Category Archives: Bik’s Non-Microbiology Picks

January 20, 2016

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Virome of children with diarrhea, bacterial communities in black truffles, arsenic biogeochemistry in an acid vapor-formed spring, distribution of microbes in microenvironments, and retraction of a PLOS ONE air microbiome paper.

Jobs and events

New job openings at Whole Biome: develops therapeutics and diagnostics targeting human microbiome, casual culture, and artisanal coffee

Human oral microbiome

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects – Jianye Zhou – PLOS ONE

Human respiratory microbiome

COPD is characterized by increased detection of Haemophilus influenzae, Streptococcus pneumoniae and a deficiency of Bacillus species – Jodie L. Simpson – Respirology

Human gut microbiome

The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin – Tung Gia Phan – Archives of Virology

Perspective: Gut microbiota and aging – Paul W. O’Toole – Science

Review: Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches – Montserrat Dueñas – MDPI Antioxidants

Animal models

Postnatal Hematopoiesis and Gut Microbiota in NOD Mice Deviate from C57BL/6 Mice – Dina Silke Malling Damlund – Journal of Diabetes Research

Bacterial profile and bone healing in rats receiving cancer therapeutic doses of bisphosphonates and corticosteroids: a pilot study – Z. Jabbour – International Journal of Oral & Maxillofacial Surgery

Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism – Robert Caesar – Journal of Lipid Research

Gut Microbiota Regulates K/BxN Autoimmune Arthritis through Follicular Helper T but Not Th17 Cells – Katharine E. Block – The Journal of Immunology

Editorial: Of Bugs and Drugs: How the Microbiome Controls Responsiveness to Antitumor Immunotherapy – Mandy L. Ford – American Journal of Transplantation

Animal microbiome

Most Low-Abundance “Background” Symbiodinium spp. Are Transitory and Have Minimal Functional Significance for Symbiotic Corals – Moo Joon Lee – Microbial Ecology

Isolation and assessment of gut bacteria from the Formosan subterranean termite, Coptotermes formosanus (Isoptera: Rhinotermitidae), for paratransgenesis research and application – Chinmay V. Tikhe – Insect Science

Plant, root, and soil microbiome

Black truffle: Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development – Aurélie Deveau – Mycorrhiza

Isolation of N2-fixing rhizobacteria from Lolium perenne and evaluating their plant growth promoting traits – Antonio Castellano-Hinojosa – Journal of Basic Microbiology

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees – J. B. Vincent – Molecular Ecology

Water, waste, and extremophile microbiome

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap – Xian Zhang – BMC Genetics

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China – Zhou Jiang – PLOS ONE

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla – Marian L. Schmidt – Environmental Microbiology

Food and cigarette microbiome

Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis – Robert E. Tyx – PLOS ONE

More microbes

Divorcing strain classification from species names – David Baltrus

Distributions of Virus-Like Particles and Prokaryotes within Microenvironments – Lisa M. Dann – PLOS ONE

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli –
Sophie J. Weiss – PLOS ONE

Microbes in the news

Satire: Dung Beetle A Bit Fed Up With Diet – The Allium

How Climate Change Endangers Microbes–And Why That’s Not a Good Thing – Aspen T. Reese – Scientific American

CDC issues guidance to help monitor pregnant women for Zika virus – Helen Branswell – STATnews

Microbes and art

These Close-Up Shots Of Kitchen Mold Are Oddly Appealing: Nikita Teryoshin, Max Slobodda / Küchendienst – FastCoDesign

Science, publishing, and career

Here are the 10 — yes, 10 — reasons PLOS ONE retracted this paper (“Metagenomic Human Repiratory Air in a Hospital Environment”) – Shannon Palus – Retraction Watch

Ten easy ways you can support diversity in academia in 2016 – Jacquelyn Gyll – The Contemplative Mammoth

Bik’s Picks

When chickens go wild. The feral chickens of Kauai provide a unique opportunity to study what happens when domesticated animals escape and evolve – Ewen Callaway – Nature
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January 18, 2016

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Skin fungi on astronauts before, during, and after a stay at the ISS, preventing obesity by stool transplants, and microbial landscapes of food production.

Human skin microbiome

Comprehensive analysis of the skin fungal microbiota of astronauts during a half-year stay at the International Space Station – Takashi Sugita – Medical Mycology

Human gut microbiome

Review: Can We Prevent Obesity-Related Metabolic Diseases by Dietary Modulation of the Gut Microbiota? – Lena K Brahe – Advances in Nutrition

Animal models

Gut microbiota lipopolysaccharide accelerates inflamm-aging in mice – Kyung-Ah Kim – BMC Microbiology

Microbiota Control of Malaria Transmission – Miguel P. Soares – Trends in Parasitology

Plant, root, and soil microbiome

Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition – J. Kohler – Journal of Environmental Management

Relevance of in vitro agar based screens to characterize the anti-fungal activities of bacterial endophyte communities – Hanan R. Shehata – BMC Microbiology

Food microbiology

A new perspective on microbial landscapes within food production – Nicholas A Bokulich – Current Opinion in Biotechnology

Metagenomics and bioinformatics

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis –
Veronika B. Dubinkina – BMC Bioinformatics

More microbiology

A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records – Tasnia Tahsin – Journal of the American Medical Informatics Association

Microbial stress priming – a meta-analysis – Diana R. Andrade-Linares – Environmental Microbiology

Microbes in the news

Corpse-eating bacteria a forensic tool – Viviane Richter – Cosmos

Olympus Voluntarily Recalls Medical Scope Accused Of Sickening Hundreds With Antibiotic-Resistant Infections – Jaleesa Baulkman – Medical Daily. See full report at Preventable Tragedies: Superbugs and How Ineffective Monitoring of
Medical Device Safety Fails Patients

Could a Poo Transplant Cure You? – Robynne Chutkan – The Huffington Post

Companies Aim to Make Drugs from Bacteria That Live in the Gut – Mike Orcutt – MIT Technology Review

Should You Eat Poop To Lose Weight? – Bruce Y. Lee – Forbes

A Judge Dismissed A Woman’s DWI Because Her Gut Makes Its Own Booze – Cat Ferguson – BuzzFeed

A Lesson in Lyme: What the Hell is a Spirochete? – Hannah Barry – The Lyme Life

Bacteria hysteria

Note: Sponsored by the Cleaning Industry Research Institute: Study Reveals High Bacteria Levels on Footwear – CIRI Science

Hotel Hygiene Exposed – Travel Math

Science, publishing, and career

Obama’s big bet on science: It’s about far more than a cancer ‘moonshot’ – Carl Zimmer – STATnews

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January 14, 2016

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Sorry for a late post today – I had a lot of meetings. Here is what I found:

Gut microbiota shaped via fecal microRNA, the microgenderome, dysbiosis in Vitiligo skin lesions, metatranscriptomics, and an 18th century Yersinia pestis.

General microbiome

Perspective: Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease – Niv Zmora – Cell Host & Microbe

The Human Microbiome: Opportunities for Dynamics, Systems, and Control
(based on the IFAC blog post Translate or Die) – Travis E. Gibson – Submitted to ACC 2016

Human skin microbiome

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects – Parul Ganju – Scientific Reports

Human oral microbiome

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing – Soo Eon Lee – Acta Odontologica Scandinavica

Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity – C Reilly – Oral Diseases

Commentary: A new association for the oral metagenome – Nicholas S Jakubovics – Oral Diseases

Human vaginal microbiome

Review: Vaginal microbiota and microbiome:- Role in health and disease – Dr Amit A. Rangari – Indian Journal of Basic and Applied Medical Research;

Human gut microbiome

Support for the Microgenderome: Associations in a Human Clinical Population – Amy Wallis – Scientific Reports

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota – Annett Klinder – Food & Function

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile – Ranjit Kumar – BMC Microbiology

Review: The microbiome and its implications in intestinal transplantation – Kroemer, Alexander – Current Opinion in Organ Transplantation

Animal models

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease – Karishma Kamdar – Cell Host & Microbe

The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell Host & Microbe

Animal microbiome

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica – Ngare Wilkinson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Culturable endophytic bacterial communities associated with field grown soybean – Karla Bianca de Almeida Lopes – Journal of Applied Microbiology

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture – Colin Averill – Global Change Biology

Water and waste microbiome

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water – Marta Gómez-Doñate – Microbiology Open

Bacterial diversity in oil-polluted marine coastal sediments – Alejandro Acosta-González – Current Opinion in Biotechnology

Spatial and temporal variability of bacterial communities in high alpine water spring sediments – Alfonso Esposito – Research in Microbiology

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation – Angelo Rubino – PLOS ONE

Metagenomics, metatranscriptomics, and bioinformatics

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – BioRxiv

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality – Yue Jiang – BMC Microbiome Journal

Viral metagenomics and blood safety – V. Sauvage – Transfusion Clinique et Biologique

Microbes in the news

Does our Microbiome Control Us or Do We Control It? – Dina Fine Maron – Scientific American

Your gut’s trick for controlling the bacteria that live in it – New Scientist

Mammals shape their microbiome to prevent disease – Science Codex

Low-Fiber Diets Cause Waves of Extinction in the Gut – Ed Yong – The Atlantic

Bad diets today can alter our great-great-grandkids’ biology – Katherine Ellen Foley – Quartz

Thoughtful and balanced comparison: mothur and QIIME – Pat Schloss – Mothur blog

Modifying the structure of wood alters plant microbiome – Science Daily

Gut Microbiome Similar in Formula- and Combination-Fed Babies – Troy Brown – MedScape

Eglin medical group first to find bacteria unseen in humans: Borrelia turicatae – Ilka Cole – US Air Force

Protecting the infant microbiome – Kathryn Kos – Examiner

Microbiology and art

Sunshine and microbiology inspire Reading artist’s work – Francesca Perryman – Get Reading

Science, publishing, and career

Re: Your Recent Email to Your Professor: Students who use emojis in their emails and write “heeeeelp!” in the subject line don’t necessarily know better.  – Paul T. Corrigan and Cameron Hunt McNabb – Inside Higher Education

ORCID: Publishers embrace scheme to end name confusion – John Bohannon – Science

Give teachers a physics test from a woman and they’ll give her worse grades – John Timmer – Ars Technica

Astronomy’s snowballing sexual harassment scandal picks up even more cases – Rachel Feltman – Washington Post

Bik’s Picks

Inside the Eye: Nature’s Most Exquisite Creation – Ed Yong – National Geographic
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January 13, 2016

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Frozen vs fresh stool transplants, the primate skin microbiome, diet-induced extinctions, bacteria in breast milk from low income Mexican-American moms, and engineered poplar tree endosphere.

Events

Tapping the Human Microbiome (Kavli Hangout) – Tuesday, Jan. 19, 1:30 pm EST, with Janet Jansson, Rob Knight, and Jeff Miller

Pregnancy and birth microbiome

Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children – Veronica Davé – Pediatric Research

Human vaginal microbiome

Review: Biotherapeutic agents and vaginal health – F. H. Al-Ghazzewi – Journal of Applied Microbiology

Human gut microbiome

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection – Christine H. Lee – JAMA

Small Intestine Bacterial Overgrowth and Environmental Enteropathy in Bangladeshi Children – Jeffrey R. Donowitz – mBio

Animal and bioreactor models

Diet-induced extinctions in the gut microbiota compound over generations – Erica D. Sonnenburg – Nature

Intestinal epithelial TLR4 signaling affects epithelial function, colonic microbiota and promotes risk for transmissible colitis – Rishu Dheer – Infection and Immunity

Modulation of the human gut microbiota by dietary fibres occurs at the species level – Wing Sun Faith Chung – BMC Biology

Animal microbiome

Diversity and evolution of the primate skin microbiome – Sarah E. Council – Proceedings of the Royal Society B

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification – N. S. Webster – Scientific Reports

Plant, root, and soil microbiome

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome – Bram Beckers – PNAS

Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests – Xiaoli Wang – Scientific Reports

Food microbiology

Seasonal and Growth-Dependent Dynamics of Bacterial Community in Radish Sprouts – Hiroshi Asakura – Journal of Food Safety

Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar – Sha Li – Applied Microbiology and Biotechnology

Transcriptomics

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline – Mark Davids – PLOS ONE

Metagenomics and bioinformatics

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome – Dingchen Li – Biology Direct

Microbes in the news

DNA Genotek’s microbiome collection and stabilization blog – Lisa Gamwell – The Microbiome Snapshot

Human trials will test freeze-dried poop pills as a weight-loss treatment – David Nield – Science Alert

What is Zika virus? Interview with Derek Gatherer – Microbe Post

E. coli Slinky: Revealed: the awful anchor that lets urinary tract infections take hold – Josh Barney – University of Virginia

Bik’s Picks

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces – Michael J. Ford – PLOS ONE

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January 9, 2016

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Microbiomes of musk deer, Tasmanian Devils, Panamanian frogs, roots of truffle-associated Douglas firs, and the Great Barrier Reef lagoon.

General human microbiome

Editorial: Getting fat from an inflamed relationship? The revenge of the holobiont
Andrew Moore – BioEssays

Perspective: Has provoking microbiota aggression driven the obesity epidemic? – Benoit Chassaing – BioEssays

Pregnancy and birth

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data – Erica Plummer- OMICS Proteomics & Bioinformatics

Review: Infection and preterm birth – Hugh C.G. Nadeau – Seminars in Fetal and Neonatal Medicine

Human gut microbiome

Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects – Radilla-Vázquez R.B. – Obesity Facts

Animal models

The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice – Jinyu Xu – Scientific Reports

Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation – Allison Agus – Scientific Reports

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior – Mark Lyte – PLOS ONE

Effects of BmCPV Infection on Silkworm Bombyx mori Intestinal Bacteria – Zhenli Sun – PLOS ONE

Antibiotic-treated versus germ-free rodents for microbiota transplantation studies – Randi Lundberg – Gut Microbes

Animal microbiome

The musk chemical composition and microbiota of Chinese forest musk deer males
Diyan Li – Scientific Reports

Pasteurellaceae bacteria from the oral cavity of Tasmanian Devils (Sarcophilus Harrisii) show high MIC values towards aminoglycosides and clindamycin – Nicole Gutman – Letters in Applied Microbiology

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis – Eria A Rebollar – The ISME Journal

Plant, root, and soil microbiome

Prokaryotic diversity in biodeteriorated wood coming from the Bükkábrány fossil forest – Katerina Nikolouli – International Biodeterioration & Biodegradation

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia – Alyssa Cornall – Environmental Toxicology and Chemistry

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum) – Gian Maria Niccolò Benucci – Mycorrhiza

Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils – Patrick L. Tomco – Environmental Toxicology and Chemistry

Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months – Daquan Sun – Applied Soil Ecology

Water and extremophile microbiome

Deep Microbial Life in High-Quality Granitic Groundwater from Geochemically and Geographically Distinct Underground Boreholes – Kohei Ino – Environmental Microbiology Reports

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication – Jesse Colangelo-Lillis – Environmental Microbiology Reports

Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community – Richard A. White III – Frontiers in Microbiology

Partitioning of fungal assemblages across different marine habitats – T.C. Jeffries – Environmental Microbiology Reports

Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities – Stéphane Jomini – Environmental Pollution

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions – Hon Lun Wong – MDPI Microorganisms

Microbial genetic diversity in soils along salinealkaline gradients at the coast of Laizhou Bay – Feng Zhao – Protistology

Influence of Zinc on Bacterial Populations and their Proteolytic Enzyme Activities in Freshwater Environments: A Cross-Site Comparison – Lauren Rasmussen – Canadian Journal of Microbiology

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events – Florent E. Angly – Peer J

Food microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Infection microbiology

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh – Shafiqul Alam Sarker – EBioMedicine

Book Chapter: Reducing pathobiomes could slow arms race between man and microbes
S. Romano-Bertrand – Microbiology 5

Bioinformatics and metagenomics

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery – Eric Marinier – BioRxiv

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities – Lisa Oberding – MDPI Microorganisms

Conference abstracts from the 2015 IEEE International Conference onBioinformatics and Biomedicine (BIBM):
Leveraging the k-Nearest Neighbors classification algorithm for Microbial Source Tracking using a bacterial DNA fingerprint library – Jeffrey D McGovern
A computational framework for integrative analysis of large microbial genomics data – Erliang Zeng
Computational challenges in microbiome research – Mihai Pop

Microbes in the news

New Year’s Resolutions for your Microbiome – Anne Estes – Mostly Microbes

West Hartford Children Museum Starts Scientific Discussion Series – Kristin Stoller – Hartford Courant

Balbriggan pair named Young Scientists of the Year: Maria Louise Fufezan and Diana Bura claim first place for research into soil fertility and nematodes – Dick Ahlstrom – The Irish Times

Body’s bacteria don’t outnumber human cells so much after all – Tina Hesman Saey – Science News

Are we really made up of more bacteria than human cells? – Lindsey Kratochwill – Popular Science

P&G granted patent for prebiotic agent-containing composition targeting skin microbiome – Andrew McDougall – Cosmetic Design-Europe.com

Science, publishing, and career

Nobel winner pulls out of Melb conference run by controversial Indian company (OMICS, EB) – Andrew Masterson – The Age

Cheer up, my academic colleagues! We’re so lucky to do this job – Anonymous Academic – The Guardian

Publishers to require ORCID identifiers for authors – EurekAlert

Bik’s Picks

Healthy Diet Helps 183-Year-Old Tortoise Feel Young Again – Jason Bittel – National Geographic

 

January 7, 2016

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A new estimate of the ratio microbial:human cells in our bodies, a 5300-year old Helicobacter genome, antibiotics alter bile metabolism, microbiota from 59 bird species, and fecal contamination of Kathmandu drinking water.

Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, which will take place in London, on the 11th and 12th of April, 2016. Early registration closes Jan 15th.

Mysterious Microbes Webinar Series 1 of 3: Microbes and the miracle of compost tea, with Noah Fierer and Ryan Heiland, on Jan 14. Learn how and why microbes are the natural secret to green lawns, lush flowers, and abundant produce

General human microbiome

Revised estimates for the number of human and bacteria cells in the body – Ron Sender – bioRxiv

Review: The human microbiota: the role of microbial communities in health and disease – Luz Elena Botero – Acta Biologica Columbiana

Pregnancy and birth microbiome

A comparative study of bifidobacteria in human babies and adults – Shadi Khonsari – Bioscience of Microbiota, Food and Health

Human oral microbiome

Salivary Antimicrobial Peptides in Early Detection of Periodontitis – Güliz N. Güncü – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

The 5300-year-old Helicobacter pylori genome of the Iceman – Frank Maixner – Science

Microbiome animal and other models

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine – Casey M. Theriot – mSphere

The Gut Microbiota Reduces Colonization of the Mesenteric Lymph Nodes and IL-12-Independent IFN-γ Production During Salmonella Infection – María Fernández-Santoscoy – Frontiers in Cellular and Infection Microbiology

Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health – Lonneke Onrust – Frontiers in Veterinary Science

Animal microbiome

Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology

Plant, root, and soil microbiome

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast –
Melike Balk – Frontiers in Microbiology

Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa – Hanan R. Shehata – Journal of Applied Microbiology

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants – Gerald Otti – Journal of Applied Microbiology

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria  – Max-Bernhard Ballhausen – Frontiers in Microbiology

Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150 – Lihua Li – MDPI Agriculture

Water and waste microbiome

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals – Galina Radeva – Canadian Journal of Microbiology

Master thesis: Evaluation of Two Culture-Independent Methods for Quantification of the Fraction of K-and r-Strategists within Water Microbial Communities – Brandsegg, Hege – Norges teknisk-naturvitenskapelige universitet

Built environment microbiome

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water – Abhilasha Karkey – PLOS Neglected Tropical Diseases

Application of the Environmental Relative Moldiness Index in Finland – Martin Täubel – Applied and Environmental Microbiology

Food microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology

Metagenomics and bioinformatics

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics – Alejandra Escobar-Zepeda – Frontiers in Genetics

Science, publishing, and career

Peer review: tips from field experts for junior reviewers – Sabina Alam – BMC Medicine

Microbes in the news

Gut bacteria from Otzi the Iceman reveals our intimate ties to one microbe – Rachel Feltman – Washington Post

Scientists unearth bacteria from stomach of 5,300-year-old iceman – Carl Zimmer – StatNews

The Famous Ancient “Iceman” Had Ulcer Bacteria In His Gut – Dan Vergano – BuzzFeed

High Stress Environments May Lead To Unhealthy Gut Microbiomes: How To Protect Yourself From The Consequences – Lecia Bushak – Medical Daily

Antibiotics Pave Way for C. Diff Infections – North Carolina State University

Jackson Laboratory Hosted Microbiome Symposium Related to Cancer and Immunology – Lexology

The Bacteria That May Be Causing Your Nasty Cold. “The most common one of them in Mycoplasma Pneumoniae Infection,” Martin explained. – Fox29

Bik’s Picks

A “Pedi” Cures All: Toenail Trimming and the Treatment of Ulcerative Dermatitis in Mice – Sean C. Adams – PLOS ONE
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December 22, 2015

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Periodontal disease associated with increased chance for breast cancer, rifaximin treatment of IBS patients, bacteria on surface of 2 different grape varieties in Spain, and a reproducible research workflow in R.

Human oral microbiome

Periodontal Disease and Breast Cancer: Prospective Cohort Study of Postmenopausal Women – Jo L. Freudenheim – Cancer Epidemiology, Biomarkers & Prevention

Distributions of Synergistetes in clinically-healthy and diseased periodontal and peri-implant niches – Xiao-Lin Yu – Microbial Pathogenesis

Human gut microbiome

Modulation of the gut microbiota composition by rifaximin in non-constipated irritable bowel syndrome patients: a molecular approach – Sara Soldi – Clinical and Experimental Gastroenterology

Roles of Sphincter of Oddi Laxity in Bile Duct Microenvironment in Patients with Cholangiolithiasis: From the Perspective of the Microbiome and Metabolome –
Tingbo Liang – Journal of the American College of Surgeons

Book chapter: Influence of Gut Microbiota on Hepatic Lipogenesis and Disease Pathogenesis – Vishal Singh – Hepatic De Novo Lipogenesis and Regulation of Metabolism

Review: Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences – Luis Vitetta – MDPI Microorganisms

Book chapter: Gut Microbiome and Stress – Winnie-Pui-Pui Liew – Beneficial Microorganisms in Medical and Health Applications

Review: Dietary and Lifestyle Factors Associated with Colorectal Cancer Risk and Interactions with Microbiota: Fiber, Red or Processed Meat and Alcoholic Drinks – Tuan J. – GastroIntestinal Tumors

Models of microbiomes

Effect of chito-oligosaccharides over human faecal microbiota during fermentation in batch cultures – Inmaculada Mateos-Aparicio – Carbohydrate Polymers

Changes in gastric microbiota induced by Helicobacter pylori infection and preventive effects of Lactobacillus plantarum ZDY 2013 against such infection – Mingfang Pan – Journal of Dairy Science

Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells – Christopher J. Day – PNAS

Research highlight: A ‘fit’ microbiota to potentiate cancer immunotherapy – Maria Rescigno – Genome Medicine

Animal microbiome

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development – Kirk E. Anderson – Host Microbe Interactions

A diverse array of new viral sequences identified in worldwide populations of the Asian citrus psyllid (Diaphorina citri) using viral metagenomics – Shahideh Nouri – Journal of Virology

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia – Jamal S. M. Sabir – Science

Comparison of Fecal Microbial Communities between White and Black Pigs – Robin B. Guevarra – Journal of Applied Biological Chemistry

Plant, root, and soil microbiome

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain) – Maria del Carmen Portillo – International Journal of Food Microbiology

Field Application of the Mycorrhizal Fungus Rhizophagus irregularis Increases the Yield of Wheat Crop and Affects Soil Microbial Functionalities – Sanâa Wahbi – American Journal of Plant Sciences

Arbuscular mycorrhizal fungi reduced the ratios of inorganic/organic arsenic in rice grains – H. Li – Chemosphere

Characteristics of rhizosphere and bulk soil microbial communities in rubber plantations in Hainan Island, China – Wang, W. B. – Journal of Tropical Forest Science

Microbial community structure and its temporal changes in Rehmannia glutinosa rhizospheric soils monocultured for different years – Linkun Wu – European Journal of Soil Biology

Exotic Plant Alnus trabeculosa Alters the Composition and Diversity of Native Rhizosphere Bacterial Communities of Phragmites australis – Xueping Chen – Pedosphere

Long-term chronological shifts in bacterial communities and hydrolytic extracellular enzyme activities in the forty years following a land-use change from upland fields to paddy fields – Nan Jiang – Pedobiologia

Water microbiome

Resilience of SAR11 bacteria to rapid acidification in the high latitude open ocean – Manuela Hartmann – FEMS Microbiology Ecology

Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities – Anna Hanke – Frontiers in Microbiology

Bioinformatics

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data – Benjamin Callahan – Pacific Symposium on Biocomputing

Techniques

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys – William Walters – mSystems

Protocol: Studying Protistan Communities in Hydrocarbon-Contaminated Environments – Julia Johnke – Springer Protocols Handbooks

Microbes in the news

Harmful bacteria can survive in sandwich crackers, cookies for months, UGA study finds – Online Athens

Tomorrow’s Heart Drugs Might Target Gut Microbes – Ed Yong – The Atlantic

Bik’s Picks

Pharmacy delivery vans targeted by thieves seeking painkillers – David Armstrong – STAT news

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October 20, 2015

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Cohabitation of helminths, bacteria, and host in the gut, diurnal sampling bias in plankton biodiversity, contaminant influence on groundwater microbiome, volatile affairs, and new tools for metagenomics.

Events

Postdoc and grad student Summit — preceding the EMBO Symposium on Aquatic Microeukaryotes: Abstract deadline October 22 – Jonathan Eisen – MicroBEnet

Human oral microbiome

Periodontal clinical and microbiological characteristics in healthy versus generalized aggressive periodontitis families – Mabelle de F. Monteiro – Journal of Clinical Periodontology

Masters Thesis: Caries and the Oral Microbiome of a Native American Population – Michael Tuan – Ohio State University

Human gut microbiome

Review: Cohabitation in the Intestine: Interactions among Helminth Parasites, Bacterial Microbiota, and Host Immunity – Lisa A. Reynolds – The Journal of Immunology

Review: Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases – Bidisha Paul – Clinical Epigenetics

Review: Intestinal Microbiota Metabolism and Atherosclerosis – Tian-Xing Liu – Chinese Medical Journal

Animal models

Colonic Lesions, Cytokine Profiles, and Gut Microbiota in Plasminogen-Deficient Mice – Bill Vestergaard – Comparative Medicine

Plant, root, and soil microbiomes

Cyanobacterial composition and spatial distribution based on pyrosequencing data in the Gurbantunggut Desert, Northwestern China – Bingchang Zhang – Journal of Basic Microbiology

Disease in apple orchards: Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis – contribution to improved aboveground apple plant growth? – Bunlong Yim – Frontiers in Microbiology

A fragrant neighborhood: Volatile mediated bacterial interactions in soil – Kristin Schulz-Bohm – Frontiers in Microbiology

Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing – Lin Chen – Frontiers in Microbiology

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California – A. C. Hollowell – Plant Microbe Interactions

Water microbiome

Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique – Satoshi Nagai – Gene

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations – Xiaofen Wu – The ISME Journal

Viral impact on prokaryotic and microalgal activities in the microphytobenthic biofilm of an intertidal mudflat (French Atlantic coast) – Hélène Montanié – Frontiers in Microbiology

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes – Christopher L. Hemme – Frontiers in Microbiology

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

Effects of Seasonal Thermal Stratification on the Functional Diversity and Composition of the Microbial Community in a Drinking Water Reservoir – Xiao Yang – Water

Extremophile microbiology

Review: Extremely Thermophilic Microorganisms as Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals – Benjamin M. Zeldes – Frontiers in Microbiology

Metagenomics and bioinformatics

Snowball: Strain aware gene assembly of Metagenomes – I. Gregor – ArXiv

PEPR: Pipelines for Evaluating Prokaryotic References – Nathan D. Olson – PeerJ preprint

cual­id: globally unique, correctable, and human­friendly sample identifiers for
comparative ­omics studies – John H Chase – PeerJ preprint

Why we need more algal metagenomes – Linda E. Graham – Journal of Phycology

Phages and viruses

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters – Jeremy J. Barr – PNAS

Microbial Ecology

Interspecies interactions are an integral determinant of microbial community dynamics –
Fatma A. A. Aziz – Frontiers in Microbiology

Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity – Caroline M. Tucker – Oikos

Review: Role of the Environment in the Transmission of Antimicrobial Resistance to Humans: A Review – Patricia M. C. Huijbers – Environmental Science & Technology

More microbiology

Self-Protected Nitrate Reducing Culture for Intrinsic Repair of Concrete Cracks –
Yusuf C. Ersan – Frontiers in Microbiology

Metabolomics

Review: Volatile affairs in microbial interactions – Ruth Schmidt – The ISME Journal

Microbes in the news

Society for Neuroscience meeting in Chicago : Probiotic bacteria may aid against anxiety and memory problems – Ian Sample – The Guardian

ID Week: How Babies’ Gut Bacteria May Help Find Treatments for C. Diff – Rachael Rettner – Live Science

Video: Speaking of Chemistry: What is the Gut Microbiome? Matt Davenport – American Chemical Society

Study reveals a key role your gut bacteria play in body’s self-defense – David Callahan – Medical Xpress

Gut Microbiome Insights; Obesity and Digestive Health Risks; Delivery Options and Predictors of Failure for Fecal Microbiota Transplantation; among Featured Topics Presented at the American College of Gastroenterology’s 80th Annual Meeting – PR NewsWire

MS conference, Barcelona: Q&A With Helen Tremlett From the University of British Columbia: Gut Microbiome And Its Role In Multiple Sclerosis -HCP Live

Virginia Tech scientists reveal more about how body copes with common gut bacterium – Augusta Free Press

High Starch Diets’ Effects on Stress Response in Horses – Casie Bazay – The Horse

These Bacteria Could Live in Europa’s Ocean – Irene Klotz – Discovery

Local news: Dozens Sick With Shigella Bacteria After Eating At San Jose Restaurant – CBS Local

The Phage is a Lonely Hunter: New research reveals that bacteriophages use slow, staccato movements to hunt bacteria on cell surfaces – Michael Price – SDSU

Creating Healthier Microbiomes, from Conception to Childhood: A Clinical Conversation with Geeta Maker-Clark, MD, and Robert Rountree, MD -Alternative and Complementary Therapies

Microbes and art

Very cool: A Microbiologist Recreated ‘Starry Night’ With Bacteria In A Petri Dish And it’s not too shabby – Priscilla Frank – Huffington Post

Bik’s Picks

Poo turns naked mole rats into better babysitters – Oestrogen in queen mole rat’s faeces drives subordinates to care for her pups – Sara Reardon – Nature News
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September 30, 2015

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Gut virome in infants, metabolome of Mediterranean diet, zebrafish gut assembly, antibiotic use and psoriasis risk, Roseobacter proteomics, and MetaPhlAn2.

Pregnancy and birth

The gut virome and bacterial microbiome—the early years – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Early life dynamics of the human gut virome and bacterial microbiome in infants –
Efrem S Lim – Nature Medicine

Human oral microbiome

Functional biomarkers for chronic periodontitis and insights into the roles of Prevotella nigrescens and Fusobacterium nucleatum; a metatranscriptome analysis – Szymon P Szafrański – NPJ Biofilms and Microbiomes

Urease and Dental Plaque Microbial Profiles in Children – Evangelia Morou-Bermudez – PLOS ONE

High prevalence of colonization of oral cavity by respiratory pathogens in frail older patients with oropharyngeal dysphagia – O. Ortega – Neurogastroenterology & Motility

Periodontal-disease-associated biofilm: A reservoir for pathogens of medical importance – Ana Paula Vieira Colombo – Microbial Pathogenesis

Human gut microbiome

High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome – Francesca De Fillippis – Gut

Review: Clinical and Pathophysiological Consequences of Alterations in the Microbiome in Cirrhosis – Jane Macnaughtan – American Journal of Gastroenterology

Animal models

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut – Sandi Wong – mBio

Antibiotics in neonatal life increase murine susceptibility to experimental psoriasis –
Peter Zanvit – Nature Communications

Plant, root, and soil microbiome

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Oily waste containing natural radionuclides: does it cause stimulation or inhibition of soil bacterial community? – Polina Galitskaya – Journal of Plant Nutrition and Soil Science

Plant diversity shapes microbe-rhizosphere effects on P mobilisation from organic matter in soil – Nina Hacker – Ecology Letters

Water microbiome

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

Extremophile microbiome

Perspective: The discovery of Antarctic RNA viruses: a new game changer – Ricardo Cavicchioli – Molecular Ecology

Metagenomics and bioinformatics

MetaPhlAn2 for enhanced metagenomic taxonomic profiling – Duy Tin Truong – Nature Methods

Metabolomics, proteomics

An automated Genomes-to-Natural Products platform (GNP) for the discovery of modular natural products – Chad W. Johnston – Nature Communications

Proteomics of the Roseobacter clade, a window to the marine microbiology landscape – Joseph A. Christie-Oleza – Proteomics

CRISPRs

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins – Joseph Bondy-Denomy – Nature

Review: CRISPR-Cas immunity in prokaryotes – Luciano A. Marraffini – Nature

Microbes in the news

Study Links Skin Microbiome to Infections – Skin Inc

Ancient ‘Superman’ microbe’s ability to withstand damage to its DNA could be key to unlocking cancer cure, Chinese scientists say – Stephen Chen – South China Morning Post

Another Frontier in Microbiome Research: Preterm Birth – Julie A. Jacob – JAMA

Science, publishing, and career

A taxonomy of authorship roles – Credit Casrai

Bik’s Picks

What if everyone lived to 100? – Georgina Peters – London Business School Review

Gene-Edited “Micropigs” to Be Sold as Pets: The institute in Shenzhen, China, that creates the pigs quoted an initial price tag of $1,600 – David Cyranoski – Scientific American / Nature

1500-Year-Old Mosaic Map Found – Rossella Lorenzi – Discovery

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September 25, 2015

Posted on by

A crowd funding project to study mind and microbes, impact of early life gut colonization, microbial aspect to terroir, and khmer sequence analysis.

Crowd funding project: Are our bacteria making us depressed or anxious? – Philip Strandwitz – Experiment.com

Pregnancy and birth

Review: The impact of early life gut colonization on metabolic and obesogenic outcomes: what have animal models shown us? – J. G. Wallace – Journal of Developmental Origins of Health and Disease

Human gut microbiome

Chronic Kidney Disease: The Influence of CKD on Colonic Microbial Metabolism – Ruben Poesen – Journal of the American Society of Nephrology

Review: Could the beneficial effects of dietary calcium on obesity and diabetes control be mediated by changes in intestinal microbiota and integrity? – J. M. G. Gomes – British Journal of Nutrition

Animal models

The microbiota shifts the iron sensing of intestinal cells – Jean-Christophe Deschemin – The FASEB Journal

Plant, root, and soil microbiome

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health – Zhong Wei – Nature Communications

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir – Sarah Knight – Scientific Reports

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil – Souichiro Kato – Scientific Reports

Food microbiology

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil
A.A.M. De-Melo – Letters in Applied Microbiology

Waste microbiology

The biotransformation of brewer’s spent grain into biogas by anaerobic microbial communities – Dina V. Malakhova – World Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

The khmer software package: enabling efficient nucleotide sequence analysis – Michael R. Crusoe – F1000 research

Microbes in the news

That Stinky Cheese Is a Result of Evolutionary Overdrive – Carl Zimmer – New York Times

Bacteria are making it harder for would-be murderers – Alexandra Petri – Washington Post

Bacteria Hysteria

Note: research sponsored by Dettol: How your child’s teddy could trigger food poisoning: 80% of cuddly toys harbour harmful bacteria – while one in four are contaminated with faeces – Lizzie Parry – Daily Mail

Science, publishing, and career

How science fairs shaped my career – Rachel Yoho – Science

Bik’s Picks

Scientists discover new system for human genome editing – Phys.org

The truth about pigs – Henry Nicholls – BBC

1 1/2-pound baby born to Utah woman on cruise ship beats odds to survive – Lindsey Whitehurst – Associated Press
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