitive PCR System – Satoshi Yoneda – American Journal of Reproductive Immunology

Human gut microbiome

Does the Intestinal Microbiota Explain Differences in the Epidemiology of Liver Disease between East and West – Nakamoto N. – Inflammatory Intestinal Diseases

Commentary: Microbiome-based companion diagnostics: no longer science fiction?
Jeroen Raes – Gut

Animal microbiome

Diary of a shrimpy kid: Dynamic changes of microbial communities in Litopenaeus vannamei cultures and the effects of environmental factors – Hao Zhang – Aquaculture

Plant, root, and soil microbiome
Substrate limitation to soil microbial communities in a subalpine volcanic desert on Mount Fuji, Japan – S. Yoshitake – European Journal of Soil Biology

Bottom-up control of fertilization on soil nematode communities differs between crop management regimes – Ting Liu – Soil Biology and Biochemistry

Interactive effects of precipitation and nitrogen spatial pattern on carbon use and functional diversity in soil microbial communities – Nianxun Xi – Applied Soil Ecology

Water and extremophile microbiome

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica – Jacqueline Goordial – The ISME Journal

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments – Petter Thureborn – PeerJ

 

Waste treatment microbiology

Metagenomic and quantitative insights into microbial communities and functional genes of nitrogen and iron cycling in twelve wastewater treatment systems – Duntao Shu – Chemical Engineering Journal

Food microbiology

High throughput sequencing identifies novel viruses in nectarine: Insights to the etiology of stem pitting disease – Dan Edward Veloso Villamor – Phytopathology

DGGE: Discrimination of post-harvest coffee processing methods by microbial ecology analyses – Yasmine Hamdouche – Food Control

Microbial Ecology

Integrating Theory and Experiment to Explain the Breakdown of Population Synchrony in a Complex Microbial Community – Emma J. Bowen – arXiv

Techniques

Poster abstract: Assembling Whole Genomes from Mixed Microbial Communities Using Hi-C – Ivan Liachko – Plant and Animal Genome Conference

Microbes in the news

Antarctic permafrost may not be habitable for microbes – so is Mars? Finding life on Mars might be harder than thought — or Martian microbes might be different – Emily Chung – CBC News

Microbes take their vitamins — for the good of science – EurekAlert

Bacteria that resist last-resort antibiotics were found in China two months ago, now they’re everywhere – Dominic Jackson – Shanghaiist

Newly Discovered Photosynthetic Bacteria Is Surprisingly Abundant – Science 2.0

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January 23, 2016

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Maturation of the mucin layer, periodontitis in Sjögren’s, Caenorhabditis elegans gut microbiota assembly, the rice-osphere, archaea in moonmilk, and microbial arsenic metabolism.

General human microbiome

The Human Microbiome and Public Health: Social and Ethical Considerations – Kieran C. O’Doherty – American Journal of Public Health

Pregnancy and birth

Review: Mucin–Microbiota Interaction During Postnatal Maturation of the Intestinal Ecosystem: Clinical Implications – Sana Rokhsefat- Digestive Diseases and Sciences

Human oral microbiome

Periodontitis prevalence and serum antibody reactivity to periodontal bacteria in primary Sjögren’s syndrome: a pilot study – Bozo Lugonja – Journal of Periodontology

Temporal Stability of the Salivary Microbiota in Oral Health – Daniel Belstrøm – PLOS ONE

Review: Immune dysregulation mediated by the oral microbiome: potential link to chronic inflammation and atherosclerosis – C. Slocum – Journal of Internal Medicine

Human gut microbiome

Review: Microbiota manipulation for weight change – Tal Dror – Microbial Pathogenesis

Review: Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances – M. P. Francino – Frontiers in Microbiology

Models of microbiome research

Modulating the Gut Microbiota Improves Glucose Tolerance, Lipoprotein Profile and Atherosclerotic Plaque Development in ApoE-Deficient Mice – Ida Rune – PLOS ONE

Dysbiosis of the fecal microbiota in the TNBS-induced Crohn’s disease mouse model – Qing He – Applied Microbiology and Biotechnology

Animal microbiome

Note that the worms did not develop into adults without having veggies to eat: Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments – Maureen Berg – The ISME Journal

Plant, root, and soil microbiome

Rice-osphere? Rice Genotype Differences in Tolerance of Zinc-Deficient Soils: Evidence for the Importance of Root-Induced Changes in the Rhizosphere – Asako Mori – Frontiers in Plant Science

A perspective on inter-kingdom signaling in plant–beneficial microbe interactions – Amanda Rosier – Plant Molecular Biology

Chemotaxis signaling systems in model beneficial plant–bacteria associations – Birgit E. Scharf – Plant Molecular Biology

Water and extremophile microbiome

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system – Helena Osterholz – The ISME Journal

Unique pioneer microbial communities exposed to volcanic sulfur dioxide – Reiko Fujimura – Scientific Reports

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential – Christoph Reitschuler – Microbial Ecology

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria – Steven Smriga – PNAS

Review: The microbial genomics of arsenic – Jérémy Andres – FEMS Microbiology Reviews

Food microbiology

Kombucha tea fermentation: Microbial and biochemical dynamics – Somnath Chakravorty – International Journal of Food Microbiology

PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment – Obinna T. Ezeokoli – International Journal of Food Microbiology

Check your fridge for Thanksgiving leftovers: Direct Dynamic Kinetic Analysis and Computer Simulation of Growth of Clostridium perfringens in Cooked Turkey during Cooling – Lihan Huang – Journal of Food Science

Bioinformatics, metagenomics, and protocols

Protocol collection: Microbial Environmental Genomics (MEG)
MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function – Kevin P. Keegan
Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler
Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip – Joy D. Van Nostrand
Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning – Céline Ribière
Fungal Communities in Soils: Soil Organic Matter Degradation – Tomáš Větrovský
GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity – Samuel Dequiedt

Microbes in the news

Exploring the human gut microbiome. Scientific interest in this diverse world of bacteria has flipped from fear to fascination – Sabin Russell – Fred Hutch

Fungi Prevalent in Urine of Women With Chronic Pelvic Pain – Pam Harrison – MedPageToday

Microscopic subway passengers with a ticket to ride: Interview with Chris Mason – Labnews

To Fight Growing Threat From Germs, Scientists Try Old-Fashioned Killer – Gautam Naik – The Wall Street Journal

http://www.cnn.com/2016/01/22/health/flint-water-legionnaires-disease/Flint hospital reports finding Legionnaires’ bacteria in water – Ralph Ellis – CNN

Breast milk protein could be used in fight against antibiotic resistance – The Guardian

Listeria outbreak: Dole packaged salad linked to 12 bacteria infections and one death – John Houck – Inquisitr

Science, publishing, and career

By a 13 year old girl: Letter to BBC Wildlife Magazine on sexism in nature conservation – Mya-Rose Craig – BirdGirl

Bik’s Picks

Secular trends in family dinner frequency among adolescents – Kathryn Walton – BMC Research Notes
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January 21, 2016

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Beards and MRSA in hospital workers, dysbiosis in Crohns Disease, non-absorbable antibiotics affect offspring in mice, bacterial sunscreens, and bacteria found in a sick-making building.

Events

2nd Annual Microbiome Symposium – January 25, 2016 – Stanford University, Palo Alto, CA

Pregnancy and birth

A necrotizing enterocolitis-associated gut microbiota is already present in the meconium: results of a prospective study – Fardou H. Heida – Clinical Infectious Diseases

Human oral microbiome

Salivary pathogen and serum antibody to assess the progression of chronic periodontitis: a 24-mo prospective multicenter cohort study – T. Morozumi – Journal of Periodontal Research

Human skin microbiome

Bacterial ecology of hospital workers’ facial hair: a cross-sectional study – E. Wakeam – Journal of hospital infection

Human respiratory microbiome

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection – Sushma K. Cribbs – Microbiome

Human gut microbiome

Changes in Colonic Bile Acid Composition following Fecal Microbiota Transplantation Are Sufficient to Control Clostridium difficile Germination and Growth – Alexa R. Weingarden – PLOS ONE

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn’s Disease – Takahashi K – Digestion

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota – Feng Wang – Cell Reports

DNA fingerprinting approaches to trace Escherichia coli sharing between dogs and owners  – Z. Naziri – Journal of Applied Microbiology

Altered intestinal microbiota as a major driving force in alcoholic steatohepatitis – Herbert Tilg – Gut

Impact of Surotomycin on the Gut Microbiota of Healthy Volunteers in a Phase 1 Clinical Trial – Diane M. Citron – Antimicrobial Agents and Chemotherapy

Microbiome animal and bioreactor models

Administration of Non-Absorbable Antibiotics to Pregnant Mice to Perturb the Maternal Gut Microbiota Is Associated with Alterations in Offspring Behavior – Shiro Tochitani – PLOS ONE

Degradation of chondroitin sulfate by the gut microbiota of Chinese individuals –
Qingsen Shang – International Journal of Biological Macromolecules

Streptococcus pneumoniae colonization disrupts the microbial community within the upper respiratory tract of aging mice – Netusha Thevaranjan – Infection and Immunity

Assessing microbial competition in a hydrogen-based membrane biofilm reactor (MBfR) using multidimensional modeling – Kelly J. Martin – Biotechnology and Bioengineering

Animal microbiome

Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs – Pedro R. Frade – PLOS ONE

Plant, root, and soil microbiome

Bacteria increase arid-land soil surface temperature through the production of sunscreens – Estelle Couradeau – Nature Communications

Historical and current climate drive spatial and temporal patterns in fungal endophyte diversity – Hannah Giauque – Fungal Ecology

Location, location, location: priority effects in wood decay communities may vary between sites – Jennifer Hiscox – Environmental Microbiology

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation – Matthew T. Agler – PLOS Biology

Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils – José A. Siles – FEMS Microbiology Ecology

Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy–upland rotation system – Hui Lin – Environmental Pollution

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing – Yajun Sun – Environmental Science and Pollution Research

Large amounts of easily decomposable carbon stored in subtropical forest subsoil is associated with r-strategy-dominated soil microbes – Yuping Chen – Soil Biology and Biochemistry

Water, waste, and extremophile microbiome

Effects of anthropogenic heavy metal contamination on litter decomposition in streams – A meta-analysis – Verónica Ferreira – Environmental Pollution

Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach – Archana Singh – Genomics Data

Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities – Meng Xiao – Scientific Reports

Occurrence of mycotoxins and yeasts and moulds identification in corn silages in tropical climate – B.F. Carvalho – Journal of Applied Microbiology

Food microbiology

Molecular diversity of bacteria in commercially available ‘‘Spirulina’’ food supplements – Elisabeth Vardaka – PeerJ

Ineffective hand washing and the contamination of carrots after using a field latrine – J M Monaghan – Letters in Applied Microbiology

Microbiological characterization using combined culture dependent and independent approaches of Casizolu pasta filata cheese – N.P. Mangia – Journal of Applied Microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon-processing plants – S. Langsrud – Journal of Applied Microbiology

Built environment microbiology

Bacteria in a water-damaged building: associations of actinomycetes and non-tuberculous mycobacteria with respiratory health in occupants – J.-H. Park – Indoor Air

Bioinformatics and metagenomics

Review: Application of multivariate statistical techniques in microbial ecology – O. Paliy – Molecular Ecology

More microbiology

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – eLIFE

Review: Within-host evolution of bacterial pathogens – Xavier Didelot – Nature Reviews Microbiology

This is NOT novel and methods are missing essential steps: A novel method to assess the biodiversity of parasites using 18S rDNA Illumina sequencing; parasitome analysis method – Akina Hino – Parasitology International

Microbes in the news

Found: Desert Hot Spots Just For Microbes – Sarah Laskow – Atlas Obscura

Beards may be more hygienic and bacteria-resistant than shaven skin, study finds – Kate Ng – Independent
Beards may not be that gross, after all – Rachel Thompson – Mashable
Are beards good for your health? – BBC News Magazine

Bacteria or virus? New diagnostic tool could curb antibiotic overuse – Eric Boodman – STAT news

Getting to know the real you – how seriously should we take the health of our internal aliens? – LabNews UK

Probiotics come with bold health claims, but the science is shaky – Megan Scudellari – STAT news

Weekend binges just as bad for the gut as a regular junk food diet, study suggests – Dan Wheelahan – Medical Xpress

Can our gut microbiota contribute to the effect healthy foods have on us? – Gut Microbiota WorldWatch

Science, publishing, and career

Are results in top journals to be trusted? – SK – Economist

The best academic acknowledgements ever – Glen Wright – Times Higher Education
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January 19, 2016

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Microbiota manipulation during stem cell transplants, meh-crobial diversity in digestive tract of two sheep breeds, eukaryotes within pitcher plants,  South Atlantic Ocean, and soil affected by the 2011 Japan Tsunami.

Events

ISME16, Montreal, Canada, 21 – 26 August 2016. Registration and Submissions now open. The deadline for submitting your abstract is 18 March.

ASM Career Development Grants for Postdoctoral Women – up to 4 awards of $1,500 each. Deadline for Nominations: February 1, 2016.

Fellowships by L’Oréal USA For Women In Science. Deadline Feb 5, 2016. Program awards five women postdoctoral scientists annually with grants of $60,000 each, in any specialty.

Human oral microbiome

Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study – Melinda L. Jackson – Sleep Science

Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian Journal

Review: Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation – Tessa M. Andermann – Current Hematologic Malignancy Reports

Review: Epigenetic Regulation of Enteric Neurotransmission by Gut Bacteria – Tor C. Savidge – Frontiers in Cellular Neuroscience

Bioreactor and animal models

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon – Guus A. M. Kortman – Frontiers in Microbiology

Video: A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities – Jacob R. Price – JOVE

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet – Kamarul Zaman Zarkasi – Microbial Ecology

Animal microbiome

Microbial diversity in the digestive tract of two different breeds of sheep – J.-L. Douglas – Journal of Applied Microbiology

Dynamics of Bacterial Community Composition in the Malaria Mosquito’s Epithelia – Majoline T. Tchioffo – Frontiers in Microbiology

Microbiota Plays a Role in Oral Immune Priming in Tribolium castaneum – Momir Futo – Frontiers in Microbiology

Plant, root, and soil microbiome

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat – Flore Ballaud – Frontiers in Microbiology

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system – Jordan D. Satler – PeerJ

Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra – Tim Lachnit – Frontiers in Microbiology

New Methods To Unravel Rhizosphere Processes – Eva Oburger – Trends in Plant Science

Soil microbial responses to forest floor litter manipulation and nitrogen addition in a mixed-wood forest of northern China – Xiao-Lu Sun – Scientific Reports

Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Water and extremophile microbiome

Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica – Valéria M. Godinho – Extremophiles

Novel Barite Chimneys at the Loki’s Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems – Ida H. Steen – Frontiers in Microbiology

High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes – Marion H. Stagars – Frontiers in Microbiology

Nutrient limitation of microbial phototrophs on a debris-covered glacier – J.L. Darcy – Soil Biology and Biochemistry

Large-scale distribution of microbial and viral populations in the South Atlantic Ocean – Daniele De Corte – Environmental Microbiology Reports

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities – Anna Hanke – Frontiers in Microbiology

A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities – Tisza A. S. Bell – Frontiers in Microbiology

Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation – Connor T. Skennerton – Frontiers in Microbiology

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami – Satoshi Hiraoka – BMC Genomics

Oil reservoir microbiome

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs – Ping Hu – mBio

Food microbiology

Dynamic changes in microbiota and mycobiota during spontaneous ‘Vino Santo Trentino’ fermentation – Irene Stefanini – Microbial Biotechnology

Other microbiology and techniques

Perspective: Adapting Koch’s postulates – Allyson L. Byrd, Julia Segre – Science

Depletion of human DNA in spiked clinical specimens to improve the sensitivity of pathogen detection by next generation sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Evaluation of a new device to simplify and standardize stool sample preparation for viral molecular testing with limited hands-on-time – Linda Feghoul – Journal of Clinical Microbiology

Review: Polymicrobial Biofilm Studies: from Basic Science to Biofilm Control – Hubertine ME Willems – Current Oral Health Reports

Review: Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts – Oleg V. Podgorny – Journal of Microbiological Methods

Book: Applications of Mass Spectrometry in Microbiology – Plamen Demirev, Todd R Sandrin – Springer

Metagenomics and bioinformatics

Searching more genomic sequence with less memory for fast and accurate metagenomic profiling – Shea N Gardner – bioRxiv

An evaluation of the accuracy and speed of metagenome analysis tools – Stinus Lindgreen – Scientific Reports

Motif-based text mining of microbial metagenome redundancy profiling data for disease classification – Yin Wang – BioMed Research International

Metabolic pathways

Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea – Romano Mwirichia – Scientific Reports

Microbes in the news

Looking at the Microbiota to Improve Intestinal Transplantation Results – Jeannette Y. Wick – HCP Live

Why do I have to share my body with so many bugs? – Michael Mosley – BBC

How Bitter Taste Receptors Defend the Body against Bacteria – Robert J Lee – Scientific American

White Paper: The Future of Microbiome Research: Out of the Lab and Into the Clinic – Global Engage

How chicory may help fight plague bacteria – Jason Tetro – Popular Science

Lethal bacteria in Christmas Island feral cats sparks warning (Leptospira) – Nicolas Perpitch – ABC Australia

Microbes and art

Subvisual Subway: The Art of New York City’s Bacterial World – Emily Driscoll – Science Friday

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January 13, 2016

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Frozen vs fresh stool transplants, the primate skin microbiome, diet-induced extinctions, bacteria in breast milk from low income Mexican-American moms, and engineered poplar tree endosphere.

Events

Tapping the Human Microbiome (Kavli Hangout) – Tuesday, Jan. 19, 1:30 pm EST, with Janet Jansson, Rob Knight, and Jeff Miller

Pregnancy and birth microbiome

Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children – Veronica Davé – Pediatric Research

Human vaginal microbiome

Review: Biotherapeutic agents and vaginal health – F. H. Al-Ghazzewi – Journal of Applied Microbiology

Human gut microbiome

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection – Christine H. Lee – JAMA

Small Intestine Bacterial Overgrowth and Environmental Enteropathy in Bangladeshi Children – Jeffrey R. Donowitz – mBio

Animal and bioreactor models

Diet-induced extinctions in the gut microbiota compound over generations – Erica D. Sonnenburg – Nature

Intestinal epithelial TLR4 signaling affects epithelial function, colonic microbiota and promotes risk for transmissible colitis – Rishu Dheer – Infection and Immunity

Modulation of the human gut microbiota by dietary fibres occurs at the species level – Wing Sun Faith Chung – BMC Biology

Animal microbiome

Diversity and evolution of the primate skin microbiome – Sarah E. Council – Proceedings of the Royal Society B

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification – N. S. Webster – Scientific Reports

Plant, root, and soil microbiome

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome – Bram Beckers – PNAS

Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests – Xiaoli Wang – Scientific Reports

Food microbiology

Seasonal and Growth-Dependent Dynamics of Bacterial Community in Radish Sprouts – Hiroshi Asakura – Journal of Food Safety

Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar – Sha Li – Applied Microbiology and Biotechnology

Transcriptomics

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline – Mark Davids – PLOS ONE

Metagenomics and bioinformatics

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome – Dingchen Li – Biology Direct

Microbes in the news

DNA Genotek’s microbiome collection and stabilization blog – Lisa Gamwell – The Microbiome Snapshot

Human trials will test freeze-dried poop pills as a weight-loss treatment – David Nield – Science Alert

What is Zika virus? Interview with Derek Gatherer – Microbe Post

E. coli Slinky: Revealed: the awful anchor that lets urinary tract infections take hold – Josh Barney – University of Virginia

Bik’s Picks

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces – Michael J. Ford – PLOS ONE

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January 9, 2016

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Microbiomes of musk deer, Tasmanian Devils, Panamanian frogs, roots of truffle-associated Douglas firs, and the Great Barrier Reef lagoon.

General human microbiome

Editorial: Getting fat from an inflamed relationship? The revenge of the holobiont
Andrew Moore – BioEssays

Perspective: Has provoking microbiota aggression driven the obesity epidemic? – Benoit Chassaing – BioEssays

Pregnancy and birth

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data – Erica Plummer- OMICS Proteomics & Bioinformatics

Review: Infection and preterm birth – Hugh C.G. Nadeau – Seminars in Fetal and Neonatal Medicine

Human gut microbiome

Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects – Radilla-Vázquez R.B. – Obesity Facts

Animal models

The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice – Jinyu Xu – Scientific Reports

Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation – Allison Agus – Scientific Reports

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior – Mark Lyte – PLOS ONE

Effects of BmCPV Infection on Silkworm Bombyx mori Intestinal Bacteria – Zhenli Sun – PLOS ONE

Antibiotic-treated versus germ-free rodents for microbiota transplantation studies – Randi Lundberg – Gut Microbes

Animal microbiome

The musk chemical composition and microbiota of Chinese forest musk deer males
Diyan Li – Scientific Reports

Pasteurellaceae bacteria from the oral cavity of Tasmanian Devils (Sarcophilus Harrisii) show high MIC values towards aminoglycosides and clindamycin – Nicole Gutman – Letters in Applied Microbiology

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis – Eria A Rebollar – The ISME Journal

Plant, root, and soil microbiome

Prokaryotic diversity in biodeteriorated wood coming from the Bükkábrány fossil forest – Katerina Nikolouli – International Biodeterioration & Biodegradation

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia – Alyssa Cornall – Environmental Toxicology and Chemistry

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum) – Gian Maria Niccolò Benucci – Mycorrhiza

Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils – Patrick L. Tomco – Environmental Toxicology and Chemistry

Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months – Daquan Sun – Applied Soil Ecology

Water and extremophile microbiome

Deep Microbial Life in High-Quality Granitic Groundwater from Geochemically and Geographically Distinct Underground Boreholes – Kohei Ino – Environmental Microbiology Reports

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication – Jesse Colangelo-Lillis – Environmental Microbiology Reports

Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community – Richard A. White III – Frontiers in Microbiology

Partitioning of fungal assemblages across different marine habitats – T.C. Jeffries – Environmental Microbiology Reports

Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities – Stéphane Jomini – Environmental Pollution

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions – Hon Lun Wong – MDPI Microorganisms

Microbial genetic diversity in soils along salinealkaline gradients at the coast of Laizhou Bay – Feng Zhao – Protistology

Influence of Zinc on Bacterial Populations and their Proteolytic Enzyme Activities in Freshwater Environments: A Cross-Site Comparison – Lauren Rasmussen – Canadian Journal of Microbiology

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events – Florent E. Angly – Peer J

Food microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Infection microbiology

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh – Shafiqul Alam Sarker – EBioMedicine

Book Chapter: Reducing pathobiomes could slow arms race between man and microbes
S. Romano-Bertrand – Microbiology 5

Bioinformatics and metagenomics

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery – Eric Marinier – BioRxiv

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities – Lisa Oberding – MDPI Microorganisms

Conference abstracts from the 2015 IEEE International Conference onBioinformatics and Biomedicine (BIBM):
Leveraging the k-Nearest Neighbors classification algorithm for Microbial Source Tracking using a bacterial DNA fingerprint library – Jeffrey D McGovern
A computational framework for integrative analysis of large microbial genomics data – Erliang Zeng
Computational challenges in microbiome research – Mihai Pop

Microbes in the news

New Year’s Resolutions for your Microbiome – Anne Estes – Mostly Microbes

West Hartford Children Museum Starts Scientific Discussion Series – Kristin Stoller – Hartford Courant

Balbriggan pair named Young Scientists of the Year: Maria Louise Fufezan and Diana Bura claim first place for research into soil fertility and nematodes – Dick Ahlstrom – The Irish Times

Body’s bacteria don’t outnumber human cells so much after all – Tina Hesman Saey – Science News

Are we really made up of more bacteria than human cells? – Lindsey Kratochwill – Popular Science

P&G granted patent for prebiotic agent-containing composition targeting skin microbiome – Andrew McDougall – Cosmetic Design-Europe.com

Science, publishing, and career

Nobel winner pulls out of Melb conference run by controversial Indian company (OMICS, EB) – Andrew Masterson – The Age

Cheer up, my academic colleagues! We’re so lucky to do this job – Anonymous Academic – The Guardian

Publishers to require ORCID identifiers for authors – EurekAlert

Bik’s Picks

Healthy Diet Helps 183-Year-Old Tortoise Feel Young Again – Jason Bittel – National Geographic

 

January 8, 2016

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Breast milk microbiota profiles, what did the Romans ever do for us, it was only a matter of thyme, and going down the wrong clay.

Pregnancy and birth

Human milk microbiota profiles in relation to birthing method, gestation and infant gender – Camilla Urbaniak – Microbiome

Early Gut Colonization of Preterm Infants: Effect of Enteral Feeding Tubes – Gómez, Marta – Journal of Pediatric Gastroenterology and Nutrition

Review: Role of the Placenta in Preterm Birth: A Review – Terry K. Morgan – American Journal of Perinatology

Human oral microbiome

Long-term efficacy of microbiology-driven periodontal laser-assisted therapy – F. S. Martelli – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human parasites in the Roman World: health consequences of conquering an empire – Piers D. Mitchell – Parasitology

Animal models

Microbiota-induced obesity requires farnesoid X receptor – Ava Parséus – Gut

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome – Scott T. Kelley – PLOS ONE

Animal microbiome

Heterogeneous size datasets of broiler intestinal microbial communities can be analyzed without normalization – I. Aranda-Olmedo – Poultry Science

Plant, root, and soil microbiome

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches
Javier Pascual – PLOS ONE

Image-based modelling of nutrient movement in and around the rhizosphere – Keith R. Daly – Journal of Experimental Botany

Unearthing the Antibacterial Mechanism of Medicinal Clay: A Geochemical Approach to Combating Antibiotic Resistance – Keith D. Morrison – Scientific Reports

Water and waste microbiology

Virome-associated antibiotic-resistance genes in an experimental aquaculture facility – Stefano Colombo – FEMS Microbiology Ecology

Biodiversity patterns of plankton assemblages at the extremes of the Red Sea – J.K. Pearman – FEMS Microbiology Ecology

Food microbiology

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes – Sebastian Liebe – FEMS Microbiology Ecology

Bioinformatics and metagenomics

Antibiotic resistance genes across a wide variety of metagenomes – David Fitzpatrick – FEMS Microbiology Ecology

Microbes in the news

You’re Probably Not Mostly Microbes – Ed Yong – The Atlantic

Scientists discover how blue and green clays kill bacteria – National Science Foundation

Heartburn pills may help grow infection-causing bacteria in gut – Lisa Rapaport – News Daily

Good Bacteria In, Bad Bacteria Out: Biofilms In Water Pipes Filter Dangerous Pathogens Out Of Drinking Water – Lizette Borreli – Medical Daily

The Next Food Fad Is Coming: Feed Your Microbiome – Andrea Hayley, Epoch Times

Enterome Announces Collaboration with Johnson & Johnson Innovation Focused on the Discovery of Novel Targets and Therapeutics for Crohn’s Disease – PR Newswire

From the gut to the eye: commensal microbes as potential triggers of autoimmune uveitis – Atlas of Science

Changes coming with QIIME 2 – Greg Caporaso – Qiime

Science, publishing, and career

DATA CHECK: For female scientists, mixed funding results at U.S. agencies – Jeffrey Mervis – Science
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January 7, 2016

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A new estimate of the ratio microbial:human cells in our bodies, a 5300-year old Helicobacter genome, antibiotics alter bile metabolism, microbiota from 59 bird species, and fecal contamination of Kathmandu drinking water.

Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, which will take place in London, on the 11th and 12th of April, 2016. Early registration closes Jan 15th.

Mysterious Microbes Webinar Series 1 of 3: Microbes and the miracle of compost tea, with Noah Fierer and Ryan Heiland, on Jan 14. Learn how and why microbes are the natural secret to green lawns, lush flowers, and abundant produce

General human microbiome

Revised estimates for the number of human and bacteria cells in the body – Ron Sender – bioRxiv

Review: The human microbiota: the role of microbial communities in health and disease – Luz Elena Botero – Acta Biologica Columbiana

Pregnancy and birth microbiome

A comparative study of bifidobacteria in human babies and adults – Shadi Khonsari – Bioscience of Microbiota, Food and Health

Human oral microbiome

Salivary Antimicrobial Peptides in Early Detection of Periodontitis – Güliz N. Güncü – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

The 5300-year-old Helicobacter pylori genome of the Iceman – Frank Maixner – Science

Microbiome animal and other models

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine – Casey M. Theriot – mSphere

The Gut Microbiota Reduces Colonization of the Mesenteric Lymph Nodes and IL-12-Independent IFN-γ Production During Salmonella Infection – María Fernández-Santoscoy – Frontiers in Cellular and Infection Microbiology

Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health – Lonneke Onrust – Frontiers in Veterinary Science

Animal microbiome

Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology

Plant, root, and soil microbiome

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast –
Melike Balk – Frontiers in Microbiology

Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa – Hanan R. Shehata – Journal of Applied Microbiology

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants – Gerald Otti – Journal of Applied Microbiology

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria  – Max-Bernhard Ballhausen – Frontiers in Microbiology

Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150 – Lihua Li – MDPI Agriculture

Water and waste microbiome

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals – Galina Radeva – Canadian Journal of Microbiology

Master thesis: Evaluation of Two Culture-Independent Methods for Quantification of the Fraction of K-and r-Strategists within Water Microbial Communities – Brandsegg, Hege – Norges teknisk-naturvitenskapelige universitet

Built environment microbiome

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water – Abhilasha Karkey – PLOS Neglected Tropical Diseases

Application of the Environmental Relative Moldiness Index in Finland – Martin Täubel – Applied and Environmental Microbiology

Food microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology

Metagenomics and bioinformatics

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics – Alejandra Escobar-Zepeda – Frontiers in Genetics

Science, publishing, and career

Peer review: tips from field experts for junior reviewers – Sabina Alam – BMC Medicine

Microbes in the news

Gut bacteria from Otzi the Iceman reveals our intimate ties to one microbe – Rachel Feltman – Washington Post

Scientists unearth bacteria from stomach of 5,300-year-old iceman – Carl Zimmer – StatNews

The Famous Ancient “Iceman” Had Ulcer Bacteria In His Gut – Dan Vergano – BuzzFeed

High Stress Environments May Lead To Unhealthy Gut Microbiomes: How To Protect Yourself From The Consequences – Lecia Bushak – Medical Daily

Antibiotics Pave Way for C. Diff Infections – North Carolina State University

Jackson Laboratory Hosted Microbiome Symposium Related to Cancer and Immunology – Lexology

The Bacteria That May Be Causing Your Nasty Cold. “The most common one of them in Mycoplasma Pneumoniae Infection,” Martin explained. – Fox29

Bik’s Picks

A “Pedi” Cures All: Toenail Trimming and the Treatment of Ulcerative Dermatitis in Mice – Sean C. Adams – PLOS ONE
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January 5, 2016

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Bacteria in breastmilk, nose/skin bacteria preventing pneumococcal infection, biofilms on pig carcasses in flowing water, Jurassic microbial mats, and Comammox Nitrospira-like bacteria in drinking water.

Pregnancy and birth

Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants – Kimberly Kozak – Gut Microbes

Review: Association Between the Gut Microbiota and Diet: Fetal Life, Early Childhood, and Further Life – D.A. Kashtanova – Nutrition

Human nose/skin microbiome

Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols – Lindsey Bomar – mBio

Human gut microbiome

A dysbiotic subpopulation of alcohol-dependent subjects – Philippe de Timary – Gut Microbes

Colorectal cancer: role of commensal bacteria and bystander effects – Xingmin Wang – Gut Microbes

Review: Gut inflammation and microbiome in spondyloarthritis – Jayakanthan Kabeerdoss – Rheumatology International

Review: Gut Microbiota and Celiac Disease – Giovanni Marasco – Digestive Diseases and Sciences

Animal models

Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice – Roman Dziarski – PLOS ONE

Plant, root, and soil microbiome

Dynamics of viral abundance and diversity in a Sphagnum-dominated peatland: temporal fluctuations prevail over habitat – Flore C. Ballaud – Frontiers in Microbiology

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession – Miao Wang – Frontiers in Plant Science

Early Jurassic microbial mats – a potential response to reduced biotic activity in the aftermath of the end-Triassic mass extinction event – Olof Peterffy – Palaeogeography, Palaeoclimatology, Palaeoecology

Water and extremophile microbiome

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals – Jennifer M. Lang – Microorganisms

Effect of water chemistry on zooplanktonic and microbial communities across freshwater ecotones in different macrophyte-dominated shallow lakes – Tomasz Mieczan – Journal of Limnology

Influences of microbial communities on groundwater component concentrations during managed artificial recharge – Wenjing Zhang – Environmental Earth Sciences

Complete metagenome sequencing based microbial diversity insights from Deccan basaltic hot spring of Unkeshwar, Maharashtra, India – Gajanan T. Mehetre – Genomics Data

Perspective: Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Built environment and waste microbiome

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System – Ameet J. Pinto – mSphere

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology – Juliana Cardinali-Rezende – Chemosphere

Food microbiology

Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration – E. Sattin – Food Microbiology

Microbes in the news

Outbreaks of Salmonellosis from Small Turtles – Maroya Spalding Walters – Pediatrics

Many of these are amazing because of microbes: 17 of the world’s weirdest water features – Marnie Hunter – CNN

Study details how good bacteria might help prevent middle ear infections and pneumonia – EurekAlert

Study: Bacteria, electrons spin in similar patterns. Bacteria streaming through a lattice behave like electrons in a magnetic material – EurekAlert
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December 17, 2015

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Effects of intranasal flu vaccine on nose microbiota, intestinal microbiota of Dutch children, fungi in dung, optical sensors, and diurnal time scales in drinking water.

General microbiome

Review: Intestinal Microbiota and Metabolic Diseases: Pharmacological Implications – Liang Shen – Trends in Pharmacological Sciences

Editorial: Immunotherapy Not Working? Check Your Microbiota – Nathan R. West – Cancer Cell

Review: Human Microbiome and Its Association With Health and Diseases – Asmaa Althani – Journal of Cellular Physiology

Infection and immunity

The microbiome of diabetic foot osteomyelitis – S. A. V. van Asten – European Journal of Clinical Microbiology & Infectious Diseases

A baleful weed and the king of fruits: tolerance, immunity, and the microbiome – Kairav Sinha – International Journal of Dermatology

Human oral microbiome

Salivary changes in oral mucosal diseases – Yazan Hassona – Periodontology 2000

Human respiratory microbiome

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles – Y. Tarabichi – Microbiome

Editorial: Precision respiratory medicine and the microbiome – Geraint B Rogers – The Lancet Respiratory Medicine

Review: The microbiome and critical illness – Robert P Dickson – The Lancet Respiratory Medicine

Human urinary tract microbiome

Intracellular Bacterial Communities: A Potential Etiology for Chronic Lower Urinary Tract Symptoms – Victoria C.S. Scott – Urology

Review: The interplay of extracellular matrix and microbiome in urothelial bladder cancer – Massimo Alfano – Nature Reviews Urology

Human gut microbiome

Composition and stability of intestinal microbiota of healthy children within a Dutch population – Tim G. J. de Meij – The FASEB Journal

Long-term risk of cardiovascular and cerebrovascular disease after removal of the colonic microbiota by colectomy: a cohort study based on the Danish National Patient Register from 1996 to 2014 – Anders Boeck Jensen – BMJ Open

Adverse events in faecal microbiota transplant: a review of the literature –
M. Baxter – Journal of Hospital Infection

Editorial: Antidiabetic drug treatment confounds gut dysbiosis associated with type 2 diabetes mellitus – David Holmes – Nature Reviews Endocrinology

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database – Jarmo Ritari – BMC Genomics

Microbiome models

Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference – Meiling Zhang – Aquaculture

Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees – Hannah J. Barbian – American Journal of Primatology

Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis – Zeneng Wang – Cell

Editorial: Immunotherapy Meets Microbiota – Jiaying Tan – Cell

Editorial: Drug the Bug! – Annika Lindskog Jonsson – Cell

Functional anatomy of the colonic bioreactor: Impact of antibiotics and Saccharomyces boulardii on bacterial composition in human fecal cylinders – Alexander Swidsinski – Systematic and Applied Microbiology

The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment – Kenneth Klingenberg Barfod – The Open Microbiology Journal

Animal microbiome

Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens – Heidi M. Luter – PeerJ

Review: Dung-inhabiting fungi: a potential reservoir of novel secondary metabolites for the control of plant pathogens – Sabrina Sarrocco – Pest Management Science

Book Chapter: Age-Related Variation in the Scent Pouch Bacterial Communities of Striped Hyenas (Hyaena hyaena) – Kevin R. Theis – Chemical Signals in Vertebrates 13

Plant, root, and soil microbiome

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata – Sunil Singh – Journal of Hazardous Materials

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil – O. Roger Anderson

Fertilizing with Animal Manure Disseminates Antibiotic Resistance Genes to the Farm Environment – Matti Ruuskanen – Journal of Environmental Quality

Water microbiome

Microbiology: lessons from a first attempt at Lake Ellsworth – D. A. Pearce – Philosophical Transactions A

Comprehensive genomic analyses of the OM43 clade including a novel species from Red Sea indicate ecotype differentiation among marine methylotrophs – Francy Jimenez-Infante – Applied and Environmental Microbiology

Built environment microbiome

Exposure to culturable and total microbiota in cultural heritage conservation laboratories – Rafał L. Górny – Int J Occup Med Environ Health

The impact of sampling, PCR, and sequencing replication on discerning changes in drinking water bacterial community over diurnal time-scales – Quyen Melina Bautista-de los Santos – Water Research

Food microbiology

The impact of yeast starter cultures on the microbial communities and volatile compounds in cocoa fermentation and the resulting sensory attributes of chocolate – Nádia Nara Batista – Journal of Food Science and Technology

Techniques

Optical sensors for sensing microbial life on a surface – M. Fischer – Applied and Environmental Microbiology

Metagenomes, viruses, and bioinformatics

Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov. – Gaël Mourembou – OMICS: A Journal of Integrative Biology

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts – Caroline De Clerck – Microbiome

MeFiT: Merging and Filtering Tool for Illumina Paired-End Reads for 16S rRNA Amplicon Sequencing – Hardik I. Parikh – ArXiv

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach – Philippe Bordron – MicrobiologyOpen

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?
Henrike Zschach – Viruses

MEEPTOOLS: A maximum expected error based FASTQ read filtering and trimming toolkit – Vishal N. Koparde – Arxiv

Microbes in the news

Book review: I, superorganism – learning to love your inner ecosystem – Jon Turney

Science, publishing, and career

South Korean professors charged over alleged plagiarism scheme: Prosecutors accuse academics of colluding with publishers to boost their standing and sell more books – David Matthews – Times Higher Education
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