Category Archives: Built Environment Microbiology

July 30, 2015

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Correct vocabulary of microbiome research, microbiome during mosquito development, microbes on Granada’s Royal Chapel stone, and microbes in Atacama desert.

General microbiome

About the proper use of “16S”, “microbiome”, and “microbiota”, and why “microflora” is not correct. Note Elies: But “microbiota” is a plant too!
The vocabulary of microbiome research: a proposal – Julian R. Marchesi – Microbiome

Human oral microbiome

Host response mechanisms in periodontal diseases – Nora Silva – Journal of Applied Oral Science

Human respiratory microbiome

The airway microbiome in patients with severe asthma: Associations with disease features and severity – Yvonne J. Huang – The Journal of Allergy and Clinical Immunology

Human gastric microbiome

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome – DeAnna E. Beasley – PLOS ONE

Microbiome models

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets – Nirupama Benis – BMC Genomics

Animal microbiome

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology

Review: The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals – A. Rodrigues Hoffmann – Veterinary Pathology

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi affect plant community structure under various nutrient conditions and stabilize the community productivity – Gaowen Yang – Oikos

Complementarity in both plant and mycorrhizal fungal communities are not necessarily increased by diversity in the other – Cameron Wagg – Journal of Ecology

Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing –
Youwei Hong – Canadian Journal of Microbiology

Genetic analysis reveals diversity and genetic relationship among Trichoderma isolates from potting media, cultivated soil and uncultivated soil – Abdullah M. Al-Sadi – BMC Microbiology

Mineralogy: Geochemical evidence of microbial activity within ooids – Mara R. Diaz – Sedimentology

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments – Isabel C. Romero – Journal of Marine Science and Engineering

Inexplicable Arsenic: Human Dimensions of Soil, Water, Food and Microbial
Resources – Ramakrishnan B – Journal of Environmetnal and Analytical Toxicology

Water microbiome

Structure of the archaeal community in the Black Sea photic zone – A. Y. Merkel – Microbiology

Review: Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes – Thomas Mock – Global Change Microbiology

Extremophiles

Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert – Maria Cecilia Rasuk – Microbial Ecology

Thesis: Microbial Ecology, Biogeochemistry, and Signatures of Life at Low Temperature in Arctic Thermokarst Lake Sediments and High Sierra Snow Fields – Matheus Carnevali, Paula B – University of Nevada, Reno

Waste and built environment microbiology

Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters – Samik Bagchi – PLOS ONE

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada – Fadwa Jroundi – PLOS ONE

Seasonal Variation on Microbial Community and Methane Production during Anaerobic Digestion of Cattle Manure in Brazil – Juliana Alves Resende – Microbial Ecology

Metagenomics and bioinformatics

deFUME: Dynamic exploration of functional metagenomic sequencing data – Eric van der Helm – BMC Research Notes

Microbial Ecology

An Economic Framework of Microbial Trade – Joshua Tasoff – PLOS ONE

Microbes in the news

Kingdoms are so 20th century: The tree of life gets a makeover: Schoolroom kingdoms are taking a backseat to life’s supergroups – Susan Milius – Science News

Soil-Dwelling Fungus Rode Joplin Tornado to Unexpected Human Home – Jennifer Frazer – Scientific American

Agave extracts show ability to shift gut microbiota: Ingredion study – Stephen DANIELLS – Nutraingredients

Bacterial Find Sheds Light on Digestive Issues, Diabetes, Obesity – American Crystallographic Association

Water At Some Olympic Venues In Rio de Janeiro Reportedly Contain Virus Levels On Par With Raw Sewage – Brad Brooks and Jeny Barchfield – Huffington Post

LASA students developing bacteria to improve carbon monoxide detectors – Calily Bien – KXAN

Bik’s Picks

A tragic death leaves just four northern white rhinos living and little hope for the species – Rachel Feltman – Washington Post

‘Once in a Blue Moon’ Happens on Friday — Why? – Geoff Gaherty – Discovery

How did you get that job: designing a parachute for NASA’s Mars rover – Elizabeth Lopatto – The Verge

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July 24, 2015

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A review about small molecules produced by human microbiota, layers of microbial life in Dead Sea sediments, fungus making “hair ice”, exploring deep microbial life in the sea, and bacterial diversity at the North Pole.

Events

3rd Microbiome R&D and Business Collaboration Forum: USA, San Diego, September 10-11, 2015

WAO Symposium on Food Allergy & the Microbiome – 5-6 December 2015, Miami, FL

Microbiome reviews

Small molecules from the human microbiota – Mohamed S. Donia, Michael A. Fischbach – Science

Editorial: Microbiota-induced T cells block allergic inflammation – Yvonne Bordon – Nature Reviews Immunology

Perspective: Promise and pragmatism in clinical microbiome research – Nadim J. Ajami – Mini-Reviews in Medicinal Chemistry

Review: The Role of Intestinal Microbiota in Graft versus Host Disease – no authors listed – Mini-Reviews in Medicinal Chemistry

Editorial: Protective role of gut microbial SCFAs – Ellen F. Carney – Nature Reviews Nephrology

Human oral microbiome

In vitro work: Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

Human gut microbiome

Agave Inulin Supplementation Affects the Fecal Microbiota of Healthy Adults Participating in a Randomized, Double-Blind, Placebo-Controlled, Crossover Trial – Hannah D Holscher – Journal of Nutrition

Plant, root, and soil microbiome

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea – C. Thomas – Geobiology

Evidence for biological shaping of hair ice – D. Hofmann – Biogeosciences

Water and extremophile microbiome

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor – F. Inagaki – Science

Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs – Samia Amarouche-Yala – Extremophiles

Bacterial diversity in snow on North Pole ice floes – Aviaja L. Hauptmann – Extremophiles

Identifying the sources of nitrate contamination of groundwater in an agricultural area (Haean basin, Korea) using isotope and microbial community analyses – Heejung Kim – Science of the Total Environment

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages – Haiwei Luo – Molecular Biology and Evolution

Built environment microbiome

Microbiological characterization of 3193 French dwellings of Elfe cohort children – S. Rocchi – Science of The Total Environment

Metagenomics and bioinformatics

For plant/animal assemblages, but might be of interest: cati: an R package using functional traits to detect and quantify multi-level community assembly processes – Adrien Taudiere – Ecography

Metabolomics and proteomics

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation – Rafael Bargiela – Proteomics

Microbes in the news

‘It’s like going to Pluto and seeing McDonald’s: ‘These microbes live more than 2 kilometers below the sea floor off the coast of Japan – Mitch Leslie – Science

It takes a village… to ward off dangerous infections? New microbiome research suggests so – MedicalXpress

Pathogenic microbiome bacteria change shape to adapt to nasopharyngeal environment – American Microbiome Institute

Rotting Fungus Creates Beautiful, Glistening ‘Hair Ice’ – Elizabeth Goldbaum – LiveScience

Not endorsing this one, full of errors and false claims: Discovery of Microbiome “Third Brain” Confirmed by Scientific Research in Japan – BusinessWire

Science, publishing, and career

New life for old bones: inventing ways to apply the DNA sequencing revolution to tissues ravaged by time. – Elizabeth Culotta – Science

Songwriting and science: Pitching songs, however, has taught me a few practical lessons about pitching papers and grant proposals: – C. Neal Stewart Jr. – Science

Bik’s Picks

Comparisons of life-history parameters between free-ranging and captive killer whale (Orcinus orca) populations for application toward species management – Todd R. Robeck – Journal of Mammalogy

Kiwi genome provides insights into evolution of a nocturnal lifestyle – Diana Le Duc – Genome Biology

A medical-toxicological view of tattooing – Peter Laux – The Lancet

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July 17, 2015

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Laser Capture Microdissection of tissue from infants with NEC, skin microbiome from Chinese subjects, paromomycin treatment effects on human gut microbiome.

General human microbiome

Prenatal exposure to systemic antibacterials and overweight and obesity in danish schoolchildren: A prevalence study – A Mor – International Journal of Obesity

Review: Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior – Peter Kramer – Perspectives on Psychological Science

Pregnancy and birth microbiome

Application of Laser Capture Microdissection and 16S rRNA Gene PCR in the Analysis of Bacteria Colonizing the Intestinal Tissue of Neonates with Necrotizing Enterocolitis – Jingli Yang – The Pediatric Infectious Disease Journal

Human oral microbiome

Checkerboard Assay: Advanced Caries Microbiota in Teeth with Irreversible Pulpitis –
Isabela N. Rôças – Journal of Endodontics

Human skin microbiome

Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups – Marcus H. Y. Leung – Scientific Reports

Human gut microbiome

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin – Femke-Anouska Heinsen – Gut Microbes

Short-term High Fat Diet Increases Postprandial Trimethylamine-N-Oxide in Humans – Nabil E. Boutagy – Nutrition Research

In Brief/ Editorial: Modifying the gut to treat liver diseases – Cláudio Nunes-Alves – Nature Reviews Microbiology

Review: Talking microbes: when gut bacteria interact with diet and host organs – Patrice D. Cani – Molecular Nutrition & Food Research

Review: Metagenomic Surveys of Gut Microbiota – Rahul Shubhra Mandal – Genomics, Proteomics & Bioinformatics

Review: The bilateral responsiveness between intestinal microbes and IgA – Andrew J. Macpherson – Trends in Immunology

Animal and other models

How free of germs is germ-free? Detection of bacterial contamination in a germ free mouse unit – Clinton A Fontaine – Gut Microbes

Microbes & Neurodevelopment – Absence of Microbiota during Early Life Increases Activity-Related Transcriptional Pathways in the Amygdala – Roman M. Stilling – Brain, Behavior, and Immunity

Exoelectrogenic capacity of host microbiota predicts lymphocyte recruitment to the gut – Aaron Conrad Ericsson – Physiological Genomics

Polyphenols-rich fruit in maternal diet modulates inflammatory markers and the gut microbiota and improves colonic expression of ZO-1 in offspring – Carina Almeida Morais – Food Research International

Defined Nutrient Diets Alter Susceptibility to Clostridium difficile Associated Disease in a Murine Model – John H. Moore – PLOS ONE

Soluble Dextrin Fibers Alter Intestinal Microbiota and Reduce Proinflammatory Cytokine Secretion in Male IL-10–Deficient Mice – Rosica Valcheva – The Journal of Nutrition

Kiwifruit fermentation drives positive gut microbial and metabolic changes irrespective of initial microbiota composition – Paul Blatchford – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

The potential roles of bacterial communities in coral defence: A case study at Talang-talang reef – Felicity W. I. Kuek – Ocean Science Journal

Soil

Land-use system shapes soil bacterial communities in Southeastern Amazon region – Lucas William Mendes – Applied Soil Ecology

Water microbiome

Seasonal progression of microbial communities on the Faroe shelf – Anni Djurhuus – Marine Biology Research

Waste treatment microbiology

Understanding the linkage between elevation and activated sludge bacterial community along a 3600 m elevational gradient in China – Lihua Niu – Applied and Environmental Microbiology

Techniques

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities – Mads Albertsen – PLOS ONE

Microbial ecology

Interaction networks for identifying coupled molecular processes in microbial communities – Magnus Bosse – BioData Mining

Microbes in the news

10 Ways to Cultivate Good Gut Bacteria and Reduce Depression – Therese Borchard – Everyday Health

Science, publishing, and career

Hundreds sign letter criticizing Science for reinforcing “damaging stereotypes” – Shannon Palus – Retraction Watch

Bik’s Picks

International report confirms: 2014 was Earth’s warmest year on record – NOAA

A second FDA approval frees Theranos to do a blood test outside lab – Roger Parloff – Fortune

Mosquitoes first sniff then attack their host – Dispatch Times

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July 16, 2015

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Biomimetic robot models of host-microbiome interactions, an eukaryotic model for astrobiology, how plants use salicylic acid to sculpt their root microbiome, and how to cook Hadza tubers.

Human oral microbiome

TLR4, NOD1 and NOD2 Mediate Immune Recognition of Putative Newly-Identified Periodontal Pathogens – Julie Marchesan – Molecular Oral Microbiology

Human respiratory microbiome

Intraalveolar Catecholamines and the Human Lung Microbiome – Robert P. Dickson – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Transforming berberine into its intestine-absorbable form by the gut microbiota – Ru Feng – Scientific Reports

I could not find information about primers or sequencing strategy, no ordination plots: Colonic bacterial composition in Parkinson’s disease – Ali Keshavarzian – Movement Disorders

Review: Role of gut microbiota in the modulation of atherosclerosis-associated immune response – Dmitry A. Chistiakov – Frontiers in Microbiology

Review: Potential role of the intestinal microbiota in programming health and disease – Olivier Goulet – Nutrition Reviews

Review: Microbiota and the gut–brain axis – John Bienenstock – Nutrition Reviews

Review: The Blood-Brain Barrier’s Gut Check – Nga Bien-Ly – Science Translational Medicine

Review: The Microbes inside Us and the Race for Colibactin – Helge B. Bode – Angewandte Chemie International Edition

Animal models

Macaques: Persistent effects of early infant diet and associated microbiota on the juvenile immune system – Nicole Narayan – Gut Microbes

Pigs: Wheat and barley differently affect porcine intestinal microbiota – Eva Weiss – Journal of the Science of Food and Agriculture

Rats: Bacterial Flora Changes in Conjunctiva of Rats with Streptozotocin-Induced Type I Diabetes – Chao Yang – PLOS ONE

Animal microbiome

Fish-like marine chordate: Diversity and composition of the bacterial community in Amphioxus feces – Minming Pan – Journal of Basic Microbiology

Plant, root, and soil microbiome

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa – Sarah L. Lebeis – Science

Silencing a key gene of the common symbiosis pathway in Nicotiana attenuata specifically impairs arbuscular mycorrhizal infection without influencing the root-associated microbiome or plant growth – Karin Groten – Plant, Cell & Environment

Water microbiome

Microbial communities related to biodegradation of dispersed Macondo oil at low seawater temperature with Norwegian coastal seawater – Odd G. Brakstad – Microbial Biotechnology

Extremophile microbiome

UV-resistant yeasts isolated from a high-altitude volcanic area on the Atacama Desert as eukaryotic models for astrobiology – André A. Pulschen – Microbiology Open

Waste management microbiology

Changes in diversity of cultured bacteria resistant to erythromycin and tetracycline in swine manure during simulated composting and lagoon storage – L. Wang – Letters in Applied Microbiology

Functional foods

Assessing digestibility of Hadza tubers using a dynamic in-vitro model – Stephanie L. Schnorr – American Journal of Physical Anthropology

Bioinformatics

Exploring Host-Microbiome Interactions using an in Silico Model of Biomimetic Robots and Engineered Living Cells – Keith C. Heyde – Scientific Reports

K-Pax2: Bayesian identification of cluster-defining amino acid positions in large sequence datasets – Alberto Pessia – Microbial Genomics

Microbes in the news

Healthy Living: Preterm Birth Disparities: Doctor Dunlop and her team have begun a five year study to examine prenatal stress, diet and a woman’s microbiome on birth outcomes – 9&10 News
Five-year study to examine the gut microbiome of premature infants – Matt Wood – Science Life University of Chicago

Plant defense hormones help sculpt root microbiome – Science Daily

Research finds diversifying your diet may make your gut healthier – Science Codex

Do you smoke? UBiome wants to study your mouthome – Claire Maldarelli – Popular Science

Bik’s Picks

Polar Bears Don’t Go Into Hibernation-Like State in Summer, Researchers Say – James Gorman – New York Times

Finally, Bacon-Flavored Health Food Has Arrived: introducing dulse, a seaweed that tastes like bacon – Elizabeth Palermo – Live Science

Why screams are scary (hint: It’s not because they’re loud) – Eryn Brown – Los Angeles Times

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July 14, 2015

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Antibiotic-induced changes in mouse gut microbiome, the lichen microbiome, and what’s floating in the airplane toilet?

Human respiratory microbiome

Common Cell Shape Evolution of Two Nasopharyngeal Pathogens – Frédéric J. Veyrier – PLOS Genetics

Human gut microbiome

Trimethylamine-N -oxide: A Novel Biomarker for the Identification of Inflammatory Bowel Disease – Aze Wilson – Digestive Diseases and Sciences

Review: Roles of commensal microbiota in pancreas homeostasis and pancreatic pathologies – Camila Leal-Lopes – Journal of Diabetes Research

Animal models of microbiome research

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile – Alyxandria M. Schubert – mBio

Animal microbiome

The Apis mellifera Filamentous Virus Genome – Laurent Gauthier – Viruses

Concentrations of viable oil-degrading microorganisms are increased in feces from Calanus finmarchicus feeding in petroleum oil dispersions – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Plant, root, and soil microbiome

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology

Indigenous trees restore soil microbial biomass at faster rates than exotic species – Chun Li – Plant and Soil

MSc Thesis: Tree Islands of Fertility Structure Bacterial Community Assembly and Functional Genes Contributing to Ecosystem Processes – Tayte Paul Campbell – Brigham Young University

Rhizosphere microbiome selection by Epichloë endophytes of Festuca arundinacea – Elizabeth Lewis Roberts – Plant and Soil

Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China – W. Y. Dong – Biogeosciences Discussions

Water microbiome

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump – S. Agusti – Nature Communications

Extremophile microbiome

Characterization of the Bacterial and Sulphate Reducing Community in the Alkaline and Constantly Cold Water of the Closed Kotalahti Mine – Malin Bomberg – Minerals

Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes – J. Comte – Biogeosciences Discussions

Built environment and waste microbiome

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance – Thomas Nordahl Petersen- Scientific Reports

Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater – Sevcan Aydin – Water Research

One-Time Addition of Nano-TiO2 Triggers Short-Term Responses in Benthic Bacterial Communities in Artificial Streams – Alexandra Ozaki – Microbial Ecology

Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure – Li Sun – Microbial Biotechnology

Characterization of the microbial community structure and the physicochemical properties of produced water and seawater from the Hibernia oil production platform – C. William Yeung – Environmental Science and Pollution Research

Archaea

The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales – Zackary J. Jay – Biology Direct

Bioinformatics

Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff – Daniel K. Manter – Bioinformatics

Swarm v2: highly-scalable and high-resolution amplicon clustering – Frederic Mahe – PeerJ

Cutting edge: Anatomy of BioJS, an open source community for the life sciences – Guy Yachdav – eLIFE

Metagenomics

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes – Sari Peura – Scientific Reports

Metabolic networks, proteomics

A Single Host-Derived Glycan Impacts Key Regulatory Nodes of Symbiont Metabolism in a Coevolved Mutualism – Min Pan – mBIO

Extracellular protein analysis of activated sludge and their functions in wastewater treatment plant by shotgun proteomics – Peng Zhang – Scientific Reports

Techniques

Scaffolding of a bacterial genome using MinION nanopore sequencing – E. Karlsson – Scientific Reports

Microbial Ecology

Biodiversity inhibits parasites: Broad evidence for the dilution effect – David J. Civitello – PNAS

Science, publishing, and career

Big Data: Astronomical or Genomical? Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. – Zachary D. Stephens – PLOS Biology

The Outrage Factor – Then and Now: There’s a lot of outrage about outrage storming around women in science and science journalism at the moment. And fear of causing it, too. – Hilda Bastian – PLOS Blogs

Microbes in the news

Aging in Microbes: bacteria are using every trick in the book to get ahead – Josh Mitteldorf

Bik’s Picks

Everything you need to know about Tuesday’s Pluto encounter – Rachel Feltman – Washington Post

Introducing the Pentaquark: Physicists Prove a New Particle Exists – Tanya Basu – Time

Neighborhood greenspace and health in a large urban center : higher health perception if you live near trees – Omid Kardan – Scientific Reports
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July 7, 2015

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A personal perspective on microbiome research, phenotypic heterogeneity in microorganisms, ruling out viruses as causes for necrotizing enterocolitis, and Robert Edgar’s USEARCH.

Job openings

Philipps-Universität Marburg and the Max-Planck Institute for Terrestrial Microbiology are looking for 2 postdocs (one experimentalist and one bioinformatician)

General microbiome

Personal perspective: From cell biology to the microbiome: An intentional infinite loop – Wendy S. Garrett – Journal of Cell Biology

Microbiome of pregnancy and birth

Cytomegalovirus and other common enteric viruses are not commonly associated with Necrotizing Enterocolitis – Thomas Skeath – Acta Paediatrica

Viremia during pregnancy and risk of childhood leukemia and lymphomas in the offspring: Nested case-control study – Davit Bzhalava – International Journal of Cancer

Human oral microbiome

The Oral Bacterial Communities of Children with Well-Controlled HIV Infection and without HIV Infection – Brittany E. Goldberg – PLOS ONE

Human respiratory microbiome

Sputum Bacterial and Fungal Dynamics during Exacerbations of Severe COPD – Jin Su – PLOS ONE

Human gut microbiome

Chemotherapy-driven dysbiosis in the intestinal microbiome – E. Montassier – Alimentary Pharmacology & Therapeutics

Animal models of microbiome research

Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine – Daniel N. Frank – PLOS ONE

Animal microbiome

NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds – J. Diaz-Real

Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations – Michaela D. J. Blyton – Applied and Environmental Microbiology

Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens – Jordan M. Casey – Scientific Reports

Plant, root, and soil microbiome

Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea) – Ahmed Abdelfattah – PLOS ONE

High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis – Paul Dijkstra – Soil Biology and Biochemistry

Earthworms modify microbial community structure and accelerate maize stover decomposition during vermicomposting – Yuxiang Chen – Environmental Science and Pollution Research

Water microbiome

Microbial Communities Associated with Zones of Elevated Magnetic Susceptibility in Hydrocarbon-contaminated Sediments – Carol L. Beaver – Geomicrobiology Journal

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability – Kathleen Brannen-Donnelly – Frontiers in Microbiology

Firmicutes is an Important Component of Microbial Communities in Water-Injected and Pristine Oil Reservoirs; Western Siberia, Russia – Yulia Frank – Geomicrobiology Journal

Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm – Runar Stokke – Environmental Microbiology

Temporal Study of the Microbial Diversity of the North Arm of Great Salt Lake, Utah, U.S. – Swati Almeida-Dalmet – Microorganisms

Diversity of the Sediment Microbial Community in the Aha Watershed (Southwest China) in Response to Acid Mine Drainage Pollution Gradients – Weimin Sun – Applied and Environmental Microbiology

Microbial Transport, Retention, and Inactivation in Streams: A Combined Experimental and Stochastic Modeling Approach – Jennifer D. Drummond – Environmental Science & Technology

Extremophile microbiome

Ribosomal tag pyrosequencing of DNA and RNA reveals ‘rare’ taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia – Pascal Weigold – Geomicrobiology Journal

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues – Talitha C. Santini – Applied and Environmental Microbiology

Built environment microbiome

A New Perspective on Microbiome and Resource Management in Wastewater Systems – Veera Gnaneswar Gude – Biotechnology & Biomaterials

Microbial Ecology

A functional perspective on phenotypic heterogeneity in microorganisms – Martin Ackermann – Nature Reviews Microbiology

Bioinformatics and statistics

USEARCH: Error filtering, pair assembly, and error correction for next-generation sequencing reads – Robert C. Edgar – Bioinformatics

Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data – Lizhen Xu – PLOS ONE

Metabolomics and metatranscriptomics

Functional metabolomics: from biomarker discovery to metabolome reprogramming – Bo Peng – Protein & Cell

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation – Michael Reck – BMC Genomics

Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism – case study of Faecalibacterium prausnitzii – Antonin Prévoteau – Scientific Reports

Techniques

A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes – Craig W. Herbold – Frontiers in Microbiology

This paper is not novel at all: An improved method for bacterial identification through 16S rDNA sequencing using double set of primers: a case study – Amanat Ali – Pak. J. Agri. Sci.,

Microbes in the news

How Bacteria Make This Underground, Awe-Inspiring Cave Shine Gold – Michele Lent Hirsch – Smithsonian

Bacteria in a bottle? AOBiome offers ways to stay clean without traditional soap – Nidhi Subbaraman – The Boston Globe

uBiome to Award Grant of up to $100k for Groundbreaking Microbiome Research – PR Web

Bik’s Picks

NASA Releases Time-Lapse Video Of Mars Rover Opportunity’s Journey: 11 Years In Just 8 Minutes – Jim Algar – Tech Times

Self-Driving ‘Robocabs’ Could Help Curb Global Warming – Wendy Koch – National Geographic

‘Vampires’ keep doctors in the dark for fear of stereotyping: study – Reuters

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July 6, 2015

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Oral microbiomes of dogs and their owners, airway mycobiome in CF patients, memory B cells and antibodies to gut microbiota, and yogurt containing seawater (?).

Human oral microbiome

Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing – Changin Oh – PLOS ONE

Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw – Shirin Kalyan – Journal of Translational Medicine

Review: Oral malodorous gases and oral microbiota: From halitosis to carcinogenesis – Naoko Tanda – Journal of Oral Biosciences

Human respiratory microbiome

A cohort study of the airway mycobiome in adult cystic fibrosis patients: differences in community structure of fungi compared to bacteria reveal predominance of transient fungal elements – Rolf Kramer – Journal of Clinical Microbiology

Review: The role of the local microbial ecosystem in respiratory health and disease – Wouter A. A. de Steenhuijsen Piters – Philosophical Transactions B

Review: The mechanism or mechanisms driving atopic asthma initiation: The infant respiratory microbiome moves to center stage – Patrick G. Holt – Journal of Allergy and Clinical Immunology

Human gut microbiome

Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota – Cornelia Lindner – Nature Immunology

Dietary modulation of the gut microbiota – a randomised controlled trial in obese postmenopausal women – Lena K. Brahe – British Journal of Nutrition

Anti-TNF treatment with adalimumab induces changes in the microbiota of Crohn’s disease – Busquets David – Journal of Crohn’s and Colitis

Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract – Mina Bashir – European Journal of Nutrition

Review: Suppression of inflammation by helminths: a role for the gut microbiota? – Paul Giacomin – Philosophical Transactions B

Review: Immune-microbiota interactions in health and disease – Noah W. Palm – Clinical Immunology

Animal models

Lentinula edodes-derived polysaccharide rejuvenates mice in terms of immune responses and gut microbiota – Xiaofei Xu – Food and Function

Effect of Lactobacillus plantarum FH185 on the Reduction of Adipocyte Size and Gut Microbial Changes in Mice with Diet-induced Obesity – Sun-Young Park – Korean Journal for Food Science of Animal Resources

In vitro probiotic characteristics of Lactobacillus plantarum ZDY 2013 and its modulatory effect on gut microbiota of mice – Renhui Huang – Journal of Dairy Science

Reduced airway microbiota diversity is associated with elevated allergic respiratory inflammation – Wenkai Yu – Annals of Allergy, Asthma & Immunology

The prebiotics 3’Sialyllactose and 6’Sialyllactose diminish stressor-induced anxiety-like behavior and colonic microbiota alterations: evidence for effects on the gut-brain axis – Andrew J. Tarr – Brain, Behavior, and Immunity

Effect of yogurt containing deep sea water on health-related serum parameters and intestinal microbiota in mice – Sun Moon Kang – Journal of Dairy Science

Animal microbiome

In situ identification and quantification of starch-hydrolyzing bacteria attached to barley and corn grain in the rumen of cows fed barley-based diets – Yun Xia – FEMS Microbiology Ecology

Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing – Lim S. – Journal of Molecular Microbiology and Biotechnology

Wolbachia influences the production of octopamine and affects Drosophila male aggression – Chelsie E. Rohscheib – Applied and Environmental Microbiology

Expanding the Entamoeba Universe: New Hosts Yield Novel Ribosomal Lineages – Alison S. Jacob – Journal of Eukaryotic Microbiology

Interactions between multiple helminths and the gut microbiota in wild rodents – Jakub Kreisinger – Philosophical Transactions B

Plant, root, and soil microbiome

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes – Pablo R. Hardoim – Microbiology and Molecular Biology Reviews

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time – Britt Koskella – Philosophical Transactions B

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States – Ederson da C. Jesus – GCB Bioenergy

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota –
Eduard Vico Oton – The ISME Journal

Composition of soil microbial communities in the rhizosphere of cucumber cultivars with differing nitrogen acquisition efficiency – Xingang Zhou – Applied Soil Ecology

Differential Decay of Wastewater Bacteria and Change of Microbial Communities in Beach Sand and Seawater Microcosms – Qian Zhang – Environmental Science & Technology

New traceability strategies based on a biological Bar Code by PCR-DGGE using bacterial and yeast communities for determining farming type of peach – Ahmed El Shobaky – Egyptian Journal of Basic and Applied Sciences

Optimization of biostimulant for bioremediation of contaminated coastal sediment by response surface methodology (RSM) and evaluation of microbial diversity by pyrosequencing – Bakthavachallam Subha – Marine Pollution Bulletin

Water microbiome

Metagenomic study of red biofilms from Diamante Lake reveals ancient arsenic bioenergetics in haloarchaea – Nicolás Rascovan – ISME Journal

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis – Benjamin Bolduc – The ISME Journal

Built Environment Microbiome

Bacteriological assessment of the hospital environment in two referral hospitals in Yaoundé-Cameroon – Kamga Hortense Gonsu – Pan African Medical Journal

Green spaces and cognitive development in primary schoolchildren – Payam Dadvand – PNAS

Food microbiology

Source Tracking and Succession of Kimchi Lactic Acid Bacteria during Fermentation –
Se Hee Lee – Journal of Food Science

House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs – Fabio Minervini – Food Microbiology

Proteomics

Estimating the computational limits of detection of microbial non-model organisms – Mathias Kuhring – Proteomics

Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation – Bernhard Tschitschko – The ISME Journal

Microbial Ecology

Paleobiological Perspectives on Early Microbial Evolution – Andrew H. Knoll – Cold Spring Harbor Perspectives in Biology

Review: Building the microbiome in health and disease: niche construction and social conflict in bacteria – Luke McNally – Philosophical Transactions B

Hypothesis: Restriction modification systems as engines of diversity – Kim Sneppen – Frontiers in Microbiology

Review: A Replisome’s journey through the bacterial chromosome – Thomas R. Beattie – Frontiers in Microbiology

Bioinformatics and metagenomics

Horizontal gene transfer in an acid mine drainage microbial community – Jiangtao Guo – BMC Genomics

ISQuest: Finding Insertion Sequences in Prokaryotic Sequence Fragment Data – Abhishek Biswas – Bioinformatics

Comparing K-mer based methods for improved classification of 16S sequences – Hilde Vinje – BMC Bioinformatics

Databases for Microbiologists – Igor B. Zhulin – Journal of Bacteriology

Techniques

Here, there, and everywhere: From PCRs to next‐generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places – Karl Gruber – EMBO Reports

Microbes in the news

Bacteria ‘Fight Club’ could help find new cures for diseases – Alexandra Ossola – Popular Science
Sold on Symbiosis: A love of the ocean lured Nicole Dubilier into science; gutless sea worms and their nurturing bacterial symbionts keep her at the leading edge of marine microbiology – Anna Azvolinsky – The Scientist

Terroir: how fungi, yeasts and bacteria affect the taste of your wine – Max Allen – The Australian

Brookline’s Maya Sekhar wins grand prize at state science fair (work on phages)

Almost half of Americans don’t understand threat of antibiotic resistance – Ginger Skinner – Consumer Reports

The Human Microbiome: do not underestimate microbes! – John Dalton – David Game College

Faecal transplants, diet on trend as society embraces gut health – Hamish Fitzsimmons – ABC.au

Aquarium Microbiome Project – Shedd Aquarium – YouTube

The Microbiology Weekly – Cesar Sanchez

This Bacteria-Slaying Light Fixture Is Perfectly Safe For Humans – Andrew Liszewski – Gizmodo

Researcher finds bacteria in pistachio trees – Angela Simental – Las Cruces Sun

Bacteria-Eating Viruses Could Be New Ally Against Superbugs In A ‘Post-Antibiotic Era’ – Ben Hirschler – Reuters / Huffington Post

Linking the microbiome and colorectal cancer: an author Q+A – Sophie Marchant – BioMedCentral blogs

Bik’s Picks

US Fish & Wildlife struggles to save remaining polar bears – Sam Catherman – News Quench

Professor: Nothing Fishy About Portuguese Man o’ War at Jersey Shore – NBC

Japan And The U.S. Are Going To Have An Actual Giant Robot Battle – Damon Beres – The Huffington Post

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July 1, 2015

Posted on by

I’ve been busy in the lab most of the day, and will be tomorrow, so my apologies for posting at weird hours.

Human oral microbiome

The Influence of Smoking on the Peri-Implant Microbiome – A.A. Tsigarida – Journal of Dental Research

Human respiratory microbiome

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma – Marcos Pérez-Losada – PLOS ONE

Commentary: Has the airway microbiome been overlooked in respiratory disease? – Olawale Salami – Genome Medicine

Review: The bacterial microbiota in inflammatory lung diseases – Gary B. Huffnagle – Clinical Immunology

Human gut microbiome

Thematic collection of abstracts: GUT in FOCUS Symposium NOBEL FORUM, Karolinska Institutet, February 2nd 2015 – Microbial Ecology in Health and Disease

Animal models

Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes – Lunxi Liang – Scientific Reports

Animal microbiome

Effects of transport, fasting and anaesthesia on the faecal microbiota of healthy adult horses – A. Schoster – Equine Veterinary Journal

Plant, root, and soil microbiome

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar – Yana Aizenberg-Gershtein – Scientific Reports

Review: Role of plant growth regulators as chemical signals in plant–microbe interactions: a double edged sword – Carla Spence – Current Opinion in Plant Biology

Water microbiome

Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d’Ivoire – Christiane Essoh – PLOS ONE

Study in 93 wells (Ha! why not 96?): Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors – Mark B. Smith – mBio

Extremophile microbiome

Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes – Naseer Sangwan – Environmental Microbiology Reports

Microbial diversity in shallow-water hydrothermal sediments of Kueishan Island, Taiwan as revealed by pyrosequencing – Li Wang – Journal of Basic Microbiology

Built Environment microbiome

Bacterial Exposures and Associations with Atopy and Asthma in Children – Maria Valkonen – PLOS ONE

Studies for antifungal activity of selected concrete sealers on white cement panels – Rajesh K. Verma – International Journal of Science, Engineering and Technology Research (IJSETR)

Bioreactor microbiology

In vitro characterisation of the fermentation profile and prebiotic capacity of gold-fleshed kiwifruit – P. Blatchford – Beneficial Microbes

Bioinformatics and metagenomics

Constructing a Boolean implication network to study the interactions between environmental factors and OTUs – Congmin Zhu – Quantitative Biology

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes – Donovan H. Parks – Genome Research

The 2015 Nucleic Acids Research annual Web Server Issue: web-based software resources for analysis and visualization of molecular biology data

Microbial Ecology

The Final Countdown? Confusion about the species richness of human gut microbiota – E. Avershina – Beneficial Microbes

Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology – Douglas Kell – F1000 Research

Microbial interspecies interactions: recent findings in syntrophic consortia – Atsushi Kouzuma – Frontiers in Microbiology

Microbes in the news

The Sum of Our Parts – Janice Dietert – The Scientist

Human Microbiome Journal Club: “Disease-specific alterations in the enteric virome in inflammatory bowel disease” [Norman et al, 2015]

Would You Eat Off These Bacteria-Covered Plates? The Petri Dishes – Diana Budds – FastCoDesign

Bik’s Picks

Personal Belief Exemptions to Vaccination in California: A Spatial Analysis – Margaret Carrel – Pediatrics
No Mating Partner? No Problem: This Flatworm Injects Sperm Directly Into Own Head To Reproduce – Jim Algar – Tech Times

Citrus fruit linked with melanoma in preliminary study – Kathryn Doyle – Reuters

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June 25, 2015

Posted on by

Vitamin B12 modulates skin microbiome transcription, viruses in fluvial systems, and a webserver for annotation of gut microbiome genes.

Human skin microbiome

Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis – Dezhi Kang – Science Translational Medicine

Human oral microbiome

Review: Shaping the oral mycobiota: interactions of opportunistic fungi with oral bacteria and the host – H Xu – Current Opinion in Microbiology

Human gut microbiome

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment – Michael B. Burns – Genome Medicine

Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome – B. P. Chumpitazi – Alimentary Pharmacology & Therapeutics

Review: Host-microbiome interactions in health and disease – Liam O’Mahony – Clinical Liver Disease

 

Review: Regulation of intestinal TH17 and Treg cells by gut microbiota – Takeshi Tanoue – Inflammation and Regeneration

Review: Gut microbial short-chain fatty acids in host defense and immune regulation – Hiroshi Ohno – Inflammation and Regeneration

Review: Gut Microbiota-derived Outer Membrane Vesicles: Under-recognized Major Players in Health and Disease? – Maurizio Muraca – Discovery Magazine

Review: The Interplay between the Microbiota and Enterohemorrhagic Escherichia coli – Reed Pifer – ASM Microbiology Spectrum

Plant, root, and soil microbiome

An in-depth analysis of actinobacterial communities shows their high diversity in grassland soils along a gradient of mixed heavy metal contamination – Tomáš Větrovský – Biology and Fertility of Soils

Review: Endophytic actinobacteria of medicinal plants: diversity and bioactivity – Patrycja Golinska – Antonie van Leeuwenhoek

Differences in Arbuscular Mycorrhizal Fungal Community Composition in Soils of Three Land Use Types in Subtropical Hilly Area of Southern China – Caihuan Wang – PLOS ONE

Water microbiome

Long-term effects of the antibacterial agent triclosan on marine periphyton communities – K. Martin Eriksson – Environmental Toxicology and Chemistry

Revealing the unexplored fungal communities in deep groundwater of crystalline bedrock fracture zones in Olkiluoto, Finland – Elina Sohlberg – Frontiers in Microbiology

Prevalence of tetracycline resistance genes among multi-drug resistant bacteria from selected water distribution systems in southwestern Nigeria – Ayodele. T. Adesoji – Annals of Clinical Microbiology and Antimicrobials

Functional gene pyrosequencing reveals core proteobacterial denitrifiers in boreal lakes –
Jatta Saarenheimo – Frontiers in Microbiology

Review: Virus ecology of fluvial systems: a blank spot on the map? – Peter Peduzzi – Biological Reviews

Built Environment Microbiome

Microbially influenced corrosion communities associated with fuel-grade ethanol environments – Charles H. D. Williamson – Applied Microbiology and Biotechnology

Metagenomics and bioinformatics

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome – Stephen Nayfach – Bioinformatics

Review: Biotechnological applications of functional metagenomics in the food and pharmaceutical industries – Laura M. Coughlan – Frontiers in Microbiology

Techniques

Label-free NIR-SERS discrimination and detection of foodborne bacteria by in situ synthesis of Ag colloids – Longyan Chen – Journal of Nanobiotechnology

Microbes in the news

How To Prevent Acne: Vitamin B12, Found In Meat And Dairy, Alters Bacteria And Leads To Pimples – Susan Scutti – Medical Daily

When Gut Bacteria Changes Brain Function: Some researchers believe that the microbiome may play a role in regulating how people think and feel – David Kohn – The Atlantic

Klaus Nielsen, scientist who tried to smuggle contagious bacteria, begins sentencing hearing – CBC News

Squares, triangles, circles: regardless of their form, bacteria can figure out where to split – TU Delft / Kavli Foundation

 

Students Find, Name Bacteriophages in Massive Team Project – Illinois Wesleyan University

BacteriaHysteria

Shocking images reveal how a Glastonbury wristband could ‘harbour 20 TIMES more bacteria than clothes’ – Daily Mail

BlackBerry Ltd May Have Plans To Develop Bacteria-Free Phones – Aman Jain – Value Walk

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June 20, 2015

Posted on by

Catching up after spending all day in the lab on Friday, and all day working on figures and text today…. Here’s your weekend digest, with the microbiome of sport schools, phasing of Illumina sequencing, and happy endings for preterm infants.

Pregnancy and birth microbiome

Preterm infant gut colonization in the Neonatal ICU and Complete Restoration two years later – Laura Moles – Clinical Microbiology and Infection

Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates – Nadim Cassir – Clinical Infectious Diseases

Human respiratory microbiome

The microbiome of the human lower airways: a next generation sequencing perspective – Velma T. E. Aho – World Allergy Organization Journal

Human skin microbiome

Poster: Noma disease: 10 years of research in the quest of a microbial etiology – P François – Antimicrobial Resistance and Infection Control

Human oral microbiome

Oral Mucositis in Pediatric Acute Lymphoblastic Leukemia Patients: Evaluation of Microbiological and Hematological Factors – Regina Maria Holanda de Mendonça – Pediatric Hematology-Oncology

Human gut microbiome

Composition and temporal stability of the gut microbiota in older persons – Ian B Jeffery – The ISME Journal

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins – Min Zhang – Applied and Environmental Microbiology

The Influence of the Gut Microbiome on Obesity, Metabolic Syndrome and Gastrointestinal Disease – Parth J Pareck – Clinical and Translational Gastroenterology

Editorial: About the gut microbiome as a pharmacological target in atherosclerosis – Julia.J. Witjes – European Journal of Pharmacology

Editorial: Diabetes, More on Merde, the Microbiome, and the Dung Beetle – Richard I. Shader – Clinical Therapeutics

Review: Effect of Dietary Resistant Starch on Prevention and Treatment of Obesity-related Diseases and Its Possible Mechanisms – Lei Zhang – Biomedical and Environmental Sciences

Animal models

In pigs: Influence of genotype and feeding strategy on pig performance, plasma concentrations of micro nutrients, immune responses and fecal microbiota composition of growing-finishing pigs in a forage-based system – A.G. Kongsted – Livestock Science

In rats: Prenatal Stress-Induced Alterations in Major Physiological Systems Correlate with Gut Microbiota Composition in Adulthood – Anna V. Golubeva – Psychoneuroendocrinology

In mice: The genetic architecture of NAFLD among inbred strains of mice – Simon T Hui – eLIFE

Animal microbiome

Cows: Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency – Kelsea A. Jewell – Applied and Environmental Microbiology

Thesis: The earthworm microbiome – Daniel Antony Pass – Cardiff University

Thesis: Gut microbiota of migratory passerines at stopover – William Lewis – University of Southern Mississippi

Plant microbiome

PERN: an EU–Russia initiative for rhizosphere microbial resources – Stéphane Declerck – Trends in Biotechnology

Review: Biological control in the microbiome era: challenges and opportunities – Haissam Jijakli – Biological Control

Plant root and soil microbiome

Impact of plant domestication on rhizosphere microbiome assembly and functions
Juan E. Pérez-Jaramillo – Plant Molecular Biology

16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity – Rongxiao Che – Journal of Soils and Sediments

Built environment microbiome

Athletic equipment microbiota are shaped by interactions with human skin – Mariah Wood – Microbiome

Food microbiology

Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes – Amira Shousha – Applied and Environmental Microbiology

Microbiological diversity associated with the spontaneous wet method of coffee fermentation – Suzana Reis Evangelista – International Journal of Food Microbiology

Chemical and microbiological characteristics of traditional homemade fresh goat cheeses from Northern Morocco – Ouiam El Galiou – Small Ruminant Research

Metagenomics and bioinformatics

Microbial bioinformatics for food safety and production – Wynand Alkema – Briefings in Bioinformatics

Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review – Felipe H. Coutinho – Peer J

Ultra-large alignments using phylogeny-aware profiles – Nam-phuong D Nguyen – Genome Biology

Techiques

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis – Liyou Wu – BMC Microbiology

Microbes in the news

Medicine’s next frontier: The microbiome – Meg Tirrell – CNBC

Microbes could be key for better yields, stronger plants – Michigan State University – AG Professional

Berkeley balcony collapse: A failure at the intersection of building science and microbiology – Brent Stephens – Microbe.net

Science, publishing, and career

Gender Differences in Physicians’ Financial Ties to Industry: A Study of National Disclosure Data – Susannah L. Rose – PLOS ONE

“If you think it’s rude to ask to look at your co-authors’ data, you’re not doing science” – C. K. Gunsalus and Drummond Rennie – Retraction Watch

Bik’s Picks

An Ant With the Right Coat for 158-Degree Weather – Sindya N. Bhanoo – New York Times

8 million mummified animals, mostly dogs, in catacombs at Egypt site – Greg Botelho – CNN

Blind Americans can now ‘see’ with a device that uses their tongues – Michelle Cortez – Mashable

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