Category Archives: Human gut

November 7, 2015

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Human oral microbiome

Dental demineralization, radiation caries and oral microbiota in patients with head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: Bacterial interactions in pathogenic subgingival plaque – Hong Min Ng – Microbial Pathogenesis

Human gut microbiome

Gut Microbiota Community and Its Assembly Associated with Age and Diet in Chinese Centenarians – Fang Wang – Journal of Microbiology and Biotechnology

Gut colonization with methanobrevibacter smithii is associated with childhood weight development – Catherine A. Mbakwa – Obesity

Review: Regulation of energy balance by a gut–brain axis and involvement of the gut microbiota – Paige V. Bauer – Cellular and Molecular Life Sciences

Animal and other models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Mice: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline – Jérôme Lluch – PLOS ONE

Sheep: Lung Microbiota Changes Associated with Chronic Pseudomonas aeruginosa Lung Infection and the Impact of Intravenous Colistimethate Sodium – David Collie – PLOS ONE

Human cells: The effect of short-chain fatty acids on human monocyte-derived dendritic cells – Claudia Nastasi – Scientific Reports

Review: Effect of dietary components on the gut microbiota of aquatic animals. A never-ending story? – E. Ringø – Aquaculture Nutrition

Animal microbiome

Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions –
Katharina Burbach – Microbiology Open

Insects: Host and Symbiont Jointly Control Gut Microbiota during Complete Metamorphosis – Paul R. Johnston – PLOS Pathogens

Plant, root, and soil microbiome

Microbial immigration across the Mediterranean via airborne dust – Riccardo Rosselli – Scientific Reports

The herbaceous landlord: integrating the effects of symbiont consortia within a single host – Roo Vandegrift – PeerJ

Review: The plant microbiome explored: implications for experimental botany – Gabriele Berg- Journal of Experimental Botany

The influence of hydrogeological disturbance and mining on coal seam microbial communities – M. J. Raudsepp – Geobiology

Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards – Paula Baptista – Environmental Microbiology Reports

Water microbiome

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes – Guillem Salazar – Molecular Ecology

Metagenomics and bioinformatics

Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome – Tanudeep Bhattacharya – PLOS ONE

Kernel-Penalized Regression for Analysis of Microbiome Data – Timothy W. Randolph – ArXiv

Infection and microbial detection

Development of a rapid and simplified protocol for direct bacterial identification from positive blood cultures by using matrix assisted laser desorption ionization time-of- flight mass spectrometry – Aleksandra Jakovljev – BMC Microbiology

Copper surfaces are associated with significantly lower concentrations of bacteria on selected surfaces within a pediatric intensive care unit – Michael G. Schmidt – American Journal of Infection Control

Microbial ecology

An equilibrium theory signature in the island biogeography of human parasites and pathogens – Kévin Jean – Global Ecology and Biogeography

Microbes in the news

‘The Secret World Inside You’ Explores the Microbial Human – William Grimes – The New York Times
I Contain Multitudes: Microbiomes at the American Museum of Natural History –
Sean Hutchinson – Inverse
Exploring the Inner Universe. A new American Museum of Natural History exhibit introduces visitors to the microbes within their bodies – Ashley P. Taylor – The Scientist

Sexed-up beer – Nature Biotechnology

Microbes aid cancer drugs – Mitch Leslie – Science

Gut microbiota regulates antioxidant metabolism – EurekAlert

Kitchen utensils can spread bacteria between foods, UGA study finds – Sydney Devine – University of Georgia
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November 6, 2015

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Dog skin, kangaroo methane emissions, flea microbiome and ecology, domestication of wine yeast, and surface reflectance by roof microbes.

Events

11th International Meeting on Microbial Epidemiological Markers (IMMEM XI), March 2016, Portugal – Abstract submission deadline: November 10

General microbiome

Microbiomes in light of traits: A phylogenetic perspective – Jennifer B. H. Martiny – Science

The ecology of the microbiome: Networks, competition, and stability – Katharine Z. Coyte – Science

What makes the gut microbiome stable? – Caroline Ash – Science

Microbiome, a new dimension in cancer research – Antonio Galvao Neto – Annals of Translational Medicine

Human gut microbiome

Characterization of the salivary microbiome in patients with pancreatic cancer – Pedro J. Torres – PeerJ

Animal microbiome

What is living on your dog’s skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis – C.M. Smith – FEMS Microbial Ecology

Decreasing methane yield with increasing food intake keeps daily methane emissions constant in two foregut fermenting marsupials, the western grey kangaroo and red kangaroo – Catharina Vendl – Journal of Experimental Biology

Evaluation of the bacterial microbiome of two flea species using different DNA isolation techniques provides insights into flea host ecology  – Andrea L. Lawrence – FEMS Microbiology Ecology

The functional gene composition and metabolic potential of coral-associated microbial communities – Yanying Zhang – Scientific Reports

Plant, root, and soil microbiome

Can commercial soil microbial treatments remediate plant–soil feedbacks to improve restoration seedling performance? – Lora B. Perkins – Restoration Ecology

Anthropogenic impact on diazotrophic diversity in the mangrove rhizosphere revealed by nifH pyrosequencing – Hongmei Jing – Frontiers in Microbiology

Phylogenetic diversity of culturable fungi in the Heshang Cave, central China –
Baiying Man – Frontiers in Microbiology

Review: Ongoing domestication of wine yeast: past, present and future – P.J. Chambers – Australian Journal of Grape and Wine Research

Built environment microbiology

Surface reflectance degradation by microbial communities – Meng-Dawn Cheng – Journal of Building Physics

Metagenomics and bioinformatics

The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data – Sandeep J Joseph – BioRxiv

Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome – Yinfeng Zhang – International Journal of Molecular Sciences

Fizzy: feature subset selection for metagenomics – Gregory Ditzler – BMC Bioinformatics

Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities – Michael A. Peabody – BMC Bioinformatics

Microbes in the news

Our Dust, Ourselves – Emily Anthes – The New Yorker
Emily Anthes writes about Wildlife of Your Homes microbiome studies in the New Yorker – Jonathan Eisen – MicroBEnet

The Hottest New Cancer Drugs Depend on Gut Microbes – Ed Yong – The Atlantic
Gut bacteria may affect the success of cancer treatments – Sam Wong – New Scientist

This New Exhibition Is a Tour of the Human Body’s ‘Hidden Organ’ – Becky Ferreira – Motherboard

Podcast (20 min) We are a constellation of our microbiome and ourselves – Meg Tirrell and Luke Timmerman – Stat News

The strange case of the man infected with tapeworm cancer – Helen Branswell – StatNews

With a picture of human cells? 30 mind-blowing facts about the microbes that live inside of you – Julia Calderone – TechInsider
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November 5, 2015

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Context and the human microbiome, review about respiratory tract, gut microbiome in UC patients, arsenic effects on mouse microbiome, and microbiome of a river-to-ocean transition.

Jobs

3 PhD fellowship in Evolutionary and Ecological Metagenomics – Natural History Museum of Denmark

General microbiome

Review: Context and the human microbiome – Daniel McDonald, Amanda Birmingham and Rob Knight – Microbiome

Pregnancy and birth

Breastfeeding and the risk of dental caries: a systematic review and meta-analysis – R Tham – Acta Paediatrica

Breastfeeding and asthma and allergies: a systematic review and meta-analysis – CJ Lodge – Acta Paediatrica

Human respiratory microbiome

Review: The Microbiome and the Respiratory Tract – Robert P. Dickson – Annual Review of Physiology

Human gut microbiome

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis – David Kevan – Journal of Crohn’s and Colitis

Extensive Modulation of the Fecal Metagenome in Children With Crohn’s Disease During Exclusive Enteral Nutrition – Christopher Quince – American Journal of Gastroenterology

Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung’s associated enterocolitis – Holger Till – Frontiers in Microbiology

eBook chapter: Human GI Tract Microbiota in Health and Disease: A Focus on Inflammatory Bowel Diseases – Clarissa Santos Rocha – Innovative Immunology

Review: Factors determining colorectal cancer: the role of the intestinal microbiota – Esther Nistal – Frontiers in Oncology

Animal models

In cattle: Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function – Shengyong Mao – Scientific Reports

In cattle: Manipulating rumen microbiome and fermentation through interventions during early life: a review – David R. Yáñez-Ruiz – Frontiers in Microbiology

 

In mice: Administration of defined microbiota is protective in a murine Salmonella infection model – Sarah-Lynn E. Martz – Scientific Reports

In mice: Arsenic induces structural and compositional colonic microbiome change and promotes host nitrogen and amino acid metabolism – Rishu Dheer – Toxicology and Applied Pharmacology

Drosophila: Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – BioRxiv

In rats: The microbiota-gut-brain axis as a potential therapeutic approach for HIV-1+ cocaine abuse – Steven B. Harrod – Drug and Alcohol Dependence

In mice: Alteration of the intestinal microbiota by short-time antibiosis protects mice from CNS-specific autoimmunity – C. Gödel – Journal of the Neurological Sciences

 

Plant, root, and soil microbiome

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem – Suvendu Das – Science of the Total Environment

Caffeine fostering of mycoparasitic fungi against phytopathogens – Akifumi Sugiyama – Plant Signaling & Behavior

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes – Kathryn M. Docherty – PLOS ONE

Fungal association and utilization of phosphate by plants: success, limitations, and future prospects – Atul K. Johri – Frontiers in Microbiology

Thesis: Manipulating the soil microbiome to increase plant health and productivity – Chaparro, Jacqueline Michelle – Colorado State University

Water and extremophile microbiome

Bacterial responses to environmental change on the Tibetan Plateau over the past half century – Yongqin Liu – Environmental Microbiology

Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient – Caroline S. Fortunato – PLOS ONE

First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea –
André Antunes – Genomics, Proteomics & Bioinformatics

Salt resistance genes revealed by functional metagenomics from brines and moderate-salinity rhizosphere within a hypersaline environment – Salvador Mirete – Frontiers in Microbiology

Research topic and call for papers: Microbiology of the rapidly changing polar environments – Frontiers in Microbiology

Food microbiology

The diversity and evolution of microbiota in traditional Turkish Divle Cave cheese during ripening – Sebnem Ozturkoglu Budak – International Dairy Journal

More microbes

Ion channels enable electrical communication in bacterial communities – Arthur Prindle – Nature

Bioinformatics

De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units – Sarah L Westcott, Patrick Schloss – PeerJ Preprint

Unpublished manuscript: Improving De Novo Metatranscriptome Assembly via Machine Learning Algorithms – Hussein Mohsen – not published

Microbes in the news

eBook: Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You – Rob DeSalle, Susan L. Perkins – eBook

Fighting Cancer With Microbes, Flagship Bets on a $35M Startup– Luke Timmerman – Forbes

Toxin Taints Crabs and Kills Sea Mammals, Scientists Warn – Jonah Bromwich – The New York Times
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November 4, 2015

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Lots of upcoming workshops and seminars, genome-wide association of the human gut microbiota, contamination of cord blood units, and bacteria with the rRNA genes on a plasmid, not on their chromosome.

Events

Webinar: The ageing microbiota by Gemma Walton and Annie-Rose Harrison-Dunn – November 17, 2015 – 10AM Paris

Mothur 3-day workshop organized by Pat Schloss – December 16-18, Detroit.

2nd Microbiome R&D and Business Collaboration Congress: Asia – February 29-March 1 2016, Kuala Lumpur, Malaysia

Early career workshop on Microbiology of the built environment (Chicago, IL) – Jack Gilbert lab – April 26-29 2016

Human oral microbiome

Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes – Meng Zhang – PLOS ONE

Human gut microbiome

In Hutterites: Genome-Wide Association Studies of the Human Gut Microbiota – Emily R. Davenport – PLOS ONE

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

Infection microbiology

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling – Luís França – PLOS ONE

More microbes

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome – Mizue Anda – PNAS

High-throughput 3D tracking of bacteria on a standard phase contrast microscope –
K.M. Taute – Nature Communications

Automated image analysis for quantification of filamentous bacteria – Marlene Fredborg – BMC Microbiology

Microbial ecology

Community rescue in experimental metacommunities – Etienne Low-Décarie – PNAS

Microbes in the news

Family dog lowers kids’ asthma risk, proving dirt and bacteria are good for children – Shelley Hazen – Inquisitr

Microbiome expert Martin Blaser to receive Georgetown’s Cura Personalis Award Nov. 3 – EurekAlert

Microbiomes could prove essential in various fields of science, study suggests – Kimberly Nielsen – The Daily Californian

Salivary microbiome of whitetail deer: Mature doe set the rut timetable – Oak Duke – Wellsville Daily Reporter

Finally! New germ exhibit opening at the American Museum of Natural History – Rebecca Rosenthal – North Jersey

Thank heavens, someone figured out which bacteria live on a donkey’s penis – Discover
http://blogs.discovermagazine.com/seriouslyscience/2015/11/03/thank-heavens-

How was the bacteria at York Hospital found?– Dylan Segelbaum – York Daily Record

Worms (and germs) may be the answer to preventing allergies – Jason Tetro – Popular Science

Two Million-Year-Old Bacteria Used Iron “Sunscreen” – Charlotte Ward – RedBrick

Bacteria infecting orange groves is driving up cost of juice; threatens nation’s supply – Sandy Miller – Fox2Now

Science, publishing, and career

EU urges science publishers to adapt to open access: European research commissioner Carlos Moedas has urged journal publishing companies to reshape their business models to an open access system. – LabNews

Supervision: Clear direction: Managing laboratory members as well as a research strategy can be difficult for early-career principal investigators, but help is at hand. – Boer Deng – Nature

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November 3, 2015

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Dog exposure and childhood asthma, earthworm poop, thermally stressed corals, and cryospheric ecosystems.

General microbiome

From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology – Pierre-Edouard Fournier – Anaerobe

Study from Sweden with patients and dogs registries: Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma – Tove Fall – JAMA Pediatrics

Human gut microbiome

Plagiarism in intro and only CFU data for E. coli and lactic acid bacteria: A Comparative Study of Gut Microbiota Profiles of Children Living in Kulon Progo and West Lombok – Siti Helmyati – Pakistan Journal of Nutrition

Microbial Signatures in Post-Infectious Irritable Bowel Syndrome – Towards Patient Stratification for Improved Diagnostics and Treatment – Jonna Jalanka – Gut Microbes

Review: Genetic Variations in Vitamin D Metabolism Genes and the Microbiome, in the Presence of Adverse Environmental Changes, Increase Immune Dysregulation – Laing BB
and Ferguson LR – Austin Journal of Nutrition & Metabolism

Animal models

In mice: Gut microbe-derived extracellular vesicles induce insulin resistance, thereby impairing glucose metabolism in skeletal muscle – Youngwoo Choi – Scientific Reports

In mice: Influence of whole-wheat consumption on fecal microbial ecology of obese diabetic mice – Jose F Garcia-Mazcorro – PeerJ Preprints

Earthworms: Characterization of the bacterial communities of casts from Eisenia andrei fed with different substrates – Manuel Aira – Applied Soil Ecology

Animals

Viral and Bacterial Epibionts in Thermally-Stressed Corals – Hanh Nguyen-Kim – J Mar Sci Eng

Plant, root, and soil microbiome

Cross-biome comparison of microbial association networks – Karoline Faust – Frontiers in Microbiology

Response of microbial communities from an apple orchard and grassland soils to the first-time application of the fungicide tetraconazole – Sławomir Sułowicz – Ecotoxicology and Environmental Safety

A Chemical Perspective on Microalgal–Microbial Interactions – Erik F.Y. Hom – Trends in Plant Science

Availability of different nitrogen forms changes the microbial communities and enzyme activities in the rhizosphere of maize lines with different nitrogen use efficiency – Laura Giagnoni – Applied Soil Ecology

Shifts in microbial communities do not explain the response of grassland ecosystem function to plant functional composition and rainfall change – Ellen L. Fry – Soil Biology and Biochemistry

Copper and temperature modify microbial communities, ammonium and sulfate release in soil – Rui Ferreira – Journal of Plant Nutrition and Soil Science

Review: Mitigating climate change through managing constructed-microbial communities in agriculture – Cyd E. Hamilton – Agriculture, Ecosystems & Environment

Extremophile microbiome

Editorial: Cryospheric ecosystems: a synthesis of snowpack and glacial research – Andy Hodson – Environmental Research Letters

Bioinformatics and metagenomics

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities – Anja Lange – PLOS ONE

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes – Mingjie Wang – Genome Biology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets – Yu-Wei Wu – Bioinformatics

Techniques

Integrated micro-optofluidic platform for real-time detection of airborne microorganisms – Jeongan Choi – Scientific Reports

Microbes in the news

Microbesity: Obesity appears linked to the gut microbiome. How and why is still a mystery—but scientists have plenty of ideas – Jenny Rood – The Scientist

Science, publishing, and career

“There’s No Crying in Academia,” Acknowledging Emotional Labour in the Academy  – Margeaux Feldman – Gender and Society

2015 Life Sciences Salary Survey – Karen Zusi and Amanda B. Keener – The Scientist
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November 2, 2015

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Overview of key players of the human microbiome in different sites, foals are born with a rich gut microbiome, biogeography of salmon microbiome, bacteria on Chinese glaciers, and the effect of X-rays on the mango microbiome.

General human microbiome

Diversity of key players in the microbial ecosystems of the human body – Ferenc Jordán – Scientific Reports

Pregnancy and birth

Intestinal microbiota in neonates requiring urgent surgery: assessing the role of probiotics using fecal DNA sequencing – Hiroshi Murakami – Pediatric Surgery International

Review: Bacterial munch for infants: potential pediatric therapeutic interventions of probiotics – Mohsin Khurshid – Future Microbiology

Review: Introduction : Microbiome in human reproduction – Jason M. Franasiak – Fertility and Sterility

Correspondence: Vaginal microbiota during pregnancy: Pathways of risk of preterm delivery in the absence of intrauterine infection? – Jeffrey A Keelan – PNAS

Reply to Keelan and Payne: Microbiota-related pathways for preterm birth – Daniel B DiGiulio – PNAS

Human oral microbiome

Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation – Brenda P.F.A. Gomes – Journal of Endodontics

Oral microbiota in patients with atherosclerosis – Frida Fåk – Atherosclerosis

Review: Intermicrobial interactions as a driver for community composition and stratification of oral biofilms – Nicholas S. Jakubovics – Journal of Molecular Biology

Review: The Fungal Biome of the Oral Cavity – Jyotsna Chandra – Candida Species

Human respiratory microbiome

Are bronchoalveolar lavages a good source for microbial profiling? Differences between throat and bronchoalveolar lavage microbiomes – Alexandra Zimmermann – Journal of Medical Microbiology

Human gut microbiome

Donor species richness determines fecal microbiota transplantation success in inflammatory bowel disease – Severine Vermeire – Journal of Crohn’s and Colitis

Gut mucosal microbiome across stages of colorectal carcinogenesis – Geicho Nakatsu – Nature Communications

Review: Gut mycobiota and adenomas – Chunguang Luan – Gut Microbes

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Animal microbiome

Development of the faecal microbiota in foals – M. C. Costa – Equine Veterinary Journal

Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment – Saria Otani – Microbial Ecology

The biogeography of the atlantic salmon (Salmo salar) gut microbiome – Martin S Llewellyn – The ISME Journal

Exposure to West Nile Virus Increases Bacterial Diversity and Immune Gene Expression in Culex pipiens – Steven D. Zink – Viruses

Plant, root, and soil microbiome

Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture – Linkun Wu – Scientific Reports

Drivers of bacterial beta diversity in two temperate forests –  Wang – Ecological Research

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing – Chris Munday – Aerobiologia

Review: Influence of soil microbiota in nurse plant systems – Susana Rodríguez-Echeverría – Functional Ecology

Review: The Role of Plant–Microbe Interactions and Their Exploitation for Phytoremediation of Air Pollutants – Nele Weyens – International Journal of Molecular Sciences

Water and extremophile microbiome

Metagenomic analysis of the bacterial community of the Sea of Azov – D. G. Matishov – Marine Biology

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India – Jhasketan Badhai – Frontiers in Microbiology

High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing – Qing Liu – Systematic and Applied Microbiology

Review: Databases of the marine metagenomics – Katsuhiko Mineta – Gene

Waste microbiology

Changes in Microbial Composition of Wastewater During Treatment in a Full-Scale Plant – Marija Kaevska – Current Microbiology

Wastewater treatment and microbial communities in an integrated photo-bioelectrochemical system affected by different wastewater algal inocula – Li Xiao – Algal Research

Review: Microbial diversity in support of anaerobic biomass valorization – M. Jobard – Critical Reviews in Biotechnology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – Barakat S M Mahmoud – Letters in Applied Microbiology

Metagenomics and bioinformatics

Poster: Alignment-free methods for metagenomic profiling – Shanshan Gao – BMC Bioinformatics

Infection microbiology

Microbial diversity on intravascular catheters from paediatric patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Phages and viruses

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile – Pierre Boudry – mBio

Microbial Ecology

Do modern theories of biodiversity fail to predict commonness and rarity among microbes? – William R. Shoemaker – PeerJ

Strongly Deterministic Population Dynamics in Closed Microbial Communities – Zak Frentz – Physical Review

Microbes in the news

Scientists debate mega-microbiome initiatives: Research standards will advance the field, proponents say, but critics counter that they will stifle creativity – Rachel Becker – Nature

Foals born with rich microbial community in their gut – study – Horsetalk

Halloween: Monster Microbiology, 101: If werewolves and other ghouls existed, they’d surely have microbiomes – Rob Dunn – Science Friday

Bacteria in space – ‘You cannot just open the window’ – Interview with Ralf Möller about microbes found on the ISS – DW

New technique could prevent biofilms on catheters and medical implants – EurekAlert

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October 30, 2015

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Cave microbiome, vaginal bacteria in cute minipigs, and “disordered” home dust microbiome, and an update on the Beard Microbiome.

Human gut microbiome

Oatmeal porridge: impact on microflora-associated characteristics in healthy subjects – Jørgen Valeur – British Journal of Nutrition

Animal models

The vaginal microbiome is stable in prepubertal and sexually mature Ellegaard Göttingen Minipigs throughout an estrous cycle – Emma Lorenzen – Veterinary Research

Biofilm-associated bacterial amyloids dampen inflammation in the gut: oral treatment with curli fibres reduces the severity of hapten-induced colitis in mice – Gertrude O Oppong – NPJ Biofilms and Microbiomes

Disease tolerance mediated by microbiome E. coli involves inflammasome and IGF-1 signaling – Alexandria M. Palaferri Schieber – Science

Cave microbiome

Microbial mediation of complex subterranean mineral structures – Nicola Tisato – Scientific Reports

Built environment microbiome

Home dust microbiota is disordered in homes of low-income asthmatic children – Christina E. Ciaccio – Journal of Asthma

Food microbiology

A Large Set of Newly Created Interspecific Saccharomyces Hybrids Increases Aromatic Diversity in Lager Beers – Stijn Mertens – Applied and Environmental Microbiology

T-RFLP: Bacterial community and proteome analysis of fresh-cut lettuce as affected by packaging – Mariasole Di Carli – FEMS Microbiology Letters

Viruses and phages

Virus Satellites Drive Viral Evolution and Ecology – Belén Frígols – PLOS Genetics

Bioinformatics and metagenomics

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Multi-view Clustering of Microbiome Samples by Robust Similarity Network Fusion and Spectral Clustering – Y. Zhang – Computational Biology and Bioinformatics, IEEE/ACM Transactions

Bacteria in the news

The strain in metagenomics: Two computational tools extract strain-level information from reams of microbial sequence data. – Tal Nawy – Nature Methods

Bacteria found to play role in cow’s milk intolerance – SunCoast news

‘Superhero’ microbiome bacteria protect against deadly symptoms during infection – Salk Institute – EurekAlert

Can changes in the brain affect your microbiome? UB researchers are investigating – Ellen Goldbaum – University at Buffalo

BacteriaHysteria

Not news at all: I-Team: Everyday items we touch are loaded with bacteria – Ryan Walsh – WWLP

Beard microbiome

This was actually funny:  Will Forte (actor from “The Last Man on Earth”) has beard swabbed for bacteria test, fails, at Jimmy Fallon show – Yahoo Video

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October 29, 2015

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Library prep technology, skin communities in urban and rural populations, rarity in aquatic microbes, and the microbiome of solar panels.

Pregnancy and birth

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons – Anuradha Ravi – Scientific Reports

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life – Tanya L Alderete – The American Journal of Clinical Nutrition

Human skin microbiome

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations – Shi Ying – PLOS ONE

Human respiratory microbiome

Review: A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS) – Mahboobeh Mahdavinia – Clinical & Experimental Allergy

Human gut microbiome

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

DGGE: The duodenal microbiota composition in children with active coeliac disease is influenced for the degree of enteropathy – F. Girón Fernández-Crehuet – Anales de Pediatría (English Edition)

Review: The microbiome and its pharmacological targets: therapeutic avenues in cardiometabolic diseases – Ana Luisa Neves – Current Opinion in Pharmacology

Review: Microbiome impact on metabolism and function of sex, thyroid,
growth and parathyroid hormones – Michał Kunc – Acta Biochimica Polonica

Review: Intestinal Microbiota: From Inflammatory Bowel Disease to Bone Marrow Transplantation – Ernst Holler – Blood

Review: Dysbiotic gut microbiome: A key element of Crohn’s disease – Styrk Furnes Øyri – Comparative Immunology, Microbiology and Infectious Diseases

Infection microbiology

Serum bacterial DNA detection in patients with cholangitis after Kasai procedure – Qianfu Luo – Pediatrics International

Deceiving title (not about microbiome but infection): Breast Implant–Associated Infections: The Role of the National Surgical Quality Improvement Program and the Local Microbiome – Cohen, Justin B. – Plastic and Reconstructive Surgery

Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration – Dagmar Chudobova – The Brazilian Journal of Infectious Diseases

Animal and bioreactor models

The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia – Tim J Schuijt – Gut

In mice: The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation – Mario M. Zaiss – Cell

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization – Malin E.V. Johansson – Cell Host & Microbe

Microbiota-Dependent Hepatic Lipogenesis Mediated by Stearoyl CoA Desaturase 1 (SCD1) Promotes Metabolic Syndrome in TLR5-Deficient Mice – Vishal Singh – Cell Metabolism

Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing – Yongchao Xie – Chemosphere

The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals – A. Schoster – Equine Veterinary Journal

A longitudinal assessment of changes in bacterial community composition associated with the development of periodontal disease in dogs – Corrin Wallis – Veterinary Microbiology

Assessment of prebiotic potential of Akpan-yoghurt-like product and effects on the human intestinal microbiota – Beatriz Gullón – Journal of Functional Foods

Relationship between inflammation, the gut microbiota, and metabolic osteoarthritis development: studies in a rat model – K.H. Collins – Osteoarthritis and Cartilage

Plant, root, and soil microbiome

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem – Claudia M. Boot – Soil Biology and Biochemistry

Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil? – Erik Verbruggen – Journal of Ecology

Editorial: Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Water microbiome

Review: Rarity in aquatic microbes: placing protists on the map – Ramiro Logares – Research in Microbiology

Waste microbiology

Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion – Eoin Gunnigle – FEMS Microbiology Ecology

An ‘omics’ approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge – D.J. Beale – Water Research

Extremophile microbiome

Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community – Alexander Crits-Christoph – BioRxiv

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city – Pedro Dorado-Morales – BioRxiv

Food microbiology

Microbial community dynamics in thermophilic undefined milk starter cultures – Eugenio Parente – International Journal of Food Microbiology

Metagenomics and bioinformatics

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition – David Koslicki – PLOS ONE

Linear-time superbubble identification algorithm for genome assembly – Ljiljana Brankovic – Theoretical Computer Science

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut – Christian Milani – Scientific Reports

Power law analysis of the human microbiome – Zhanshan (Sam) Ma – Molecular Ecology

More microbiology

Bioactive natural products from novel microbial sources – Victoria L. Challinor – Annals of the New York Academy of Sciences

Conference report: Bacterial Networks in Cells and Communities – Victor Sourjik – Journal of Molecular Biology

Self-establishing communities enable cooperative metabolite exchange in a eukaryote – Kate Campbell – eLife

Techniques

Library preparation methodology can influence genomic and functional predictions in human microbiome research – Marcus B. Jones – PNAS

Microbes in the news

Scientists Urge National Initiative on Microbiomes – Carl Zimmer – New York Times

Fecal transplant pills: Large-scale production begins: Nonprofit stool bank launched by MIT researchers completes first dose-finding study – GlobeNewsWire
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October 28, 2015

Posted on by

A global microbiome initiative, diversity of bumblebee gut microbes and rhizophere, and the microbiome of Brazilian banknotes.

General microbiome

Microbiology: Create a global microbiome effort – Nicole Dubilier, Margaret McFall-Ngai& Liping Zhao – Nature

A unified initiative to harness Earth’s microbiomes – A. P. Alivisatos – Science

Human gut microbiome

Two healthy diets modulate gut microbial community improving insulin sensitivity in a human obese population – Carmen Haro – Journal of Clinical Endocrinology & Metabolism

Animal microbiome

Mollusk: Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod – Ajit Kumar Ngangbam – PLOS ONE

Bees: Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris) – Annelies Billiet – Insect Science

Plant, root, and soil microbiome

Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth – Mangal Singh – Scientific Reports

Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields – Li Bai – Microbiological Research

Plant Invasions Associated with Change in Root-Zone Microbial Community Structure and Diversity – Richard R. Rodrigues – PLOS ONE

Water microbiome

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing – Joel F. Gibson – PLOS ONE

Food microbiome

A Novel Bacteriophage Targeting Cronobacter sakazakii is a Potential Biocontrol Agent in Foods – Ju-Hoon Lee – Applied and Environmental Microbiology

Money microbiome

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces –
Tairacan Augusto Pereira da Fonseca – Int. J. Environ. Res. Public Health

Microbial Ecology, more microbes

Fungal communities as an experimental approach to Darwin’s naturalization hypothesis –
María Camila Morales – Research in Microbiology

Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses – Lu Han – Scientific Reports

Techniques

DNA Barcoding through Quaternary LDPC Codes – Elizabeth Tapia – PLOS ONE

Metagenomics

Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life – Philippe Lopez – Biology Direct

Microbes in the news

Hey Obama, Can We Have a Unified Microbiome Initiative? Yours, the microbiologists – Ed Yong – The Atlantic

Intestinal Worms ‘Talk’ With Gut Bacteria – Talal Al-Khatib – Discovery

Intestinal Worms May Boost Our Immune System By Communicating With Gut Bacteria – Ed Cara – Medical Daily

Collecting dust from the International Space Station: an author Q+A – Sophie Marchant – BioMedCentral Blogs

Antarctic Bacteria Prove Resilient – Glacier Hub

Bacteria-Powered Shirts Vent When You Sweat – Glenn McDonald – Discovery

New Sherwin-Williams paint kills infection-causing bacteria – Nathan Bomey – USA Today

Bacteria Hysteria

Nasty Bacteria Found In Halloween Masks – MSN
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October 27, 2015

Posted on by

Gut biogeography, soil transplants, donkey penises, Chicago public beaches, deep-sea mussels, dust particles in the International Space Station, and red pepper influence on kimchi microbiology

Events

About the world within us: This week, Penn Vet, Penn Medicine, and the Children’s Hospital of Philadelphia will host their second annual microbiome symposium – Sandy Bauers – Philly.com

Call for Volunteers: Gut Microbiota Samples – AGA is now recruiting volunteers to have their gut analyzed. Submit your name by Dec. 7 to be considered

General human microbiome

Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches – José E. Belizário – Frontiers in Microbiology

Pregnancy and birth microbiome

The Early Intestinal Microbiota of Healthy Korean Newborns – Eu Kyoung Lee – Iran J Pediatr

Human oral microbiome

Microbiome interaction with sugar plays an important role in relapse of childhood caries –
Jing Tian – Biochemical and Biophysical Research Communications

Human respiratory microbiome

The microbiome of the maxillary sinus and middle nasal meatus in chronic rhinosinusitis – O.A. Ivanchenko – Rhinology

Human skin microbiome

The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients – Charles W. Lynde – Journal of Cutaneous Medicine and Surgery

Human gut microbiome

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India – Anna Johnning – BMC Microbiology

Regulation of lung immunity and host defense by the intestinal microbiota – Derrick R. Samuelson – Frontiers in Microbiology

Intestinal Microbiota Profiles of Healthy Pre-School and School-Age Children and Effects of Probiotic Supplementation – Wang C. – Annals of Nutrition and Metabolism

Effect of Whole-Grain Barley on the Human Fecal Microbiota and Metabolome – Maria De Angelis – Applied and Environmental Microbiology

Microbiota studies in the bile duct strongly suggest a role for H. pylori in extrahepatic cholangiocarcinoma – Francisco Avilés-Jiménez- Clinical Microbiology and Infection

Review: A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Toward Dietary Interventions Targeting Bacterial Genes – Yueqiong Ni – mBio

Review: Gut biogeography of the bacterial microbiota – Gregory P. Donaldson – Nature Reviews Microbiology

Review: The Microbiome in Mental Health: Potential Contribution of Gut Microbiota in Disease and Pharmacotherapy Management – Stephanie A. Flowers – Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy

Review: Impact of Gut Microbiota on Obesity, Diabetes, and Cardiovascular Disease Risk – Luca Miele – Current Cardiology Reports

Editorial: Faecal transplants – Tim Spector, Rob Knight – British Medical Journal

Microbiome models

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection – Jason L. Kubinak

Diet drives quick changes in the metabolic activity and composition of human gut microbiota in a validated in vitro gut model – Marisol Aguirre – Research in Microbiology

The effect of diet and host genotype on ceca microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Frontiers in Microbiology

Review: Selective manipulation of the gut microbiota improves immune status in vertebrates – Ana Montalban-Arques – Frontiers in Immunology

Animal microbiome

With a picture of the sampling site! Bacterial and fungal microflora on the external genitalia of male donkeys (Equus asinus) – Carla L. Carleton – Animal Reproduction Science

Zoo animals: Human Staphylococcus aureus lineages among Zoological Park residents in
Greece – E. Drougka – Open Veterinary Journal

Insects: Microbial ecology-based methods to characterize the bacterial communities of non-model insects – Erica M. Prosdocimi – Journal of Microbiological Methods

Cattle: The nasopharyngeal microbiota of feedlot cattle – Devin B. Holman – Scientific Reports

Cattle: The rumen microbial metagenome associated with high methane production in cattle – R. John Wallace – BMC Genomics

Goose: Comparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing – Wen Wang – Microbiological Research

Bats: Bacterial diversity indicates dietary overlap among bats of different feeding habits – Sunil Banskar – Microbiological Research

Copepods: Biotransformation of petroleum hydrocarbons and microbial communities in seawater with oil dispersions and copepod feces – Ingvild Fladvad Størdal – Marine Pollution Bulletin

Mussels: Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels – Lizbeth Sayavedra – eLIFE

Snail: Enrichment and Identification of Cellulolytic Bacteria from the Gastrointestinal Tract of Giant African Snail, Achatina fulica – Kiran D. Pawar – Applied Biochemistry and Biotechnology

Coral: Intraspecific diversity among partners drives functional variation in coral symbioses – John Everett Parkinson – Scientific Reports

Coral: Variations in the abundance and structural diversity of microbes forming biofilms in a thermally stressed coral reef system – Huda Mahmoud – Marine Pollution Bulletin

Coral: Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria – Julie L Meyer – The ISME Journal

Zebrafish: Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine – W. Zac Stephens – mBio

Arthropod: The microbiome of Folsomia candida: an assessment of bacterial diversity in a Wolbachia-containing animal – V. Agamennone – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Dynamics of bacterial community structure on intertidal sandflat inhabited by the ghost shrimp Nihonotrypaea harmandi (decapoda: Axiidea: Callianassidae) in tomioka bay, amakusa, Japan – Minoru Wada – Gene

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest –
Dulce Flores-Rentería – Soil Biology and Biochemistry

Long lasting effects of the conversion from natural forest to poplar plantation on soil microbial communities – Francesco Vitali – Microbiological Research

Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China – Weibing Xun – Environmental Microbiology

Microbial responses to southward and northward Cambisol soil transplant – Mengmeng Wang – Microbiology Open

Review: Incorporating the soil environment and microbial community into plant competition theory – Po-Ju Ke – Frontiers in Microbiology

Review: Root Microbiome Assemblage is Modulated by Plant Host Factors – Venkatachalam Lakshmanan – Advances in Botanical Research

Water microbiome

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats – Hon Lun Wong – Scientific Reports

Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches – Kema Malki – Data in Brief

Cyanobacterial reuse of extracellular organic carbon in microbial mats – Rhona K Stuart – The ISME Journal

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton – Sedimentology

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan – Takuro Nunoura – Environmental Microbiology

Do phages impact microbial dynamics, prokaryotic community structure and nutrient dynamics in Lake Bourget? – Antony Meunier, Stéphan Jacquet – Biology Open

Active populations of rare microbes in oceanic environments as revealed by bromodeoxyuridine incorporation and 454 tag sequencing – Koji Hamasaki – Gene

Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment – Tao He – Applied Microbiology and Biotechnology

[Mini review] metagenomic studies of the Red Sea – Hayedeh Behzad – Gene

Marine bacteria from the French Atlantic coast displaying high forming-biofilm abilities and different biofilm 3D architectures – Ibtissem Doghri – BMC Microbiology

Genome-wide tuning of protein expression levels to rapidly engineer microbial traits – Emily F. Freed – ACS Synthetic Biology

Built Environment microbiology

Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities – Aleksandra Checinska – Microbiome

Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing – Jing You – Applied Microbiology and Biotechnology

Food microbiology

The influence of red pepper powder on the density of Weissella koreensis during kimchi fermentation – Bo Kyoung Kang – Scientific Reports

Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant – Maria Calasso – Food Microbiology

Extremophile microbiology

Hot spring deposits: Tracing Biosignature Preservation of Geothermally Silicified Microbial Textures into the Geological Record – Kathleen A. Campbell – Astrobiology

Microbiome composition and geochemical characteristics of deep subsurface high-pressure environment, Pyhäsalmi mine Finland – Hanna Miettinen – Frontiers in Microbiology

Bioinformatics and metagenomics

mBLAST: Keeping up with the Sequencing Explosion for (Meta) Genome Analysis – Curtis Davis – Journal of Data Mining in Genomics & Proteomics

Identification and resolution of microdiversity through metagenomic sequencing of parallel consortia – William C. Nelson – Applied and Environmental Microbiology

V-GAP: Viral genome assembly pipeline – Yoji Nakamura – Gene

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community – Robert M. Bowers – BMC Genomics

MinION Analysis and Reference Consortium: Phase 1 data release and analysis [version 1; referees: awaiting peer review] – Camilla L.C. Ip – F1000 Research

Review: Machine learning for metagenomics: methods and tools – Hayssam Soueidan, Macha Nikolski – Arxiv

Review: Novel Computational Technologies for Next-Generation Sequencing Data Analysis and Their Applications – Chuan Yi Tang – International Journal of Genomics

Microbes in the news

Potentially Dangerous Bacteria Thrive At The International Space Station, NASA Warns
– Katrina Pascual – Tech Times
What’s In The Microbiome Of Space? – Science 2.0

Decoding the DNA of lung bacteria to keep you healthy – Leah Cuthbertson – Imperial College London

US researchers delve into make-up of gut bacteria in horses – HorseTalk

Microbial engineering finds a home at SEAS: genetic engineering on biofilms – Adam Zewe – Harvard

Cultures: a small magazine tackling big issues – Special Kids Edition – ASM

Hurricane Patricia Victims Use Chlorine To Fight Bacteria – Operation Blessing

Bacteria can communicate like brain cells. This is a bacterial world. We just live in it. – Bradley J. Fikes – San Diego Union Tribune

Jessica Richman Wants People to Track Their Microbiomes – Wall Street Journal

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