Monthly Archives: June 2017

June 18, 2017

Posted on by

Quite a large Digest for a Sunday, with most picks being on soil microbiome and some interesting animal papers including how microbial genetic composition may tune host longevity (Bing Han – Cell)

General microbiome

Reply to Wang and Chen: An ancient origin of magnetotactic bacteria – Wei Lin – Proceedings of the National Academy of Sciences of the United States of America

Microbiome and Longevity: Gut Microbes Send Signals to Host Mitochondria – Jan Gruber – Cell

Human gut microbiome

The Human Microbiome and the Missing Heritability Problem – Santiago Sandoval-Motta – Frontiers in Genetics

Bacteriophages important for FMT efficacy – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Postmortem succession of gut microbial communities in deceased human subjects – Jennifer M. DeBruyn – Peerj

Urinary metabolic insights into host-gut microbial interactions in healthy and IBD children – Francois-Pierre Martin – World Journal of Gastroenterology

Animal experiments

Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Vitamin A deficiency in mice results in a hypermetabolic state, dysbiosis and alterations in bacterial metabolism – Yuan Tian – The Journal of Immunology

Host–microbiota interactions in Caenorhabditis elegans and their significance – Michael Shapira – Current Opinion in Microbiology

Microbial Genetic Composition Tunes Host Longevity – Bing Han – Cell

Probabilistic Invasion Underlies Natural Gut Microbiome Stability – Benjamin Obadia – Current Biology

Animal microbiome

Metagenomic survey of bacteria associated with the invasive ladybird Harmonia axyridis (Coleoptera: Coccinellidae) – Krzysztof Dudek – European Journal of Entomology

Plant, root, and soil microbiome

Microbial mechanisms controlling the rhizosphere effect of ryegrass on degradation of polycyclic aromatic hydrocarbons in an aged-contaminated agricultural soil – Meixia Guo – Soil Biology and Biochemistry

Illumina-Based Analysis of Bulk and Rhizosphere Soil Bacterial Communities in Paddy Fields Under Mixed Heavy Metal Contamination – HE Huaidong  – Pedosphere

Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) – Zheng-Fei Yan – International Journal of Systematic and Evolutionary Microbiology

The role of Plant Growth Promoting Bacteria in improving nitrogen use efficiency for sustainable crop production: a focus on wheat – Nilde Antonella Di Benedetto – AIMS Microbiology Special Issue: Plant probiotic bacteria: solutions to feed the World

Molecular Communication and Nutrient Transfer of Arbuscular Mycorrhizal Fungi, Symbiotic Nitrogen-Fixing Bacteria, and Host Plant in Tripartite Symbiosis – Chunling Chang – Legume Nitrogen Fixation in Soils with Low Phosphorus Availability

Experimental study on the effects of underground CO2 leakage on soil microbial consortia – Fu Chen – International Journal of Greenhouse Gas Control

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

In vitro and in silico characterization of metagenomic soil-derived cellulases capable of hydrolyzing oil palm empty fruit bunch – Laura Marcela Palma Medina – Biotechnology Reports

The impacts of organic amendments: Do they confer stability against drought on the soil microbial community? – F. Bastida – Soil Biology and Biochemistry

Techniques

Review: Harnessing Whole Genome Sequencing in Medical Mycology – Christina A Cuomo – Current Fungal Infection Reports

From complex gut communities to minimal microbiomes via cultivation – Thomas Clavel – Current Opinion in Microbiology

Microbes in the news

Microbiome ‘fingerprint’ shows donor microbes persist in fecal transplant recipients –R Kumar – Healio Gastroenterology

New Pasteurization Alternative Sanitizes Milk Without Killing Good Bacteria – Luke Dormehl – Digitaltrends

Gut Bacteria May Help Slow Down Process of Ageing – NDTV

Gut microbiota – Tiny helpers against Samonella – Innovations-report

June 17, 2017

Posted on by

Today: A few job searches, a lot of microbes in the news (as we all ponder our bread choices), and some articles about microbes in the wild.

Events and jobs

Assistant Professor-Microbiology (Tenure-Track) – The College of New Jersey

Microbiology Technician – Matchtech, England

Microbiology Analyst – Stericycle, Massachusetts

Animal microbiome

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Springer et al, Ecology and Evolution

Water and extremophile microbiome

Undocumented Potential For Primary Productivity In A Globally-Distributed Bacterial Photoautotroph – Graham et al, bioRxiv (pre-print)

Microbes in the news

White or Whole Wheat Bread Study May Shed Light on Diet Failure – Patrick Keeffe, HealthLine

Gene transfer keeps bacteria fit – University of Basel, Phys.org

In dying, blood-starved heart, bacteria injections offer cellular life support – Beth Mole, Ars Technica

New antibiotic effective against drug-resistant bacteria – Rutgers University, Science Daily

June 16, 2017

Posted on by

Gut microbiome focus: Differences in the gut microbiome between children and adults can mediate the metabolism of arsenic possibly leading to differences in exposure risk, the gut microbiome’s ability to protect against salmonella infection is dependent on the IFNy producing bacteria, the microbiome of insoluble fibre is characterized, and a new in vitro technique to interrogate intestinal transport of microbiota and antigens. Plus an overview of the world data centre for microorganisms, and MicroScope for microbial genome annotation. 

  • Events and jobs

Microbiology Technologist OR Microbiology Medical Technologist – Orlando Florida  

*****************************

  • General microbiome

Conference: Current concepts in chronic inflammatory diseases: Interactions between microbes, cellular metabolism, and inflammation – Holger Garn – Allergy and Clinical Immunology

  • Human oral microbiome

Characterisation of Roseomonas mucosa isolated from the root canal of an infected tooth – Nina Diesendorf – BMC Research Notes

  • Human gut microbiome

* Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model – Naiyi Yin – Chemosphere

* Inter-individual differences determine the outcome of wheat bran colonization by the human gut microbiome – Kim De Paepe – Environmental Microbiology

Review: Microbiota Therapy for Clostridium difficile and Antibiotic Resistant Enteric Infections – Brittany Lewis – Annual Review of Microbiology

*****************************

  • Animal experiments

* Enhancement of IFNγ Production by Distinct Commensals Ameliorates Salmonella-Induced Disease – Sophie Thiemann – Cell Host and Microbe

Efficacy of antibiotic treatment of implant-associated Staphylococcus aureus infections with moxifloxacin, flucloxacillin, rifampin, and combination therapy: an animal study – Felix Greimel – Drug Design, Development and Therapy

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam Burns – Current Opinion in Microbiology

IL-17 Receptor A Maintains and Protects the Skin Barrier To Prevent Allergic Skin Inflammation – Achilleas Floudas – The Journal of Immunology

Irf4-dependent CD103+CD11b+ dendritic cells and the intestinal microbiome regulate monocyte and macrophage activation and intestinal peristalsis in postoperative ileus – Judith-Mira Pohl – Gut

  • Animal microbiome

Effect of three lactobacilli with strain-specific activities on the growth performance, faecal microbiota and ileum mucosa proteomics of piglets – Yating Su – Journal of Animal Science and Biotechnology

  • Plant, root, and soil microbiome

Characterization of the regulation of a plant polysaccharide utilization operon and its role in biofilm formation in Bacillus subtilis – Cameron Habib – PLOSone

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function – Sebastian Flues – Environmental Microbiology

Green alder (Alnus viridis) encroachment shapes microbial communities in subalpine soils and impacts its bacterial or fungal symbionts differently – G Schwob – Environmental Microbiology

The role of organic acids on microbial deterioration in the Radix pseudostellariae rhizosphere under continuous monoculture regimes – Hongmiao Wu – Scientific Reports

Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization – María Eugenia Salas – Environmental Microbiology

  • Water and extremophile microbiome

Cascading influence of inorganic nitrogen sources on DOM production, composition, lability and microbial community structure in the open ocean – SJ Goldberg – Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment, and water bacterial communities – Arthur Escalas – Environmental Microbiology

*****************************

  • Phages and viruses

Preprint: Bacteria defend against phages through type IV pilus glycosylation – Hanjeong Harvey- bioRxiv

  • Techniques

Dissecting the human microbiome with single-cell genomics – Andrew Tolonen – Genome Medicine

* A human intestinal M-cell-like model for investigating particle, antigen and microorganism translocation – Ana Beloqui – Nature Protocols

  • Metagenomics

* World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide – Linhuan Wu – Nucleic Acids Research

* MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes – David Vallenet – Nucleic Acids Research

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome – Fergus Collins – Scientific Reports

Screening and characterization of a novel thermostable lipase with detergent-additive potential from the metagenomic library of a mangrove soil – Leli Tang – Gene

  • Microbial Physiology

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

Preprint: Campylobacter jejuni transcriptome changes during loss of culturability in water – Christina Bronowski – bioRxiv

*****************************

  • Microbes in the news

You Are What You Eat, And What You Eat Is Millions of Microbes – Kyle Frischkorn – Smithsonian.com

John Bartlett’s Take on Critical Infectious Disease Topics: Part 3 – John Bartlett – Medscape

Placental Microbiome – Sally Robertson – Life Sciences News

Light-activated bacteria protect rats from heart attacks – Michael Price – Science

These light-eating bacteria could one day help us survive heart attacks – Alessandra Potenza – The Verge

Scientists image molecular machinery never before seen in bacteria – Brooke Hays – UPI

June 15, 2017

Posted on by

Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

June 14, 2017

Posted on by

Still quite a few articles on rhizosphere, and antibiotic resistance remains a hot topic, both in the literature and media. How about a Micro-lympics?

Jobs

Microbiology Technician – Seattle Washington

Events

*Annual Microbiology Retreat µlympics – Indiana University

General microbiology

*Commentary: History of Medicine: Origin of the Term Microbiome and why it Matters – Susan L. Prescott – Human Microbiome Journal

A Stoichioproteomic Analysis of Samples from the Human Microbiome Project – Briana Vecchio-Pagan – Frontiers in Microbiology

Adaptor protein mediates dynamic pump assembly for bacterial metal efflux – Ace George Santiago et al. – PNAS

Press: E. coli bacteria’s defense secret revealed – Bill Steele – Phys.org

Uncharacterized bacterial structures revealed by electron cryotomography – Megan J. Dobro et al. – Journal of Bacteriology

Press: Researchers discover new structures in bacteria, seek to determine function – Phys.org

Microbots decorated with silver nanoparticles kill bacteria in aqueous media – Diana Vilela et al. – Applied Materials and Interfaces

Human gut microbiome

Book chapter: The gut microbiome and inflammatory bowel disease – Maire A. Conrad et al. – Pediatric Inflammatory Bowel Disease (Ed. Petar Mamula et al.)

Quantitative systems pharmacology and the personalized drug-microbiota-diet axis – Ines Thiele et al. – Current Opinion in Systems Biology

Human nearly-sterile sites

Endometrial microbiota—new player in town – Inmaculada Moreno & Jason M. Franasiak – Fertility and Sterility

Contributions of the maternal oral and gut microbiome to placental microbial colonization in overweight and obese pregnant women – Luisa F. Gomez-Arango et al. – Scientific Reports

Plant, root and soil microbiome

Stability and dynamics of enzyme activity patterns in the rice rhizosphere: Effects of plant growth and temperature – Tida Ge et al. – Soil Biology and Biochemistry

Doctoral thesis: Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes – Hua Xiao – Virginia Tech

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac – Jinping Wu et al. – World Journal of Microbiology and Biotechnology

*Fishing bacteria with a nanonet – F. De Cesare et al. – Materials Today

Isolation, identification, characterization, and screening of rhizospheric bacteria for herbicidal activity – Charles Oluwaseun Adetunji et al. – Organic Agriculture

Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US – Chuntao Yin et al. – Phytobiomes

*Dispersal enhances beta diversity in nectar microbes – Rachel L. Vannette & Tadashi Fukami – Ecology Letters

Temporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes – Florine Degrune et al. – Frontiers in Microbiology

Water and extremophile microbiome

Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste – German A. Estrada-Bonilla et al. – Systematic and Applied Microbiology

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor – Noah Stern et al. – Applied and Environmental Microbiology

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – I.L. Angell et al. – Letters in Applied Microbiology

Built environment

The bacterial composition of ventilation filter dust in Norwegian pre-school nurseries – Anders B Nygaard & Colin Charnock – Indoor and Built Environment

Factors Determining the Biodiversity of Halophilic Microorganisms on Historic Masonry Buildings – Anna Otlewska et al. – Microbes and Environments

Phages and viruses

The pepper virome: natural co-infection of diverse viruses and their quasispecies – Yeonhwa Jo et al. – BMC Genomics

Bioinformatics

A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni et al. – Journal of Microbiological Methods

*PrePrint: Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software – Alexander Sczyrba et al. – bioRxiv

Microbes in the news

Live antibiotics use bacteria to kill bacteria – Elizabeth Eaton – Science News

Will a New Drug to Fight Antibiotic Resistant Bacteria Really Work? – Shawn Radcliffe – Healthline news

Former Pfizer Scientist Is Resurrecting Projects To Solve The Multidrug Resistant Bacteria Problem – John LaMattina – Forbes

The Algae That Devastated Florida’s Coasts Also Contained 28 Kinds Of Bacteria, Study Finds – Kate Stein – WGCU

Microbes on the market

DoggyBiome: studying the microbiome to improve dog health – AnimalBiome – Backerkit

Science, career and publishing

Book chapter: Women of Science – Laura E. Willis – Viewpoints on Media Effects: Pseudo-reality and Its Influence on Media Consumers (Ed. Carol M. Madere)

PrePrint: An elective course for medical students on innovation and entrepreneurship – Erik Reinertsen et al. – bioRxiv

June 13, 2017

Posted on by

Excellent reviews across all sections, with many from the Nature Journals. Also, multiple articles on the tree of life and animal experiments.

General microbiome
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life – Supratim Mukherjee – Nature Biotechnology

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes – Violette Da Cunha – PLoS Genetics

Review: Natural Products and the Gene Cluster Revolution – Paul R. Jensen – Trends in Microbiology

Pregnancy and early life
Review: How nutrition and the maternal microbiota shape the neonatal immune system – Andrew J. MacPherson – Nature Reviews Immunology

Multi-site human microbiome
Review: Role of oral and gut microbiome in nitric oxide mediated colon motility – Miriam Y. Walker – Nitric Oxide

Human skin microbiome
Review: Chemical signaling in mosquito–host interactions: the role of human skin microbiota – William Takken – Current Opinion in Insect Science

Human oral microbiome
Reduced Susceptibility to Antiseptics Is Conferred by Heterologous Housekeeping Genes – Supathep Tansirichaiya – Microbial Drug Resistance

Human gut microbiome
*Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae – Derrick R. Samuelson – PLoS Pathogens

Review: Fungal dysbiosis: immunity and interactions at mucosal barriers – Ilian D. Iliev – Nature Reviews Immunology

Review: Transmission of the gut microbiota: spreading of health – Hilary P. Browne – Nature Reviews Microbiology

Editorial: Post-dieting weight gain: the role of persistent microbiome changes – Christoph A Thaiss – Future Microbiology

Animal experiments
*Thermoneutral housing exacerbates nonalcoholic fatty liver disease in mice and allows for sex-independent disease modeling – Daniel A. Giles – Nature Medicine

*Cold-induced conversion of cholesterol to bile acids in mice shapes the gut microbiome and promotes adaptive thermogenesis – A. Worthmann – Nature Medicine

Integrated Metagenomic Analyses of the Rumen Microbiome of Cattles Reveals Key Biological Mechanisms Associated with Methane Traits – Haiying Wang – Methods

Long-term multi-species Lactobacillus and Bifidobacterium dietary supplement enhances memory and changes regional brain metabolites in middle-aged rats – Caroline O’Hagan – Neurobiology of Learning and Memory

Soy compared with milk protein in a Western diet changes fecal microbiota and decreases hepatic steatosis in obese OLETF rats – Matthew R. Panasevich – Journal of Nutritional Biochemistry

Targeted metabolomics analysis of aromatic amino acids and their gut microbiota-host co-metabolites in rat serum and urine by liquid chromatography with tandem mass spectrometry – Yifeng Zeng – Journal of Separation Science

Effect of cocoa’s theobromine on intestinal microbiota of rats – Sandra Martin-Pelaez – Molecular Nutrition and Food Research

Water and extremophile microbiome
Review: Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems – Alan W. Decho – Frontiers in Microbiology

Review: Linking genes to microbial biogeochemical cycling: lessons from arsenic – Yong-Guan Zhu – Environmental Science and Technology

Food microbiology
Review: Extremozymes from metagenome: Potential applications in food processing – Mahejibin Khan – Critical Reviews in Food Science and Nutrition

Phages and viruses
Review: Interplay between viruses and bacterial microbiota in cancer development – Dariia Vyshenska – Seminars in Immunology

Bioinformatics
A novel method to determine the minimum number of sequences required for reliable microbial community analysis – Jiajia Ni – Journal of Microbiological Methods

Power and sample size calculations for high-throughput sequencing-based experiments – Chung-I Li – Briefings in Bioinformatics
Only a short section on microbiome.

Techniques
*A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis – Spencer R. Scott – Nature Microbiology

Body fluid prediction from microbial patterns for forensic application – Eirik Nataas Hanssen – Forensic Science International: Genetics

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinIONTM portable nanopore sequencer – Alfonso Benítez-Páez – GigaScience

Review: Phenotyping of gut microbiota: Focus on capillary electrophoresis – Manuel Ferrer – Electrophoresis

Review: Panacea in progress: CRISPR and the future of its biological research introduction – Michael Carroll – Microbiological Research

June 12, 2017

Posted on by

An unusually quiet Monday to start your week of microbiome literature. In the methods section, some new protocols from Springer’s “Diagnostic Bacteriology” volume. Enjoy!

General microbiome

Review: Influences of environmental bacteria and their metabolites on allergies, asthma and host microbiota
G Jatzlauk et al. – Allergy

Human gut microbiome

Microbiome and NAFLD: Potential Influence of Aerobic Fitness and Lifestyle Modification
Matthew R. Panasevich – Physiological Genomics

Mucosa-associated microbiota signature in colorectal cancer
R. Gao et al. – European Journal of Clinical Microbiology & Infectious Diseases

Microbial diseases

Pre-print: Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA
Maho Yokoyama et al. – bioRxiv

Animal experiments

Alteration of gut microbiota in association with cholesterol gallstone formation in mice
Qihan Wang et al – BMC Gastroenterology

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts
Meriem Belheouane et al. – Microbiome

Animal microbiome

Symbionts in waiting: the dynamics of incipient endosymbiont complementation and replacement in minimal bacterial communities of psyllids
Jennifer L. Morrow et al – Microbiome

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome
Sara M. Wolff et al – Microbiome

Plant, root, and soil microbiome

Novel microbial assemblages dominate weathered sulfide-bearing rock from copper-nickel deposits in the Duluth Complex, Minnesota, USA
DS Jones et al. – Applied and Environmental Microbiology

Water, estuarine and sediment microbiome

Colonization habitat controls biomass, composition, and metabolic activity of attached microbial communities in the Columbia River hyporheic corridor
N Stern et al. – Applied and Environmental Microbiology

Microbial biotechnology

Efficacy of Bacillus amyloliquefaciens as biocontrol agent to fight fungal diseases of maize under tropical climates: from lab to field assays in south Kivu
Parent Zihalirwa Kulimushi et al. – Environmental Science and Pollution Research

Food microbiology

RNA-based amplicon sequencing highlights the impact of the processing technology on microbiota composition of artisanal and industrial PDO Lard d’Arnad
I Ferrocino et al. – Applied and Environmental Microbiology

General microbiology and evolution

Nitrogen-source stabilization of quorum sensing in the Pseudomonas aeruginosa bioaugmentation strain SD-1
M Wang et al – Applied and Environmental Microbiology

Phages and viruses

Pre-print: Gene networks provide a high-resolution view of bacteriophage ecology
Jason Shapiro & Catherine Putonti – bioRxiv

Bioinformatics and statistics

MetabolitePredict: a de-novo human metabolomics prediction system and its applications in rheumatoid arthritis
Quan Qiu Wang & Rong Xu – Journal of Biomedical Informatics

Techniques and methods

Protocol: Detection of Helicobacter pylori in the Gastric Mucosa by Fluorescence In Vivo Hybridization
Silvia Fontenete et al. – Diagnostic Bacteriology

Protocol: Detection of Helicobacter pylori DNA in Formalin-Fixed Paraffin-Embedded Gastric Biopsies Using Laser Microdissection and qPCR
María Fernanda Loayza Villa et al. – Diagnostic Bacteriology

Protocol: Characterization of Sinus Microbiota by 16S Sequencing from Swabs
Thad W. Vickery et al. – Diagnostic Bacteriology

Protocol: Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples
Amanda Claire Brown & Mette T. Christiansen

Microbes in the news

Bacteria Behind Legionnaires’ Disease Found at New York Police Station
Ashley Southall – The New York Times

Science, publishing, and career

Microbiology Graduate Program – University of California

11 June, 2017

Posted on by

Events and jobs

Doctoral researcher in Microbiology/Virology – Helmholtz Centre for Environmental Research – UFZ – Germany

General microbiome

Review: Role of Gut Microbiota in Rheumatoid Arthritis – Y. Maeda – Journal of Clinical Medicine
Review: The Mycobiome: Impact on Health and Disease States –  N. El-Jurdi – Microbiology Spectrum

Pregnancy and early life

Review: Early-Life Host–Microbiome Interphase: The Key Frontier for Immune Development – N. Amenyogbe – Frontiers in Pediatrics

Human skin microbiome

Temporal Dynamics Of Relative Abundances And Bacterial Succession In Chronic Wound Communities – C.D. Tipton – Wound Repair and Regeneration

Human vaginal microbiome

Therapeutic Opportunities in the Vaginal Microbiome – G. Reid – Microbiology Spectrum

Human gut microbiome

Review: Microbial Impact on Host Metabolism: Opportunities for Novel Treatments of Nutritional Disorders? – H. Plovier – Microbiology Spectrum
Nickel-resistant bacteria isolated in human microbiome – E.A. Lusi – New Microbes and New Infections

Animal experiments

Keratin 8 reduces colonic permeability and maintains gut microbiota homeostasis, protecting against colitis and colitisassociated tumorigenesis – C. Liu – Oncotarget
Evolution of commensal bacteria in the intestinal tract of mice – A. Sousa – Current Opinion in Microbiology

Animal microbiome

Gut Microbiota Dysbiosis in Postweaning Piglets: Understanding the Keys to Health – R. Gresse – Trends in Microbiology
Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome – S.M. Wolff – Microbiome

Plant, root, and soil microbiome

Community analysis of Persian oak fungal microbiome under dust storm conditions – N.H. Doust – Fungal Ecology
Maternal effects on phenotype, resistance and the structuring of fungal communities in Eucalyptus grandis – M. Vivas – Environmental and Experimental Botany
Review: Iron and Immunity – E.H. Verbon – Annual Review of Phytopathology
Dispersal enhances beta diversity in nectar microbes – R.L. Vannette – Ecology Letters

Water and extremophile microbiome

Application of long amplicon propidium monoazide-PCR to assess the effects of temperature and background microbiota on pathogens in river water – A. Banihashemi – Journal of Water and Health

Microbes in the news

Gut bacteria can stop cancer drugs from working – S. Reardon – Nature News
Fungi revive starving bacteria – K. Evans – Labroots
Did the microbiome help drive human evolution? – S.E. Erdman – STAT news

June 10, 2017

Posted on by

Jobs and events

Two tenure-track assistant professor or associate professors – Department of Plant and Microbial Biology – College of Biological Sciences, University of Minnesota

Sign up for the webinar by Edward Messick, GENEWIZ – Topic: Metagenomics for Biomarker Discovery: Applications in Precision Medicine – Webinar date and time: June 14, 2017 at 5 PM

 

General microbiome

Ferrous Iron Efflux Systems in Bacteria – H Pi – Metallomics

Metagenomics of microbial and viral life in terrestrial geothermal environments – A Strazzulli – Reviews in Environmental Science and Bio/Technology

Bacterial Infections in Neonates Following Mupirocin-Based MRSA Decolonization: A Multicenter Cohort Study – R Pierce – Infection Control & Hospital Epidemiology

 

Human gut microbiome

Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model –  N Yin – Chemosphere

Report: Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases – SC Kleiman – European Eating Disorders Review

 

Animal experiment

A Targeted Metabolomics Analysis Identifies Intestinal Microbiota-Derived Urinary Biomarkers of Colonization Resistance in Antibiotic-Treated Mice – ME Obrenovich – Antimicrobial Agents and Chemotherapy

 

Animal microbiome

Molecular dialogues with the microbiota: Lessons from the zebrafish intestine – K Guillemin – Mechanisms of Development

 

Plant, root and soil microbiome

The nodule microbiome; N2-fixing rhizobia do not live alone  – P  Martínez-Hidalgo – Phytobiomes Journal

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity – X Zhang – Global Change Biology

Turnover of carbon and phosphorus in the microbial biomass depending on phosphorus availability – M Spohn – Soil Biology and Biochemistry

Effect of soil preparation techniques on the biochemical properties and microbial communities of a citrus orchard after replanting and conversion into organic management – A Pérez-Piqueres – Applied Soil Ecology

 

Water microbiome and extremophile

Review: The Vulnerability and Resilience of Reef-Building Corals – HM Putnam – Current Biology

Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing – X Lin – Acta Oceanologica Sinica

Genetic diversity of nitrate reducing bacteria in marine and brackish water nitrifying bacterial consortia generated for activating nitrifying bioreactors in recirculating aquaculture systems – PG Preena – Aquaculture Research

 

Techniques

Integrated transcriptomic, proteomic and epigenomic analysis of Plasmodium vivax salivary-gland sporozoites – A Jex – bioRxiv

Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis – NE Dina – Journal of Raman Spectroscopy

 

Metabolomics

Comparative metabolomics in vanilla pod and vanilla bean revealing the biosynthesis of vanillin during the curing process of vanilla –  F Gu – AMB Express

 

Phages

A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome – BJ O’ Hara – PLoS Genetics

 

Built environment microbiome

Warm and wet: robust lipase-producing bacteria from the indoor environment – K Tanner – bioRxiv

Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater – M Liu – Water Research

 

More microbes

Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances – PGE Kennedy – Viruses

Protozoa and microbiome  – SL Burgess – Infection and Immunity

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens  – JE Heindl – bioRxiv

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans – J Kaspar – bioRxiv

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle – SL Sokol – bioRxiv

 

Microbes in news

Engineering ‘good’ bacteria to kill bad ones – The Straits Times

White or wholemeal? It depends on your gut bacteria – A Middleton – Cosmos

Ixcela Announces Partnership with ORACLE TEAM USA to Improve Athletes’ Internal Health and Performance – Business Wire

New Study Finds Gut Bacteria May Inhibit Cancer Drugs – K Lant – Futurism

Therapy could stop superbugs on farms – P Ghosh – BBC News

SHU students travel to present phages research – P Parise – Setonian Online

June 9, 2017

Posted on by

Effects of prebiotics on body fat and gut microbiota of children, a review on the phage community of the human gut, a metabolomics study of the rodent brain to analyze the influence of gut bacteria.

Pregnancy and early life

Clostridium difficile colonization and/or infection during infancy and the risk of childhood allergic diseases – Sun Hwa Lee – Korean Journal of Pediatrics

Human vaginal microbiome

Association of vaginal dysbiosis and biofilm with contraceptive vaginal ring biomass in African women – Liselotte Hardy – PLOS ONE

Human gut microbiome

Age-Related Changes in the Composition of Gut Bifidobacterium Species – Kumiko Kato – Current Microbiology

Review: The low FODMAP diet: recent advances in understanding its mechanisms and efficacy in IBS – Heidi M Staudacher – Gut

Animal experiments

Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut – H J Wisselink – Poultry Science

Weaned beef calves fed selenium-biofortified alfalfa hay have an enriched nasal microbiota compared with healthy controls – Jean A Hall – PLOS ONE

The artificial sweetener acesulfame potassium affects the gut microbiome and body weight gain in CD-1 mice – Xiaoming Bian – PLOS ONE

Effects of different n-6 to n-3 polyunsaturated fatty acids ratio on reproductive performance, fecal microbiota and nutrient digestibility of gestation-lactating sows and suckling piglets – Jia Yin – Animal Science Journal

Nucleotide-binding oligomerization domain-containing protein 2 (Nod2) modulates T1DM susceptibility by gut microbiota – Yang-yang Li – Journal of Autoimmunity

Plant, root, and soil microbiome

Kinetic analysis of aerobic biotransformation pathways of a perfluorooctane sulfonate (PFOS) precursor in distinctly different soils – Lilan Zhang – Environmental Pollution

Plant breeding goes microbial – Zhong Wei – Trends in Plant Science

Atrazine, chlorpyrifos, and iprodione effect on the biodiversity of bacteria, actinomycetes, and fungi in a pilot biopurification system with a green cover – Sebastian Elgueta – Journal of Environmental Science and Health, Part B

Probiotics/prebiotics

Prebiotic Reduces Body Fat and Alters Intestinal Microbiota in Children With Overweight or Obesity – Alissa C Nicolucci – Gastroenterology

Phages and viruses

Review: The Human Gut Phage Community and Its Implications for Health and Disease – Pilar Manrique – Viruses

Metabolomics

Application of 1H NMR spectroscopy to the metabolic phenotyping of rodent brain extracts: A metabonomic study of gut microbial influence on host brain metabolism – J R Swann – Journal of Pharmaceutical and Biomedical Analysis

More microbes

Multi-locus and ultra-long amplicon sequencing approach to study microbial diversity at species level using the MinION(TM) portable nanopore sequencer – Alfonso Benítez-Páez – bioRxiv

ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species – Thomas M Nero – bioRxiv

Microbes in the news

Microbiology: Many forks make light work – ScienceDaily

Fungi awake bacteria from their slumber – ScienceDaily

Microbes on the market

Seres Completes Enrollment for SER-287 Phase 1b Clinical Trial in Patients with UC – Daniela Semedo – IBD News Today