Category Archives: Microbiome of Death

September 17, 2018

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In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

July 30, 2018

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Today’s digest features the microbiomes of a XVIII century mummy (Krásna Hôrka, Slovakia), an interesting initiative out of Belgium (Disbiome, a database of microbiota-disease associations), exciting news from Kamagata lab about improved culturing of environmental samples, promising findings on gut bacteria byproduct that protects against Salmonella, and much more. Happy reading!

Human microbiome

*Disbiome database: linking the microbiome to disease – Yorick Janssens – BMC Microbiol.

*The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment – Lucia Kraková – Environ Microbiol.

Gut microbiome

*A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection – Amanda Jacobson – Cell Host & Microbe

Simulation and modeling of dietary changes in the infant gut microbiome – Daniel Medina – FEMS Microbiol Ecol.

Human gut bacteria as potent class I histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid – Samantha Yuille – PLoS One

Review: An update on the role of gut microbiota in chronic inflammatory diseases, and potential therapeutic targets – Bobbi Laing – Expert Rev Gastroenterol Hepatol.

A step ahead: Exploring the gut microbiota in inpatients with bipolar disorder during a depressive episode – Annamaria Painold – Bipolar Disord.

Review: The Gut-Brain Axis, the Human Gut Microbiota and Their Integration in the Development of Obesity – Edward Bliss – Front Physiol.

Fungal dysbiosis in cirrhosis – Jasmohan S Bajaj – Hepatology

Urinary tract microbiome

The bacterial microbiota in first-void urine from men with and without idiopathic urethritis – Maria Frølund – PLoS One

Lung microbiome

Lower respiratory tract microbial composition was diversified in Pseudomonas aeruginosa ventilator-associated pneumonia patients – Xiaoling Qi – Respir Res.

Plant microbiome

Bacterial community assemblages in the rhizosphere soil, root endosphere and cyst of soybean cyst nematode-suppressive soil challenged with nematodes – Muzammil Hussain – FEMS Microbiology Ecology

Exploring plant-microbe interactions of the rhizobacteria Bacillus subtilis and Bacillus mycoides by use of the CRISPR-Cas9 system – Yanglei Yi – Environ Microbiol.

Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling – Garcia Joshua – Front Microbiol.

Water microbiome

Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater – Roland Wilhelm – Environ Microbiol.

Techniques

*Isolation of Previously Uncultured Slow-growing Bacteria by Using a Simple Modification in Preparation of Agar Media – Souichiro Kato – Applied and Environmental Microbiology

Review: The role of the gut microbiota on animal model reproducibility – Patricia Turner – Animal Model Exp.

Review: Environmental enrichment and mouse models: Current perspectives – Kathryn Bayn – Animal Model Exp.

Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface – Marta Calatayud Arroyo – J Vis Exp.

Bioprinting microbial communities to examine interspecies interactions in
time and space – William Frederick Hynes – Biomed. Phys. Eng. Express

January 19, 2018

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Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table

June 24, 2017

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An early life focus today: Interesting papers on the effects of a pre-term cesarian birth on the gut microbiome and the impact of the infant gut microbiome on food allergies. Also highlighted, the relationship between the gut microbiome and social stress vulnerability in mice, the role of the gut microbiome in mosquito development, and evidence of a permanent transfer of prokaryotic virus sequences to the mammalian brain.

  • Pregnancy and early life

Review: Perinatal Group B Streptococcal Infections: Virulence Factors, Immunity, and Prevention Strategies – Jay Vornhagen – Trends in Microbiology

* Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants – Christopher Stewart – Frontiers in Microbiology

* A prospective microbiome-wide association study of food sensitization and food allergy in early childhood – Jessica Savage – Allergy

  • Human respiratory microbiome

Psl Produced by Mucoid Pseudomonas aeruginosa Contributes to the Establishment of Biofilms and Immune Evasion – Christopher Jones – mBio

  • Human skin microbiome

Isotretinoin and lymecycline treatments modify the skin microbiota in acne – Hanna-Lenna Kelhala – Experimental Dermatology

  • Human oral microbiome

Potassium is a key signal in host-microbiome dysbiosis in periodontitis – Susan Yost – PLOS Pathogens

  • Human gut microbiome

The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue – Rebecca Schugar – Cell Reports
In vitro modulation of gut microbiota by whey protein to preserve intestinal health – Sanchez-Moya – Food and Function

Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis – Gregory Young – Frontiers in Cellular and Infection Microbiology

NOD2 genetic variants predispose one of two familial adenomatous polyposis siblings to pouchitis through microbiome dysbiosis – Kathleen Schieffer – Journal of Crohn’s and Colitis

The Bacteroides fragilis pathogenicity island links virulence and strain competition – Benjamin Casterline – Gut Microbes

Diversity analysis of gut microbiota in osteoporosis and osteopenia patients – Jihan Wang – PeerJ

Gut microbiota of liver transplantation recipients – Li-Ying Sun – Scientific Reports

Review: Microbiome: A Potential Component in the Origin of Mental Disorders – George Stefano – Medical Science Monitor

Review: Impact of mycotoxins on the intestine: are mucus and microbiota new targets? – Herve Robert – Journal of Toxicology and Environmental Health

Review: Microbiota, Inflammation and Colorectal Cancer – Cecily Lucas – International Journal of Molecular Sciences

Review: The Enteric Network: Interactions between the Immune and Nervous Systems of the Gut – Bryan Yoo – Immunity

  • Cadaver microbiome

Function of bacterial community dynamics in the formation of cadaveric semiochemicals during in situ carcass decomposition – Javier Pascual – Environmental Microbiology

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  • Animal experiments

* Implications of the gut microbiota in vulnerability to the social avoidance effects of chronic social defeat in male mice – Joanna Kasia Szyszkowicz – Brain, Behavior, and Immunity

Intestinal microbial dysbiosis aggravates the progression of Alzheimer’s disease in Drosophila – Shih-Cheng Wu – Nature Communications

Fructo-oligosaccharides and intestinal barrier function in a methionine-choline-deficient mouse model of nonalcoholic steatohepatitis – Kotaro Matsumoto – PLOS One

Spirulina Protects against Hepatic Inflammation in Aging: An Effect Related to the Modulation of the Gut Microbiota? – Audrey Neyrinck – Nutrients

Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice – C.J Chang – International Journal of Obesity

Topical antimicrobial treatments can elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors – Adam SanMiguel – Antimicrobial Agents and Chemotherapy

Temporal microbiota changes of high-protein diet intake in a rat model – Chunlong Mu – Anaerobe

  • Animal microbiome

Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2 – Guowei Zhou – Environmental Microbiology

Effects of dietary supplementation of red pepper (Schinus terebinthifolius Raddi) essential oil on performance, small intestinal morphology and microbial counts of weanling pigs – Pedro Leon Gomes Cairo – Science of Food and Agriculture

Identification of Bufadienolides from the Boreal Toad, Anaxyrus boreas, Active Against a Fungal Pathogen – Kelly Barnhart – Microbial Ecology

* Bacteria-mediated hypoxia functions as a signal for mosquito development – Kerri Coon – PNAS

  • Plant, root, and soil microbiome

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation – Eduardo de Siva Fonseca – Microbial Ecology

  • Water and extremophile microbiome

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses – Vera Thiel – Frontiers in Microbiology

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  • Phages and viruses

* A prokaryotic viral sequence is expressed and conserved in mammalian brain – Yang-Hui Yeh – PNAS

  • Techniques

Solid Sampling with a Diode Laser for Portable Ambient Mass Spectrometry – Yeni Yung – Analytical Chemistry

January 12, 2017

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uBiome blog

Losing Weight is the Most Popular New Year’s Resolution – Could Probiotics Help? – Julie Taylor – uBiome

Video: Young Microbiome Researchers: Celsius & Beyond – uBiome
For the uBiome team, working with other scientists is always rewarding, but we particularly enjoyed our recent collaboration with a team of researchers, many of whom were swamped by their lab coats and blue nitrile gloves.

Jobs

Postdoctoral Research Fellow, Microbiology – California Academy of Sciences

Pregnancy and early life

* A molecular portrait of maternal sepsis from Byzantine Troy – Alison M Devault – eLIFE

The Generation R Study: design and cohort update 2017 – Marjolein N. Kooijman – European Journal of Epidemiology

Human oral microbiome

On the ecosystemic network of saliva in healthy young adults – Egija Zaura – The ISME Journal

Human gut microbiome

Seven brief reviews: Topical Issue of the Journal of Immunology: The Macro Influence of the Microbiome – Pamela J. Fink – The Journal of Immunology

Review: Microbiome and the future for food and nutrient security – Brajesh K. Singh – Microbial Biotechnology

Animal experiments

Neuroblastoma causes alterations of the intestinal microbiome, gut hormones, inflammatory cytokines, and bile acid composition – Christoph Castellani – Pediatric Blood & Cancer

Routine assessment of the gut microbiome to promote preclinical research reproducibility and transparency – Hannah R Wardill – Gut

Animal microbiome

Postnatal changes in the relative abundance of intestinal Lactobacillus spp. in newborn calves – Tadashi Takino – Journal of Veterinary Medical Science

Population- and growth-related differences in helminthic fauna of finless porpoises (Neophocaena asiaeorientalis) in five Japanese populations – Akira Shiozaki – Journal of Veterinary Medical Science

Antifeedants Produced by Bacteria Associated with the Gut of the Pine Weevil Hylobius abietis – Karolin Axelsson – Microbial Ecology

Plant, root, and soil microbiome

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel – Binu M. Tripathi – Microbial Ecology

Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil – Eoin Gunnigle – Scientific Report

Foliar application of the leaf-colonizing yeast Pseudozyma churashimaensis elicits systemic defense of pepper against bacterial and viral pathogens – Gahyung Lee – Scientific Reports

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes – Joana P. Fernandes – Science of the Total Environment

Biodegradation of the veterinary antibiotics enrofloxacin and ceftiofur and associated microbial community dynamics – Diogo A.M. Alexandrino – Science of the Total Environment

* Redox conditions and marine microbial community changes during the end-Ordovician mass extinction event – Justyna Smolarek – Global and Planetary Change

Use of plant growth promoting bacterial strains to improve Cytisus striatus and Lupinus luteus development for potential application in phytoremediation – María Balseiro-Romero – Science of the Total Environment

Response of microbial communities colonizing salt marsh plants rhizosphere to copper oxide nanoparticles contamination and its implications for phytoremediation processes -Joana P. Fernandes – Science of the Total Environment

Communication of Sedentary Plant-Parasitic Nematodes With Their Host Plants – T. Hewezi – Advances in Botanical Research

Book chapter: Application of Microbiology in Dryland Agriculture – Minakshi Grover – Innovations in Dryland Agriculture

Water and extremophile microbiome

Potential Activity of Subglacial Microbiota Transported to Anoxic River Delta Sediments – Karen A. Cameron – Microbial Ecology

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring – Laura Ward – The ISME Journal

* Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics – Abraham G. Moller – PeerJ

Abundance of microorganisms and enzyme activity in the rapids-pool-benchland systems in natural Douliu River of China – Zhen Hong Wang – PeerJ Preprint

Distinct sensitivity of fungal freshwater guilds to water quality – Oliver Röhl – Mycological

Food microbiology

Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses – Jing Li – BMC Microbiology

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation – Peter R Sternes – bioRxiv

Waste and pollution microbiology

Microbial community structure in a full-scale anaerobic treatment plant during start-up and first year of operation revealed by high-throughput 16S rRNA gene amplicon sequencing – Else Marie Fykse – Bioresource Technology

Bioinformatics

* MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes – Wei Ma – Scientific Reports

Microbial ecology

Review: Where less may be more: how the rare biosphere pulls ecosystems strings – Alexandre Joussett – ISME Journal

Microbes in the news

Gut science is radically changing what we know of the human body – Pat Rich – University Affairs Canada

Renowned microbiology expert to visit West Florida. Claire Fraser will present, “The Human Gut Microbiome in Health and Disease” – SR Press Gazette

Microbiomes Move Standard Plate Count One Step Forward – Gregory Siragusa – Food Safety Tech

Researchers develop new compound to fight cytomegalovirus – EurekAlert

Eating red meat six times a week could increase chances of getting painful bowel disease – Daisy Dunne – Mirror

This looks intriguing: Microbiota and the masses: a love story – S. B. Divya – MacMillan

Microbes on the market

Gut microbiome profiling tests propelled by customer demand – Vijay Shankar – Nature Biotechnology

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business

Bik’s non-microbiology picks

UCSF Receives Historic Half-Billion-Dollar Donation – Lindsey Hoshaw – KQED

This is a tragic/comic read, but note that the original post contained some offending language, that was removed after protests on e.g. Twitter. The Rise and Fall of a Shrimp Biologist – David Scholnick – Scientific American

January 11, 2017

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Vaginal microbial  communities associated with HIV acquisition or protection, evolution and function of the appendix, microbes and bird evolution, soil microbes followed for 17 years, and bone microbiome and cause-of-death of an 18th century child.
Jobs

Faculty Position in Microbiome Research – National University of Singapore – Science Careers

Pregnancy and early life

The Role of Early Life Nutrition in the Establishment of Gastrointestinal Microbial Composition and Function – Erin C. Davis – Gut Microbes

Human vaginal microbiome

* Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women – Christina Gosmann – Immunity

Diagnosis and microecological characteristics of aerobic vaginitis in outpatients based on preformed enzymes – Zhi-liang Wang – Taiwanese Journal of Obstetrics & Gynecology

Human respiratory microbiome

Review: The microbiome in mechanically ventilated patients – Yin, Yudong – Current Opinion in Infectious Diseases

Human gut microbiome

* Morphological evolution of the mammalian cecum and cecal appendix – Heather F. Smith – Comptes Rendus Palevol

Exploring the Efficacy of Pooled Stools in Fecal Microbiota Transplantation for Microbiota-Associated Chronic Diseases – Abbas Kazerouni – PLOS ONE

Review: Role of Vitamin D in the Hygiene Hypothesis: The Interplay between Vitamin D, Vitamin D Receptors, Gut Microbiota, and Immune Response – Allison Clark – Frontiers in Immunology

Review: Bacterial Signaling to the Nervous System via Toxins and Metabolites – Nicole J. Yang – Journal of Molecular Biology

Animal experiments

Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior – Caleb Fischer – eLIFE

Gut Microbiota Mediates Protection Against Enteropathy Induced by Indomethacin – Xue Xiao – Scientific Reports

Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change – P. Grimm – Animal

Characterisation of Early-Life Fecal Microbiota in Susceptible and Healthy Pigs to Post-Weaning Diarrhoea – Samir Dou – PLOS ONE

Animal microbiome

Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum – A.V. Nedoluzhko – Genomics Data

* Review: Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history – Jessica K. Evans – Hormones and Behavior

Archaeology microbiome

* The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing – Valeria D’Argenio – International Journal of Molecular Sciences

Plant, root, and soil microbiome

Phyllosphere Methylobacterium bacteria contain UVA-absorbing compounds – Shigenobu Yoshida – Journal of Photochemistry and Photobiology B: Biology

Major Crop Species Show Differential Balance between Root Morphological and Physiological Responses to Variable Phosphorus Supply – Yang Lyu – Frontiers in Plant Science

* Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change – Emma J. Sayer – Ecology and Evolution

Water and extremophile microbiome

Two microcrustaceans affect microbial and macroinvertebrate-driven litter breakdown – Sophie Chambord – Freshwater Biology

Biofilms Confer Resistance to Simulated Extra-terrestrial Geochemical Extremes – Adam H Stevens – bioRxiv Preprint

Bioinformatics, statistics, and metagenomics

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer – Aaron Weimann – mSystems

Structural zeros in high-dimensional data with applications to microbiome studies – Abhishek Kaul – Biostatistics

More microbiology

Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response – Robert Heler – Molecular Cell

Press: Researchers Learn to Enhance Bacteria’s Ability to Form Genetic Memories – SciCasts

Microbes in the news
Meet Canada’s ‘poop lady’: “I got to know people up there very well over the years, said Girard, 28. – EurekAlert

A new year for our journal club! – Fiona Whelan – Human Microbiome Journal Club

Oral bacteria linked to preterm labor in Hawaiʻi – Desiree Uyeda – University of Hawai’i News

Mayo’s microbiome study targets diabetes – Brett Boese – Post Bulletin

MicrobEYEome: Liver Cancer Patients Have a Signature Microbiome – GastroEndo News

Presentation: The role of the microbiome in Porcine Reproductive & Respiratory Syndrome (PRRS) – Megan Niederwerder – YouTube

Based on the title this appears to be a good candidate for the “Overselling The Microbiome Award” by Jonathan Eisen: How Sexual Attraction Is Shaped by Gut Bacteria, Infectious Diseases, and Parasites – Kathleen McAuliffe – BigThink

Latest Dengue Update: Bacteria Strain That Stops Dengue Transmission In Mosquitoes Dies In Hot Environment – Minnow Blythe – Counsel Heal

Microbes on the market

Allergan (AGN) Enters Licensing Agreement with Assembly Biosciences (ASMB) to Obtain Worldwide Rights to GI Programs – StreetInsider

Ferring Partners with Intralytix to Develop Bacteriophage Treatments for Conditions Associated with the Microbiome and Drug-Resistant Bacteria – BusinessWire

La Roche-Posay Introduces Prebiotic Skincare Line – PR NewsWire

Indigo’s Preliminary Commercial Data Demonstrate Significant Yield Gains for Growers with Plant Microbiome Product – PR NewsWire

Bik’s non-microbiology picks

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study – Mustafa Chopan – PLOS ONE

December 16, 2016

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General microbiome

Forging new links between the microbiome and cancer – Bryn Nelson – Cancer Cytopathology

Pregnancy and early life

Review: Planting the seed: Origins, composition, and postnatal health significance of the fetal gastrointestinal microbiota – Lisa F. Stinson – Critical Reviews in Microbiology

Human respiratory microbiome

Review: The respiratory tract microbiome and lung inflammation: a two-way street – G B Huffnagle – Mucosal Immunology

Human gut microbiome

Influence of potassium-competitive acid blocker on the gut microbiome of Helicobacter pylori-negative healthy individuals – Taketo Otsuka – Gut

High Prevalence of Gut Microbiota Colonization with Broad-Spectrum Cephalosporin Resistant Enterobacteriaceae in a Tunisian Intensive Care Unit – Elaa Maamar – Frontiers in Microbiology

Review: Linking Dietary Patterns with Gut Microbial Composition and Function – Amy M. Sheflin – Gut Microbes

Review: The role of the gastrointestinal tract in the pathogenesis of rheumatic diseases – Francesco Ciccia – Best Practice & Research Clinical Rheumatology

Animal experiments

Alteration in the Gut Microbiota Provokes Susceptibility to Tuberculosis – Nargis Khan – Frontiers in Immunology

Animal microbiome

Faecal virome of red foxes from peri-urban areas – Ivana Lojkić – Comp Immunol Microbiol Infect Dis

The Underlying Ecological Processes of Gut Microbiota Among Cohabitating Retarded, Overgrown and Normal Shrimps – Jinbo Xiong – Microbial Ecology

Faecal virome of red foxes from peri-urban areas – Comp Immunol Microbiol Infect Dis

Plant, root, and soil microbiome

Vertical stratification of the foliar fungal community in the world’s tallest trees – Joshua G. Harrison – American Journal of Botany

Impact of mowing management on nitrogen mineralization rate and fungal and bacterial communities in a semiarid grassland ecosystem – Jiangye Li – Journal of Soils and Sediments

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil – Lei Wang – Frontiers in Microbiology

Temporal Variations in Diazotrophic Communities and nifH Transcripts Level Across the Agricultural and Fallow Land at Jaipur, Rajasthan, India – Sushma Sharma – Indian Journal of Microbiology

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC) – Rosa Margesin – Microbial Ecology

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils – S. Emilia Hannula – Frontiers in Microbiology

Water and extremophile microbiome

Life in deep subsurface – Grégoire Galès – E2S Web of Conferences

Microbiology of cultural heritage

Microbial Life and Death in a Foxing Stain: a Suggested Mechanism of Photographic Prints Defacement – Maria Carla Sclocchi – Microbial Ecology

Microbiology of death

Artful decomposition: the microbial necrobiome – Kevin Lyons – People, peas and pathogens

Microbes in the news

It takes guts: Lawrence David explains unconventional research on microbiome – Jackie Dillon – Duke Chronicle

Water filters could increase bacteria in Flint water, researchers say – Oona Goodin-Smith – Mlive

How is the gut microbiome established? – Philip Dube – Taconic

Soil Bacteria Could Help Absorb Natural Gas Leaks – Aaron Sidder – EOS

Microbes on the market

The Microbiome Defined and Understood Using A.I. – Nanalyze

Microbiome Therapeutics Market Size To Reach USD 433.5 Million By 2025: Grand View Research, Inc. – SAT PR News

September 13, 2016

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Infant gut microbiome and allergy risk, gut microbiome in mice and susceptibility to Plasmodium, microbiome of a stranded striped dolphin, cadavers in Canada, rRNA operon copy numbers.

Events

(repeat posting) 4th Microbiome R&D Business collaboration Forum & Probiotics Congress, October 3-4, 2016, La Jolla,San Diego, USA. Use discount code: ALLONG for a special rate of $399.

Pregnancy and birth

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation – Kei E Fujimura – Nature Medicine

Press: Infant gut microbiome appears to shape allergy risk by altering immune responses – EurekAlert
Newborn gut microbiome predicts later allergy and asthma, study finds. Microbial byproducts link particular early-life gut microbes to immune dysfunction – Science Daily
Clues in microbiome of infants point to future allergies and asthma – Yvette Brazier – Medical News Today
Neonatal Gut Bacteria Might Promote Asthma. Byproducts of gut microbes in some 1-month–old babies trigger inflammation that is linked to later asthma development, researchers find. – Anna Azvolinsky – The Scientist

Human urinary tract microbiome

Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance – Asha Rani – Translational Research

Human gut microbiome

Gut bacterial microbiota in psoriasis: A case control study – Doaa Masallat – African Journal of Microbiology Research

Review: Cognitive Function and the Microbiome – M.G. Gareau – International Review of Neurobiology

Review: Advances in Gut Microbiome Research and Relevance to Pediatric Diseases – Lindsey Albenberg – The Journal of Pediatrics

Animal experiments

Monitoring perinatal gut microbiota in mouse models by mass spectrometry approaches: parental genetic background and breastfeeding effects – Stefano Levi Mortera – Frontiers in Microbiology

Functional characteristics of the gut microbiome in C57BL/6 mice differentially susceptible to Plasmodium yoelii – Joshua M. Stough – Frontiers in Microbiology

Modulation of the bifidobacterial communities of the dog microbiota by zeolite – Alberto Sabbioni – Frontiers in Microbiology

Animal microbiome

The microbiome of a striped dolphin (Stenella coeruleoalba) stranded in Portugal – Filipa Godoy-Vitorino – Research in Microbiology

Book Chapter: Microbial Interactions on Coral Surfaces and Within the Coral Holobiont – Max Teplitski – The Cnidaria, Past, Present and Future

Book Chapter: Association of Coral-Microbes, and the Ecological Roles of Microbial Symbionts in Corals – Wei Sun – The Cnidaria, Past, Present and Future

Human Lice in Paleoentomology and Paleomicrobiology – Rezak Drali – ASM Microbiology Spectrum

Plant, root, and soil microbiome

Resource partitioning between bacteria, fungi and protists in the detritusphere of an agricultural soil – Susanne Kramer – Frontiers in Microbiology

Composition and activity of soil microbial communities in different types of temperate forests – Marcin Chodak – Biology and Fertility of Soils

The effect of the Falcon 460 EC fungicide on soil microbial communities, enzyme activities and plant growth – Małgorzata Baćmaga – Ecotoxicology

Review: Plant microbe interactions in post genomic era: perspectives and applications – Jahangir Imam – Frontiers in Microbiology

Water microbiome

Quantification of viral and prokaryotic production rates in benthic ecosystems: a methods comparison – Eugenio Rastelli – Frontiers in Microbiology

Microbiome of death

Cadavers in Canada: Book Chapter: Changes in Soil Microbial Activity Following Cadaver Decomposition During Spring and Summer Months in Southern Ontario – Heloise A. Breton – Soil in Criminal and Environmental Forensics

Wastewater and pollution microbiology

Poster: MiDAS: A curated database for the microorganisms of activated sludge and anaerobic digesters – Simon Jon McIlroy – Water Engineering and Biofilm IWA Specialist Conference, 2016

Probiotics

Layer-by-Layer Encapsulation of Probiotics for Delivery to the Microbiome – Aaron C. Anselmo – Advanced Materials

Food microbiology

Book: Functional Nucleic Acids Detection in Food Safety: Theories and Applications – Wentao Xu – Springer

Microbial ecology

Aligning the Measurement of Microbial Diversity with Macroecological Theory – James C. Stegen – Frontiers in Microbiology

Editorial: Insights into microbe-microbe interactions in human microbial ecosystems: strategies to be competitive – Nuria Salazar – Frontiers in Microbiology

Bioinformatics and metagenomics

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies – Benjamin R.K. Roller – Nature Microbiology

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers – Michelle Davison – PLOS ONE

SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes – Carmen H.S. Chan – Computational Biology and Chemistry

Review: Advances in biodiversity: metagenomics and the unveiling of biological dark matter – Robert J. Robbins – Standards in Genomic Sciences

Microbes in the news

What we have in common with corals and their unexplored microbial world – Alejandra Hernandez – The Conversation

August 27, 2016

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Gut microbiome in pre-Columbian mummies, spacecraft assembly cleanrooms, smokeless tobacco products, time series data, and a return of the Musical Microbes.

Human skin microbiome

Skin fungal community and its correlation with bacterial community of urban Chinese individuals – Marcus H. Y. Leung – Microbiome

Human oral microbiome

High-throughput quantitative method for assessing coaggregation among oral bacterial species – E. Levin-Sparenberg – Letters in Applied Microbiology

Human gut microbiome

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies – Tasha M. Santiago-Rodriguez – FEMS Microbiology Ecology

Note: unclear definition of “redemption”; means that a medication prescription was filled. Broad-Spectrum Antibiotic Treatment and Subsequent Childhood Type 1 Diabetes: A Nationwide Danish Cohort Study – Tine D. Clausen – PLOS ONE

Animal experiments

Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits – Y. Zhu – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Endolithic microbial diversity in sandstone and granite from the McMurdo Dry Valleys, Antarctica – Stephen D. J. Archer – Polar Biology

Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System – Rodrigo Gouvêa Taketani – Microbial Ecology

Review: Bacteria in decomposing wood and their interactions with wood-decay fungi – Sarah R. Johnston – FEMS Microbiology Ecology

Water microbiome

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution – Francisco J. R. C. Coelho – Molecular Ecology

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities – Anders Lanzén – Molecular Ecology

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification – Eric A. Dubinsky – Water Research

Spacecraft microbiome

Functional metagenomics of spacecraft assembly cleanrooms: Presence of virulence factors associated with human pathogens – Mina Bashir – Frontiers in Microbiology

Tobacco microbiome

Bacterial Populations Associated with Smokeless Tobacco Products – Jing Han – Applied and Environmental Microbiology

Bacteria in smokeless tobacco products may be a health concern – American Society for Microbiology
http://www.asm.org/index.php/journal-press-releases/94525-bacteria-in-smokeless-tobacco-products-may-be-a-health-concern
Proteomics

Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS – Jing Wu – Journal of Proteome Research

Bioinformatics, metagenomics, and statistics

Modeling time-series data from microbial communities – Benjamin J Ridenhour – bioRxiv

Improving ancient DNA genome assembly – Alexander Seitz – PeerJ Preprint

More microbiology

The Musical Microbes are back! Influence of a mono-frequency sound on bacteria can be a function of the sound-level – Vijay Kothari – bioRxiv

Microbes in the news

Focus: California drought reducing beach bacteria: Reduced runoff has meant fewer health advisories, data show – Daniel Wheaton – San Diego Union Tribune
Mystery Solved: How Lyme Disease Bacteria Spread Around the Body – Rachael Rettner – LiveScience

In sub-Saharan Africa, cancer can be an infectious disease – ScienceDaily

#BacteriaHysteria: You Should Never Ask For a Slice Of Lemon In Your Drink – Alice Sholl – Yahoo

Science, publishing, and career

There Was A Huge Outpouring Of Support For This Little Girl Who Got Bullied For Loving Bugs. Let Sophia play with her bugs! – Ishmael N. Daro – BuzzFeed

August 24, 2016

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Revisiting obesity and microbiome links, movies of Vibrio growing in biofilms, and decomposing chickens (yum)!

My apologies for not having had a lot of time to keep up with the literature. I’m now running all searches after work hours. This week we have friends over from Europe, and after 7 pm, my friends go before work ! Here is what I have so far, but it’s not as recent as I would like it to be. Hopefully I will have some time in the weekend to catch up.

Jobs and events

Postdoc Position in Bioinformatics, Metagenomics and the Human Microbiome – Jeroen Raes group, Leuven, Belgium

Human Microbiome Journal Club, Friday August 26: What is the most appropriate method for associating microbiome data with health and disease?

Human gut microbiome

Previously on bioRxiv, now published: Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome – Marc A. Sze, Patrick D. Schloss – mBio

No, your gut bacteria ISN’T making you fat: Scientists find ‘no difference’ between the microbes in obese and thin people’s stomachs – Daily Mail

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Systematic Review: Adverse Events of Fecal Microbiota Transplantation – Sinan Wang – PLOS ONE

Animal microbiome

Nutrition mediates the expression of cultivar–farmer conflict in a fungus-growing ant – Jonathan Z. Shik – PNAS

Water microbiome

Distinct bacterial communities in surficial seafloor sediments following the 2010 Deepwater Horizon blowout – Tingting Yang – Frontiers in Microbiology

Microbiome of death

Effect of Substrate on Identification of Microbial Communities in Poultry Carcass Composting and Microorganisms Associated with Poultry Carcass Decomposition – Jie Wang – Journal of Agricultural and Food Chemistry

Bioinformatics and metagenomics

Using Dendritic Heat Maps to Simultaneously Display Genotype Divergence with Phenotype Divergence – Matthew Kellom – PLOS ONE

Microbial Ecology

Review: Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System – Adrian Ho – Frontiers in Microbiology

More microbiology

Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging – Jing Yan – PNAS

Comparative genomics of biotechnologically important yeasts – Robert Riley – PNAS

Microbes in the news

Great Moments in Science: The microscopic high-tech wizardry of bacteria – Karl Kruszelnicki – ABC Australia

Bacteria are the probably cause of barnacles sticking to boats – battling biofouling with biology – Mary Beth Griggs – PopSci

Bacteria Hysteria

Your Bed Is A Hotbed Of Bacteria – Joy D’Souza – Huffington Post Canada
Bacteria in your Bed – “study” sponsored by AmeriSleep (huge CoI)

Science, publishing, and career

Including Diverse Voices in Science Stories –  Christina Selby – The Open Notebook