Category Archives: Metagenomics & Bioinformatics

July 9, 2016

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Bacteroidales from homeothermic animals, 136 microbial genomes from the Red Sea, corrosion of concrete sewers, and the microbiology lab in 2050 (still sexist!).

Pregnancy and birth

Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome – Zhanshan (Sam) Ma – Scientific Reports

Review: The Microbiome, Antibiotics, and Health of the Pediatric Population – Ravi S Misra- EC Microbiology

Human oral microbiome

Metagenomic Analysis of Sputum Microbiome as a Tool Towards Culture-independent Pathogen Detection of Patients with Ventilator-associated Pneumonia – Qiulong Yan – American Journal of Respiratory and Critical Care Medicine

Human respiratory microbiome

Smoking Cessation and the Microbiome in Induced Sputum Samples from Cigarette Smoking Asthma Patients – Christian Munck – PLOS ONE

Association of sputum microbiota profiles with severity of community-acquired pneumonia in children – Melinda M. Pettigrew – BMC Infectious Diseases

Human gut microbiome

Review: Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease – Darrell W. Cockburn – Journal of Molecular Biology

Review: Microbiota at the crossroads of autoimmunity – Oded Shamriz – Autoimmunity Reviews

Editorial: A Role for Chemists in Microbiome Research – Courtney C. Aldrich – ACD Infectious Diseases

Animal experiments

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection – Alison Morris – Microbiome

Animal microbiome

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals – Kate L. Ormerod – Microbiome

Biodiversity and Activity of the Gut Microbiota across the Life History of the Insect Herbivore Spodoptera littoralis – Bosheng Chen – Scientific Reports

Long-term effect of heavy-metal pollution on diversity of gastrointestinal microbial community of Bufo raddei – Wenya Zhang – Toxicology Letters

Plants, roots, and soil microbiome

Multiscale assemblage of an ectomycorrhizal fungal community: The influence of host functional traits and soil properties in a 10-ha miombo forest – David Bauman – FEMS Microbiology Ecology

Impact of Soil Salinity on the Structure of the Bacterial Endophytic Community Identified from the Roots of Caliph Medic (Medicago truncatula) – Mahmoud W. Yaish – PLOS ONE

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis – Maya Ofek-Lalzar – FEMS Microbiology Ecology

The effect of bullet removal and vegetation on mobility of Pb in shooting range soils – Abioye O. Fayiga – Chemosphere

Water and extremophile microbiome

A catalogue of 136 microbial draft genomes from Red Sea metagenomes – Mohamed F. Haroon – Scientific Data

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples – Miguel I. Uyaguari-Diaz – Microbiome

Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada) – Marie-Ève Garneau – FEMS Microbiology Ecology

Built environment microbiome

Wastewater Enhanced Microbial Corrosion of Concrete Sewers – Guangming Jiang – Environmental Science & Technology

Bioreactors

The bioleaching potential of a bacterial consortium – Mauricio Latorre – Bioresource Technology

Biofilms

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – SpringerPlus

Bioinformatics and metagenomics

GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis – Mitchell J. Brittnacher – PLOS ONE

Icarus: visualizer for de novo assembly evaluation – Alla Mikheenko – Bioinformatics

deBGA: read alignment with de Bruijn Graph-based seed and extension – Bo Liu – Bioinformatics

ConsPred – a rule-based (re-)annotation framework for prokaryotic genomes – Thomas Weinmaier – Bioinformatics

Proteomics

Review: Metaproteomic data analysis at a glance: advances in computational microbial community proteomics – Expert Review of Proteomics

Bik’s Picks

A typical day working in a laboratory in 2050: Are microbiologists becoming chemists and serene workers? – Daniele Sohier – Current Opinion in Food Science

Napa native on space mission showed early signs of promise – Jonathan Bloom – ABC News

 

 

July 8, 2016

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The highly anticipated microbiome statistical workflow from the Holmes lab at Stanford, lichen planus, chronic lung disease, and the beneficial microbes of buildings.

Bioinformatics

Preprint, awaiting peer review: Bioconductor workflow for microbiome data analysis: from raw reads to community analyses  – Ben J. Callahan – F1000 Research

Human oral microbiome

The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus – Yun Sik Choi – Scientific Reports

Human respiratory microbiome

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx – R. L. Marsh – Microbiome

Review: Commensal–Pathogen Interactions along the Human Nasal Passages – Silvio D. Brugger – PLOS Pathogens

Animal experiments

Structural Change in Microbiota by a Probiotic Cocktail Enhances the Gut Barrier and Reduces Cancer via TLR2 Signaling in a Rat Model of Colon Cancer – Eugene Dogkotenge Kuugbee – Digestive Diseases and Sciences

Adaptive immunity against gut microbiota enhances apoE-mediated immune regulation and reduces atherosclerosis and western-diet-related inflammation – Diego Saita – Scientific Reports

Animal microbiome

The Fecal Microbial Communities of Dairy Cattle Shedding Shiga Toxin–Producing Escherichia coli or Campylobacter jejuni – Dong Hee-Jin – Foodborne Pathogens and Disease

Press: Microbiology of cattle poop – Doug Powell – BarfBlog

Characterization of the microbial communities along the gastrointestinal tract of sheep by 454 pyroseqencing analysis – Jin Wang – Asian-Australasian Journal of Animal Sciences

Microbial Composition in Different Gut Locations of Weaning Piglets Receiving Antibiotics – Kaifeng Li – Asian-Australasian Journal of Animal Sciences

Plant, root, and soil microbiome

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities – James P. J. Hall – PNAS

Built environment microbiome

Review: Buildings, Beneficial Microbes, and Health – Jordan Peccia – Trends in Microbiology

Press: Invite good bacteria into home: scientists – MSN
Should architecture take our microbial health into account? – Coby McDonald – Popular Science

Microbes in the news

Gut Bacteria Are Different in People With Chronic Fatigue Syndrome – Nicholas Bakalar – NY Times

An Algorithm To Predict Which Bacteria Are Good For You. For a more targeted microbiome fix than a fecal transplant – Alexandra Ossola – Vocativ

Purdue students hope new bacteria stops toxic algae blooms – Washington Times

Japanese and Chinese scientists team up against infectious diseases – Tetsuya Abe – Nikkei Asian Review

The Microbiome’s New Frontier: The Rest of the Animal Kingdom – Conservation Magazine

July 7, 2016

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Genetic variation and airway microbiome, Thai vegetarians, social wasps carry local yeast strains, classifying infections by host response, profiling of arbuscular mycorrhizal fungi.

Pregnancy and birth

Research Highlight: First steps in the infant gut microbiota – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Human respiratory microbiome

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome – Catherine Igartua – bioRxiv

Human gut microbiome

A Disease-associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients – Jonathan P. Jacobs – CMGH Cellular and Molecular Gastroenterology and Hepatology

Microbial community of healthy Thai vegetarians and non-vegetarians, their core gut microbiota and pathogens risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Animal experiments

Personality composition alters the transmission of cuticular bacteria in social groups – Carl N. Keiser – Biology Letters

Oat products modulate the gut microbiota and produce anti-obesity effects in obese rats – Ji-lin Dong – Journal of Functional Foods

Animal microbiome

Social wasp intestines host the local phenotypic variability of Saccharomyces cerevisiae strains – Leonardo Dapporto – Yeast

Spatial and temporal investigation of the microbiome of the Caribbean octocoral Erythropodium caribaeorum – Erin P McCauley – FEMS Microbiology Ecology

Bacterial and fungal symbionts of parasitic Dendroctonus bark beetles – Loïc Dohet – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Active microorganisms in forest soils differ from the total community yet are shaped by the same environmental factors: the influence of pH and soil moisture – Karl J. Romanowicz – FEMS Microbiology Ecology

High-resolution community profiling of arbuscular mycorrhizal fungi – Klaus Schlaeppi – New Phytologist

Mycorrhizal associations and soil properties of native Allanblackia stuhlmannii stands in the Eastern Usambara Mountains, Tanzania – P. Fransson – Annals of Applied Biology

Hierarchical neighbor effects on mycorrhizal community structure and function – Holly V. Moeller – Ecology and Evolution

Review: The role of plant-microbiome interactions in weed establishment and control – F. Trognitz – FEMS Microbiology Ecology

Water and extremophile microbiome

Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya – Anne Kelly Kambura – BMC Microbiology

Spatial distribution of aquatic marine fungi across the western Arctic and sub-arctic – Brandon T. Hassett – Environmental Microbiology

Metagenomics and bioinformatics

Metagenome Mining: A Sequence Directed Strategy for the Retrieval of Enzymes for Biocatalysis – Jack W. E. Jeffries – Chemistry Select

Reaching saturation in 16S rRNA sequences: After All, Only Millions? – Rudolf Amann – mBio

More microbiology

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics – Timothy E. Sweeney – Science Translational Medicine

Press: A Blood Test To Determine When Antibiotics Are Warranted: Scientists can assay gene activity to distinguish between bacterial and viral infections – Alison F. Takemura – The Scientist

Editorial: Linking Ecosystem Function to Microbial Diversity – Anne E. Bernhard – Frontiers in Microbiology

Microbes in the news

Meet Angus, the C. difficile-sniffing dog trained to detect superbugs – CBC News

Researchers, farmers collaborate to prevent E. coli – Science Daily

How the bacterial protective shell is adapted to challenging environments – Phys.org

Could E.Coli be used to fight disease? Bacteria could transport next-generation vaccines, experts reveal – Daily Mail

Single microbe may restore social behaviors in mice – Ann Griswold – Spectrum

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

Discovery of new bacterium brings laurels to Palamuru University – The Hindu

July 5, 2016

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Circadian rhythm, resistant starch, mock communities, sea turtle microbiome, tea rhizosphere.

General microbiome

Review: The Metronome of Symbiosis: Interactions Between Microbes and the Host Circadian Clock – Elizabeth A. C. Heath-Heckman – Integrative & Comparative Biology

Human oral microbiome

Microbial Ecosystem Analysis in Root Canal Infections Refractory to Endodontic Treatment – Luiz Carlos Feitosa Henriques – Journal of Endodontics

Human gut microbiome

Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions – Bijaya Upadhyaya – Scientific Reports

Press: Essential Science: Taking on metabolic disorders with starch – Tim Sandle – Digital Journal

Editorial: serologic microbial-associated markers to predict Crohn’s disease behaviour – A. G. Fraser – Alimentary Pharmacology & Therapeutics

Review: Microbiota and Liver – Kazumichi Abe – The Liver in Systemic Diseases

Animal experiments

A Role for Timp3 in Microbiota-Driven Hepatic Steatosis and Metabolic Dysfunction – Maria Mavilio – Cell Reports

Animal microbiome

A first insight into the gut microbiota of the sea turtle Caretta caretta – Khaled F. Abdelrhman – Frontiers in Microbiology

News and views: Co-evolution of marine worms and their chemoautotrophic bacterial symbionts: unexpected host switches explained by ecological fitting? – A. Brune – Molecular Ecology

Bacterial communities of oceanic sea star (Asteroidea: Echinodermata) larvae – Madeline R. Galac – Marine Biology

Gut bacteria differentially affect egg production in the anautogenous mosquito Aedes aegypti and facultatively autogenous mosquito Aedes atropalpus (Diptera: Culicidae) – Kerri L. Coon – Parasites & Vectors

Review: Better with your parasites? Lessons for behavioural ecology from evolved dependence and conditionally helpful parasites – Kelly L. Weinersmith – Animal Behaviour

Plant, root, and soil microbiome

Response of soil properties and microbial communities to agriculture: Implications for primary productivity and soil health indicators – Pankaj Trivedi – Frontiers in Plant Science

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Yanchun Li – Journal of Applied Microbiology

Water and extremophile microbiome

Oil sands tailings ponds harbour a small core prokaryotic microbiome and diverse accessory communities – S.L. Wilson – Journal of Biotechnology

The Ocean Microbiome: Metabolic Engine of the Marine Carbon Cycle – Elizabeth B. Kujawinski – Microbe

Biofilms

Relevant for Cystic Fibrosis: Temperate phages both mediate and drive adaptive evolution in pathogen biofilms – Emily V. Davies – PNAS

Press: Tiny viruses speed-up evolution of bacteria causing infections in cystic fibrosis patients – News Medical

Techniques

Droplet barcoding for massively parallel single-molecule deep sequencing –
Freeman Lan – Nature Communications

Transcriptomics

Comparative transcriptomics across the prokaryotic tree of life – Ofir Cohen – Nucleic Acids Research

Bioinformatics and metagenomics

PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets – Shareef M. Dabdoub – Scientific Reports

Optimization of 16S amplicon analysis using mock communities: implications for
estimating community diversity – Andrew Krohn – PeerJ

Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data – Philip T. L. C. Clausen – Journal of Antimicrobial Chemotherapy

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies – Shalabh Thakur – BMC Bioinformatics

Editorial: Nucleic Acids Research annual Web Server Issue in 2016 – Nucleic Acids Research

June 30, 2016

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Mycorrhizal fungi and CO2, pathogen defense in the gut, Mississippi River plume.

Animal experiments

Defensive Mutualism Rescues NADPH Oxidase Inactivation in Gut Infection – Gratiela Pircalabioru – Cell Host & Microbe

Press: Good gut relationships key in defence against pathogens – Medical Xpress

Plant, root, and soil microbiome

Mycorrhizal association as a primary control of the CO2 fertilization effect – César Terrer – Science

Press: Study finds that plant growth responses to high carbon dioxide depend on symbiotic fungi – EurekAlert

Grassland to woodland transitions: Dynamic response of microbial community structure and carbon use patterns – Courtney A. Creamer – Journal of Geophysical Research

The interaction between arbuscular mycorrhizal fungi and endophytic bacteria enhances plant growth of Acacia gerrardii under salt stress – Abeer Hashem – Frontiers in Microbiology

Water and extremophile microbiome

Mississippi River plume enriches microbial diversity in the northern Gulf of Mexico – Olivia U. Mason – Frontiers in Microbiology

Editorial: Anthropogenic impacts on the microbial ecology and function of aquatic environments – Maurizio Labbate – Frontiers in Microbiology

Unanticipated geochemical and microbial community structure under seasonal ice cover in a dilute, dimictic Arctic lake – Ursel Schuette – Frontiers in Microbiology

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – Jacqueline Goordial – Environmental Microbiology

Metagenomics and bioinformatics

Bioinformatic Characterization of Mosquito Viromes within the Eastern United States and Puerto Rico: Discovery of Novel Viruses – Kenneth G. Frey – Evolutionary Bioinformatics

Review: Reconstructing single genomes from complex microbial communities – Dongwan D. Kang – it-Information Technology

Review: A history of DNA sequence assembly – Eugene W. Myers Jr – it-Information Technology

Review: Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes – Miklós Bálint – FEMS Microbiology Reviews

Microbes in the news

Stanford undergrads cook up a biotech startup to develop new antibiotics for drug-resistant superbugs – Rosemary Mena-Werth – Stanford News

From the Evolution Conference, talk by Danielle Whittaker: Bacteria give bird its sexy smells – Patrick Monahan – Science

Australia’s Melbourne takes selfie of its microbiome – i4U News

The Microbiome and Bronchiolitis: An Unusual Pairing or Is It? – Lewis First – AAP Gateway

An Ounce of (Water) Prevention: microbial fuel degradation – Katherine Vanover – Fuel Market News

New study shows chronic fatigue isn’t just in your head. It may have to do with your gut – Ariana Eunjung Cha – Washington Post

Resistance to antibiotics and to immune system are interconnected in bacteria – EurekAlert

In times of great famine, microalgae digest themselves. AWI researchers decipher the connection between nutrient availability and algae growth – EurekAlert

Researchers develop effective strategy for disrupting bacterial biofilms – EurekAlert

How a germ catches a virus – Phys.org

Coming Soon: Gut Bacteria That Actually Cure Your Disease: The $34 billion probiotics market includes some dubious products. This crop looks different – Deena Shanker – Bloomberg

TV weatherman retracts story about toxic bacteria at Northwest Florida beaches – The Destin Log

Bik’s non-microbiology Picks

Former Relman lab member: NASA Astronaut Kate Rubins Prepares for First Trip to Space – Alison Thoet – ABC News

107 Nobel laureates sign letter blasting Greenpeace over GMOs – Joel Achenbach – Washington Post

The Academic Hermit – What are you going to do with your tool?: installation as the Frederick G. Novy Collegiate Professor of Microbiome Research at the University of Michigan – Pat Schloss

June 29, 2016

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Two new papers on multiple sclerosis and breast tissue, cross-respiration, the Boston urban transit microbiome, and plastic debris.

Human respiratory microbiome

Review: The respiratory microbiome of HIV-infected individuals – MB Lawawni – Expert Review of Anti-infective Therapy

Human skin microbiome

The microbiota of breast tissue and its association with tumours – Camilla Urbaniak – Applied and Environmental Microbiology

Human gut microbiome

Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications

Review: Gut microbiota and hematopoietic stem cell transplantation: where do we stand? – D Zama – Bone Marrow Transplantation

Review: The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? – Roman M. Stilling – Neurochemistry International

Animal and in vitro experiments

A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration – Apollo Stacy – mBio

Press: Cross-respiration between oral bacteria leads to worse infections – EurekAlert

Microbiota-Regulated IL-25 Increases Eosinophil Number to Provide Protection during Clostridium difficile Infection – Erica L. Buonomo – Cell Reports

Animal microbiome

Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host – Yan Wang – Molecular Biology and Evolution

In barn swallows: Stress response, gut microbial diversity and sexual signals correlate with social interactions – Iris I. Levin – Biology Letters

Plant, root, and soil microbiome

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation – Natalie Christian – Microbial Ecology

Perspective: Soil immune responses – Jos M. Raaijmakers – Science

Water and extremophile microbiome

Microbes in mercury-enriched geothermal springs in western North America – Gill G. Geese – Science of The Total Environment

Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton – Cristina M. Herren – mSystems

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments – Marina N. Mato – Environmental Microbiology

Built environment microbiome

Commentary: Avoiding Pandemic Fears in the Subway and Conquering the Platypus – A. Gonzalez – mSystems

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems

Press: ‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – EurekAlert

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Food microbiology

Culture-independent bacterial community profiling of carbon dioxide treated raw milk – Raquel Lo – International Journal of Food Microbiology

Metagenomics and bioinformatics

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation – David Koslicki – mSystems

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – Microbial Genomics

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees – Maxime Hebrard – PLOS ONE

Proteomics and metabolomics

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses – Ernesto S. Nakayasu – mSystems

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria – Maria Maansson – mSystems

Techniques

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform – Fiona Fouhy – BMC Microbiology

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses – Lindsey A. Moser- mSystems

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Microbes in the news

Germs in the Subway Are the Harmless Kind – Nicholas Bakalar – New York Times

An Industrial Microbiologist Who Adds Biofuel to the Fire – Nandita Jayaraj – The Wire India

Interview of Faculty of Clinical Microbiology, Prof. Generalov Igor Ivanovich, at VSMU, Belarus – LinkedIn

 

June 26, 2016

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Pregnancy and birth

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development – Takahiro Matsuki – Nature Communications

Necrotizing enterocolitis and preterm infant gut bacteria – Barbara B. Warner – Seminars in Fetal & Neonatal

Human oral microbiome

Identification of Veillonella Species in the Tongue Biofilm by Using a Novel One-Step Polymerase Chain Reaction Method – Izumi Mashima – PLOS ONE

Human respiratory microbiome

Bacterial Microbiota Analysis Present in the Nose and Pharynx of a Mexican Young Population – Ana Karina Rodríguez-Vicente – Int J Curr Microbiol App Sci

Human gut microbiome

Significant Differences Found in Short Nucleotide Sequences of Human Intestinal Metagenomes of Northern-European and Chinese Origin – Balázs Szalkai – Biochimica et Biophysica Acta (BBA) – General Subjects

Analysis of the effects of microbiome-related confounding factors on the reproducibility of the volatolomic test – Marcis Leja – Journal of Breath Research

Campylobacter concisus utilizes blood but not short chain fatty acids despite showing associations with Firmicutes taxa – Nadeem O. Kaakoush – Microbiology

Review: Links Between the Microbiome and Bone – C.J. Hernandez – Journal of Bone and Mineral Research

Review: Microbiome, Metabolome and Inflammatory Bowel Disease – Ishfaq Ahmed – Microorganisms

Comment: Ethics of exploring the microbiome of native peoples – Maria G. Dominguez-Bello – Nature Microbiology

Microbes found in blood

I’m skeptical about this review: A Bacterial Component to Alzheimer’s-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease – Etheresia Pretorius – Journal of Alzheimer’s Disease

Animal experiments

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion – George M. H. Birchenough – Science

Gut microbiota drive the development of neuro-inflammatory response in cirrhosis – Dae Joong Kang – Hepatology

Bacteriophage infections of microbiota can lead to leaky gut in an experimental rodent model – George Tetz – Gut Pathogens

The Effects of LW-AFC on Intestinal Microbiome in Senescence-Accelerated Mouse Prone 8 Strain, a Mouse Model of Alzheimer’s Disease – Jianhui Wang – Journal of Alzheimer’s Disease

Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Megan C. Niederwerder – Veterinary Microbiology

Press: College of Veterinary Medicine researchers examine microbiome associations related to disease expression in swine – Kansas State University

Supplementing Blends of Sugars, Amino Acids, and Secondary Metabolites to the Diet of Termites (Reticulitermes flavipes) Drive Distinct Gut Bacterial Communities – Xing-Feng Huang – Microbial Ecology

Letter: Does Intestinal Microbiota Protect Mice Against Acute/Binge Drinking-Induced Liver Injury? – Tao Zeng – Alcoholism: Clinical and Experimental Research

Animal microbiome

DGGE: Influence of Starvation on the Structure of Gut-Associated Bacterial Communities in the Chinese White Pine Beetle (Dendroctonus armandi) – Xia Hu – Forests

Plant, root, and soil microbiome

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Effectiveness of ecological rescue for altered soil microbial communities and functions – Kadiya Calderón – ISME Journal

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition – Carles Castaño – Mycorrhiza

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters – Weichen Bao – Scientific Reports

Water and extremophile microbiome

Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River Basin, Yangtze River Delta – Wei Cai – Water Science and Technology

Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora – Neelu Nawani – Biologia

Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam – Wei Huang – Int. J. Environ. Res. Public Health

Bioreactor and wastewater microbiology

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water – Junying Tang – Ecotoxicology and Environmental Safety

Food microbiology

Effect of Simulated Sanitizer Carryover on Recovery of Salmonella from Broiler Carcass Rinsates – Gary R. Gamble – Journal of Food Protection

Press: USDA Salmonella Bacteria on Chicken Testing Severely Flawed, New Study Finds – Emily Monaco – Organic Authority

Potential applications of metagenomics to assess the biological effects of food structure and function – Tasha Santiago-Rodriguez – Food & Function

Bioinformatics and metagenomics

A comparison of tools for the simulation of genomic next-generation sequencing data – Merly Escalona – Nature Reviews Genetics

Hessian Regularization Based Symmetric Nonnegative Matrix Factorization for Clustering Gene Expression and Microbiome Data – Yuanyuan Ma – Methods

Techniques

Grown, Printed, and Biologically Augmented: An Additively Manufactured Microfluidic Wearable, Functionally Templated for Synthetic Microbes – Christoph Bader – 3D Printing and Additive Manufacturing

Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning – Lucia Kraková – Extremophiles

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – Springer Plus

More microbiology

Applying landscape genetics to the microbial world – Rachael Y. Dudaniec – Molecular Ecology

A metapopulation model for the spread of MRSA in correctional facilities – Marc Beauparlant – Infectious Disease Modelling

Biological Dual-Use Research and Synthetic Biology of Yeast – Angela Cirigliano – Science and Engineering Ethics

Microbes in the news

Fabulous Pacific coast and the latest digestive diseases research: BMC Medicine joins DDW2016 – Alessandro Recchioni – BioMedCentral blog

The Unseen – Millions of microbes are yet to be discovered. Will one hold the ultimate cure? – Raffi Khatchadourian – The New Yorker

Indicator of chronic fatigue syndrome found in gut bacteria – Krishna Ramanujan – Cornell Chronicle

Fermentation Fervor: Here’s How Chefs Boost Flavor And Health – Allison Aubrey – NPR Morning Edition

Beneficial bacteria may protect breasts from cancer – ASM – EurekAlert

Economics in Mind, Evolution Has Allowed Some Bacteria to Evolve Sublime Genomes – Aswin Sai Narain Seshasayee – The Wire

Old Technology Successfully Reduce Salmonella in Meat Products by 90 Percent –  John Raphael – Nature World News

Bright Minds Battling Dark Diseases: San Diego is home to world-class biomedical scientists focused on cutting-edge projects touted by president – Gary Robbins – The San Diego Union Tribune

Liquid eyeliner recalled, contains bacteria – CTV News Winnipeg

June 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 21, 2016

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An invertebrate gets its amino acids from microbial symbionts, microbiota and allograft rejection, high-altitude Andes lakes, and determining absolute microbiota abundances by spiking-in bacteria.

Jobs and events

Postdoctoral Researcher Microbial Ecology & Bioinformatics – NIOO-KNAW, WUR, Wageningen, The Netherlands

Report from the Microbiome R&D and Business Collaboration Forum, April 11–12, 2016, London, UK – Duc H. Le – EBioMedicine

General microbiome

Review: Diversity at low abundance: The phenomenon of the rare bacterial biosphere – M. Yu. Skopina – Microbiology

Workshop report: Culture-Independent Diagnostics for Health Security – Doggett Norman A.- Health Security

Viewpoint: Addressing Infectious Disease Challenges by Investigating Microbiomes – Emily P. Balskus – ACS Infectious Diseases

Human oral microbiome

Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing – Yumi Imabayashi – Scientific Reports

Human reproductive tract microbiome

Review: Chlamydia trachomatis Genital Tract Infections: When Host Immune Response and the Microbiome Collide – Noa Ziklo – Trends in Microbiology

Human gut microbiome

Review: Microbes, Immunity and Behaviour: Psychoneuroimmunology Meets the Microbiome – Timothy G Dinan – Neuropsychopharmacology

Review: Emerging roles for antigen presentation in establishing host–microbiome symbiosis – Nicholas J. Bessman – Immunological Reviews

Book Chapter: The Effect of H. pylori Infection on the Gastric Microbiota – Hyun Jin Jo – Helicobacter Pylori (Springer book)

Animal and in vitro experiments

The composition of the microbiota modulates allograft rejection – Yuk Man Lei – The Journal of Clinical Investigation

Press: Microbiota affect the rate of transplant acceptance and rejection – MedicalXpress

Maternal Metabolic Syndrome Programs Mitochondrial Dysfunction via Germline Changes across Three Generations – Jessica L. Saben – Cell Reports

Press, extrapolated conclusion: Obese Pregnant Women With Poor Diets May Worsen The Childhood Obesity Epidemic: Study – Samantha Olson – Medical Daily

Diet-dependent, microbiota-independent regulation of IL-10-producing lamina propria macrophages in the small intestine – Takanori Ochi – Scientific Reports

Characterization of Cimex lectularius (bedbug) defensin peptide and its antimicrobial activity against human skin microflora – Akanksha Kaushal – Biochemical and Biophysical Research Communications

Variability of arsenic bioaccessibility and metabolism in soils by human gut microbiota using different in vitro methods combined with SHIME – Naiyi Yin – Science of The Total Environment

Transient activation of mucosal effector immune responses by resident intestinal bacteria in normal hosts is regulated by interleukin-10 signalling – Cong Wu – Immunology

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community – Prabhakar D. Pandit – Bioresource Technology

Review: Strategies to modulate the intestinal microbiota of Tilapia (Oreochromis sp.) in aquaculture: a review – Alyssa M. Haygood – Reviews in Aquaculture

Animal microbiome

Seasonality and Locality Affect the Diversity of Anopheles gambiae and Anopheles coluzzii Midgut Microbiota from Ghana – Jewelna Akorli – PLOS ONE

A Nightmare for Males? A Maternally Transmitted Male-Killing Bacterium and Strong Female Bias in a Green Lacewing Population – Masayuki Hayashi – PLOS ONE
http://journals.plos.org/plosone/article?

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows
– Camilo Escallón – Functional Ecology

The dominant detritus-feeding invertebrate in arctic peat soils derives its essential amino acids from gut symbionts – Thomas Larsen – Journal of Animal Ecology

Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp – Yong Wang – Environmental Microbiology

Review: Is gastrointestinal microbiota relevant for endogenous mercury methylation in terrestrial animals? – R.C. Rodríguez Martín-Doimeadios – Environmental Research

Plant, root, and soil microbiome

Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient – Anders Lanzén – Scientific Reports

Integrated analysis of root microbiomes of soybean and wheat from agricultural fields – Nicolás Rascovan – Scientific Reports

Dark stains on rock surfaces in Driny Cave (Little Carpathian Mountains, Slovakia)
Rafał Ogórek – Extremophiles

Water and extremophile microbiome

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes – Júlia Margit Aszalós – Extremophiles

Microbial interactions lead to rapid micro-scale successions on model marine particles –
Manoshi S. Datta – Nature Communications

Bacteriophages in Arctic and Antarctic low-temperature systems – S. N. Filippova – Microbiology

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka) – A. Y. Merkel – Microbiology

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey) – Seval Çınar – Extremophiles

Techniques

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria – 
Frank Stämmler – Microbiome

Metagenomics and bioinformatics

Data Labours: How the Sequence Databases GenBank and EMBL-Bank Make Data – Tahani Nadima – Science as Culture

Principle, analysis, application and challenges of next-generation sequencing: a review – Khalid Raza – arXIv

Microbes in the news

Does a pipette work in space? with NASA Astronaut Dr Kate Rubins – Microbe Talk – Microbe Post

An Antarctic sponge offers new hope against deadly MRSA infection – Matt Windsor – UAB

Dental Microbes Not All in the Family. Kids often acquire cavity-causing bacteria from non-family members, researchers report at the American Society for Microbiology annual meeting – Tanya Lewis – The Scientist

Never-Before Human-Detected, Potentially Pathogenic Bacterium Found in Children With Acute Leukemia Human Microbiology Institute investigates potential role of previously unknown bacteria – PR Newswire

Geisinger’s Donna Wolk recognized for work in microbiology – Daily Item

Microbial mass extinctions were kicked off by human evolution – Andy Coghlan – New Scientist

Global Microbiome Initiative Explores Subways for Drug-Resistance Markers:
MetaSUB Consortium will collect DNA and RNA samples from high-traffic areas in subway systems, buses, and parks in 54 cities worldwide – GenEngNews

June 20, 2016

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The temperate tree phyllosphere, Qaanaaq Glacier, effect of human activities on Hong Kong coast microbes, and genome assembly from read clouds.

Events

Microbiome R&D and Business Collaboration Forum: USA, October 3-4, San Diego

Pregnancy and birth

Putative periodontopathic bacteria and herpesviruses in pregnant women: a case-control study – Haixia Lu – Scientific Reports

Human gut microbiome

Letter to Editor: Reduction of antibiotic resistance genes in intestinal microbiota of recurrent Clostridium difficile patients after fecal microbiota transplantation – Hanne Jouhten – Clinical Infectious Diseases Advance Access

Review: The Gut Microbiota and Inflammatory Bowel Diseases – Jun Miyoshi – Translational Research

Review: Links Between the Microbiome and Bone – C.J. Hernandez – Journal of Bone and Mineral Research

Animal models

Interactions between the colonic transcriptome, metabolome and microbiome in mouse models of obesity-induced intestinal cancer – Anna C. Pfalzer – Physiological Genomics

Plant, root, and soil microbiome

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure – Isabelle Laforest-Lapointe – Microbiome

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations – Quan Li – Scientific Reports

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan – E. V. Pershina – Eurasian Soil Science

A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands – Austin B. Harbison – FEMS Microbiology Letters

Water and extremophile microbiome

Microbial community variation in cryoconite granules on Qaanaaq Glacier, NW Greenland – Jun Uetake – FEMS Microbiology Ecology

Mechanisms driving Antarctic microbial community responses to ocean acidification: a network modelling approach – Roshni C. Subramaniam – Polar Biology

Video article: Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR – Enrico Tatti – Journal of Visualized Experiments

Waste and pollution microbiology

Microorganisms in heavy metal bioremediation: strategies for applying microbial-community engineering to remediate soils – Jennifer L. Wood – AIMS Bioengineering

Impacts of Human Activities on Distribution of Sulfate Reducing Prokaryotes and Antibiotic Resistance Genes in Marine Coastal Sediments of Hong Kong – Feng Guo – FEMS Microbiology Ecology

Shotgun metagenomic profiles have a high capacity to discriminate activated sludge according to wastewater type – Federico M. Ibarbalz – Applied and Environmental Microbiology

Characteristics of Sediment Bacterial Community in Response to Environmental Impacts in a Sewage Polluted River – Jialin Li – Journal of Coastal Research

Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil – Jakub Ridl – Frontiers in Microbiology

Food microbiology

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane – Francois J. Duvenage – Journal of the Science of Food and Agriculture

Book: Acetic Acid Bacteria: Ecology and Physiology – Springer

Metagenomics and bioinformatics

Genome assembly from synthetic long read clouds – Volodymyr Kuleshov – Bioinformatics

Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method – Yun Liu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Bioreactor microbiology

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

From ASM Microbe 2016: Bacteria Can Persist on Gloves, Transfer to Surfaces – Neil Osterweil – Medscape

Ischemic stroke therapy – does the gut microbiota hold the key? – Sara Adães – PLOS Neuro Community

French microbiologist hopes CRISPR/Cas9 can be used medically, with Emmanuelle Charpentier – Focus Taiwan

Chipotle Bosses Accused Of Insider Trading During Bacteria Scandals – Scott Heins – Gothamist

Bik’s Not-Microbiology Picks

Why Did Scientists Release Dead Sea Turtles into Chesapeake Bay? – Erica Tennenhouse – The Science Explorer