January 27, 2015

Review (could also be filed under plant microbiome): Is there a role for symbiotic bacteria in plant virus transmission by insects? – Patricia V. Pinheiro – Current Opinion in Insect Science

Plant microbiome

Endophytic fungi from the genus Colletotrichum are abundant in the Phaseolus vulgaris and have high genetic diversity – L.L. Gonzaga – Journal of Applied Microbiology

Bioreactor microbiome

Effect of hygienization treatment on the recovery and/or regrowth of microbial indicators in sewage sludge – M. Pascual-Benito – Journal of Applied Microbiology

Metabolomics and Proteomics

Review: New aspects on the metabolic role of intestinal microbiota in the development of atherosclerosis – Ioannis Drosos – Metabolism

Not in microbes, but of note: Tissue-based map of the human proteome – Mathias Uhlén – Science

Microbial detection general

First Experience of a Multicenter External Quality Assessment of Molecular 16S rRNA Gene Detection in Bone and Joint Infections – Chloé Plouzeau – Journal of Clinical Microbiology

Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identification of Molds of the Fusarium Genus – David Triest – Journal of Clinical Microbiology

A combined light sheet fluorescence and differential interference contrast microscope for live imaging of multicellular specimens – R.P. Baker – Journal of Microscopy

Infection and Immunity

Twin study @Stanford: Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences – Petter Brodin – Cell

Hidden costs of infection: Chronic malaria accelerates telomere degradation and senescence in wild birds – M. Asghar – Science

Review: Advances in Laboratory Methods for Detection and Typing of Norovirus – Jan Vinjé – Journal of Clinical Microbiology

Combating the emerging viral infectious diseases – Shibo Jiang, Peter J. Hotez – Microbes and Infection

Phages, viruses, CRISPRs

Transcriptional regulator-mediated activation of adaptation genes triggers CRISPR de novo spacer acquisition – Tao Liu – Nucleic Acids Research

Microbes in the news
Breathing in Bacteria – The healthy lung receives microbes from the mouth, a new model suggests – Jenny Rood – The Scientist

Viruses may play unexpected role in inflammatory bowel diseases – Science Daily

Researchers See IBD-related Shifts in Individuals’ Gut Viromes – GenomeWeb

How gut bacteria may affect brain health – ScienceCodex

New microbiome drug candidate licensed by major manufacturer – Healio.com

When the Microbiome Stages a Coup – GenomeWeb

Environment, not genes, plays starring role in human immune variation, study finds – Stanford Medicine

Dirty Mouth? Chewing Gum Removes Millions Of Bacteria, But With One Catch – Philip Ross – International Business Times

We’ve found a strange box at our student microbiology lab… – AwesomeScience – Imgur

Immune system promotes digestive health by fostering community of ‘good’ bacteria – EurekAlert

The New Measles – One of the most infectious viruses on the planet is making a comeback in the United States, and many doctors have never even seen it – Adrienne Lafrance – The Atlantic

Science, publishing, and career

Intel Science Talent Search finalists: 9 of 40 from Bay Area – James Urton and Sharon Noguchi – Mercury News

Should Teachers be Allowed to Touch Students? – Jessica Lahey – The Atlantic

Science and art

100 Years of National Geographic Maps: The Art and Science of Where – Cathy Newman – National Geographic

Kitty Microbiome – Artologica – Etsy

Bik’s Picks

Major breakthrough in reading ancient scrolls – Science Daily

The geometry of their shells keeps turtles from getting stuck on their back – Seriously Science – Discover Magazine

Scottish scientists slow down speed of light – Robert Ferris – CNBC

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January 22, 2015

Posted on January 22, 2015 by eliesbik

The enteric virome is more diverse in patients with Crohn’s Disease and ulcerative colitis, measuring how fecal transplants are portrayed in Canadian media, and bacteria and archaea in sugarcane soils.

Human gut microbiome

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease – Jason M. Norman – Cell

Media Discourse on the Social Acceptability of Fecal Transplants – Kim H. Chuong – Qualitative Health Research

Perspective: Cancer and the gut microbiota: An unexpected link – Laurence Zitvogel – Science Translational Medicine

Editorial: Bugs, Guts, and Glia: How Microbiota Influence Enteric Gliogenesis and Migration – Meenakshi Rao – Neuron

Animal models

MyD88 Signaling in T Cells Directs IgA-Mediated Control of the Microbiota to Promote Health – Jason L. Kubinak – Cell Host & Microbe

Soil microbiome

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil – Kanako Tago – Microbes and Environments

Metabolomics

Global biogeographic sampling of bacterial secondary metabolism – Zachary Charlop-Powers – eLIFE

Ecology

Perspective: The physiology and ecological implications of efficient growth – Benjamin RK Roller and Thomas M Schmidt – ISME Journal

Metagenomics and bioinformatics

Pollux: platform independent error correction of single and mixed genomes – Eric Marinier – BMC Bioinformatics

Microbes in the news

When bacteria-killing viruses take over, it’s bad news for the gut – Tina Hesman Saey – ScienceNews

Immune system promotes digestive health by fostering community of ‘good’ bacteria – NewsWise

Gut microbes may trigger autoimmune disease later in life – PuneMirror

Scientists claim breakthrough in taming genetically modified E.coli bacteria – Joel Achenbach – Washington Post

Have we found alien life? Microbes that eat and breath electricity have forced scientists to reimagine how life works – on this planet and others – Corey S. Powell – Popular Science

Science, publishing, and career

Origin stories of the scientists – Adam Ruben – Science

Bik’s Picks

The Science of Mmm – How food and drink tickle the brain’s pleasure centers – John McQuaid – Slate

Will this put an end to a very old discussion? Is glass a true solid? New research suggests it is – Science Daily

Which state f*cking loves science the most? – Phil Edwards – Vox

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January 21, 2015

Posted on January 21, 2015 by eliesbik

Today’s digest features the microbiome of chewing gum, infants of stressed-out moms, growing segmented filamentous bacteria, and a YouTube video with Jack Gilbert.

Chewing gum microbiome

Quantification and Qualification of Bacteria Trapped in Chewed Gum – Stefan W. Wessel – PLOS ONE

Human gut microbiome

Review: Gut microbial metabolism and colon cancer: Can manipulations of the microbiota be useful in the management of gastrointestinal health? – Antoaneta Belcheva – BioEssays

Microbiome of pregnancy and birth

Maternal Prenatal Stress is Associated with the Infant Intestinal Microbiota – Maartje A.C. Zijlmans – Psychoneuroendocrinology (which is a nice word for Scrabble or Hangman)

Animal and other models of microbiome research

Growth and host interaction of mouse segmented filamentous bacteria in vitro – Pamela Schnupf – Nature

Signaling between two interacting sensor kinases promotes biofilms and colonization by a bacterial symbiont – Allison N. Norsworthy and Karen L. Visick – Molecular Microbiology

Soil microbiome

Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea – Jong-Shik Kim – Microbiology Open

Water microbiome

Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek’s watershed – A.L. Barkovskii – Journal of Applied Microbiology

Immunology

Reduced neonatal regulatory T cell response to microbial stimuli associates with subsequent eczema in high-risk infants – Intan H. Ismail – Pediatric Allergy and Immunology

Metagenomics

Biological interpretation of genome-wide association studies using predicted gene functions – Tune H. Pers – Nature Communications

Microbes in the news

YouTube video with Jack Gilbert: Invisible Influence: A Bacterial Guide to Your Health – Argonne OutLoud on YouTube

Commensal Defense: Beneficial gut bacteria have evolved resistance to antimicrobial peptides that hosts release to fight pathogens – Kate Yandell – The Scientist

GM microbes created that can’t escape the lab – Engineered bacteria kept in check with a designer diet – Elie Dolgin – Nature

SDSU Hosts the “Year of the Phage” – Jeneene Chatowsky and Michael Price – San Diego State University

Novel IBD microbiome drug advanced to phase 1 trial – Healio

Optibiotix unlocking the mysteries of the human microbiome – Ian Lyall – Proactive Investors

New bacterial ‘language’ discovered: Previously unknown communication pathway – Science Daily

Science, publishing and career

Turning point: Swati Padmaraj – Scott Kraft – Nature

Time management: Seize the moment – Jeffrey M. Perkel – Nature

How to recruit a good bioinformatician – Opiniomics

Science and Art

Micro Masterpiece: The artful science of Tom Deerinck, a micrographer who consistently places in Nikon’s Small World competition – Jef Akst – The Scientist

Bik’s Picks

The Science Behind Deflated Footballs – Erin Blakemore – Smithsonian

Science gets its moment in Obama’s 2015 State of the Union – David Malakoff – Science

The Namer: Carl Linnaeus’s lasting impact on biological science – Kerry Grens – The Scientist

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January 20, 2015

Posted on January 20, 2015 by eliesbik

Today we will honor #PenguinAwarenessDay with an older paper, but all others links are brand new. There is the cave microbiome, bacteria in fermented yak milk, and a warning about comparing data obtained in mouse models. Here we go:

Perspective: Where Next for Microbiome Research? – Matthew K. Waldor – PLOS Biology

Review: The Microbiome and Graft Versus Host Disease – Nathan Mathewson, Pavan Reddy – Current Stem Cell Reports

Review: The microbiome mutiny hypothesis: can our microbiome turn against us when we are old or seriously ill? – Lajos Rózsa – Biology Direct

Review: Prevention of Microbial Communities: Novel Approaches Based Natural Products – George D. Mogosanu – Current Pharmaceutical Biotechnology

Human respiratory microbiome

Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome – Arvind Venkataraman – mBio

Review (behind paywall, even at Stanford): Immunology, genetics and microbiota in the COPD pathophysiology: potential scope for patient stratification – Rajneesh Malhotra, and Henric Olsson – Expert Review of Respiratory Medicine

Human gut microbiome

Helicobacter pylori infection as a protective factor against multiple sclerosis risk in females – Marzena J Fabis Pedrini – J Neurol Neurosurg Psychiatry

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers – A Lavelle – Gut

Review: The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases? – Gerardo Nardone, Debora Compare – United European Gastroenterology Journal

Pregnancy and birth

Review: Human Milk: Mother Nature’s Prototypical Probiotic Food? – Michelle K McGuire, and Mark A McGuire – Advances in Nutrition

Animal models of microbiome research

Perspective: How informative is the mouse for human gut microbiota research? – Thi Loan Anh Nguyen – Disease Models & Mechanisms

Attenuated portal hypertension in germ-free mice: Function of bacterial flora on the development of mesenteric lymphatic and blood vessels – Sheida Moghadamrad – Hepatology

High-throughput 16S rRNA gene sequencing reveals alterations of mouse intestinal microbiota after radiotherapy – Young Suk Kim – Anaerobe

Antibiotic perturbation: An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile – Matthew Miezeiewski – ISME J

Animal microbiome

This is a 2013 article, but I included it to honor today’s #PenguinAwarenessDay:
Interspecific variations in the gastrointestinal microbiota in penguins – Meagan L. Dewar – MicrobiologyOpen

Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata using functional metagenomics – María Alcaide – Applied and Environmental Microbiology

Plant microbiome

Structure, variation, and assembly of the root-associated microbiomes of rice – Joseph Edwards – PNAS USA

Rhizosphere microbial community composition affects cadmium and zinc uptake of the metal-hyperaccumulating plant Arabidopsis halleri – E. Marie Muehe – Applied and Environmental Microbiology

Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics – Martin Grube – ISME J

Soil microbiome

Profiling microbial communities in manganese remediation systems treating coal mine drainage – Dominique L. Chaput – Applied and Environmental Microbiology

Bacterial succession in paddy soils derived from different parent materials – Rong Sheng – Journal of Soils and Sediments

Main factors controlling microbial community structure and function after reclamation of a tailing pond with aided phytostabilization – R. Zornoza – Geoderma

Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA# – Swathi A. Turlapati – Frontiers in Microbiology

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust – Alberto Robador – Frontiers in Microbiology

Water microbiome

Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean – Mary Thaler and Connie Lovejoy – Applied and Environmental Microbiology

The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly – Chuck Pepe-Ranney, Ed Hall – BioRxiv

Catchment-scale biogeography of riverine bacterioplankton – Daniel S Read – ISME J

Microbiome of the built environment

Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas – I. Gandolfi – Applied Microbiology and Biotechnology

The community distribution of bacteria and fungi on ancient wall paintings of the Mogao Grottoes – Yantian Ma – Nature Scientific Reports

A long-term study examining the antibacterial effectiveness of Agion silver zeolite technology on door handles within a college campus – B.A. Potter – Letters in Applied Microbiology

Bioreactor microbiology

Groundwater Chemistry Determines the Prokaryotic Community Structure of Waterworks Sand Filters – Christian N. Albers – Environmental Science & Technology

Impact of Organic Load Shock on the Dynamic Transition of Microbial Communities During the Anaerobic Start-up Process – Jie Li – Energy Procedia

Food microbiology

High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk – Wenjun Liu – Annals of Microbiology

Viruses and phages

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome – Bonnie L Hurwitz – ISME J

BSc thesis: Metagenomic study of the human gut virome during the first year of life – David Mayo Muñoz – Universitat Politecnica de Valencia

Metagenomics

Strong spurious transcription likely a cause of DNA insert bias in typical metagenomic clone libraries – Kathy N Lam, Trevor C Charles – BioRXiv

Commentary: Capturing bacterial chromosome conformation – Andrea Du Toit – Nature Reviews Microbiology

Metabolomics

Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury – Pilib Ó Broin – International Journal of Radiation Oncology

Investigation of biotechnological potential of sponge-associated bacteria collected in Brazilian coast – O.C.S. Santos – Letters in Applied Microbiology

Review: The Role of Colonic Bacteria in the Metabolism of the Natural Isoflavone Daidzin to Equol – Fatemeh Rafii – Metabolites

Microbes in the news

Can the Microbiome Mutiny? – Carl Zimmer – National Geographic

Fast-Paced Microbiome (about Rob Knight) – Genome Web

Researchers urge caution in studies of mice and microbes – Sarah DeWeerdt – SFARI

Gut microbes trigger autoimmune disease later in life in mice – Science Codex

Ulcer Bacteria Tied to Lower Multiple Sclerosis Risk in Women – HealthDay

Breweries partner with bacteria-detecting Philadelphia start-up – Diane Mastrull – Philly.com

New Species Discovered Beneath Ocean Crust – Robert Perkins – Pressroom USC

Ancient Viruses Gain New Functions in the Brain – Andrea Alfano – Scientific American

Science, publishing, and career

Is it Ph.D. or PhD? And are PhDs who act like MDs a special kind of douchebag? Twitter debates – Chris Seper – MedCityNews

Is the Debate and “Pause” on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? – Julie K. Pfeiffer – mBio

Don’t be that dude: Handy tips for the male academic – Tenure She Wrote

Science and art

Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu – Jonathan Eisen – The Tree of Life

Bik’s Picks

Exercise at depth alters bradycardia and incidence of cardiac anomalies in deep-diving marine mammals – Terrie M. Williams – Nature Communications

What’s Up With That: Birds Bob Their Heads When They Walk – Nick Stockton – Wired

Over 80 percent of Americans support “mandatory labels on foods containing DNA” – Ilya Somin – Washington Post

The Discoloration of the Taj Mahal due to Particulate Carbon and Dust Deposition – M. H. Bergin – Environmental Science & Technology

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January 19, 2015

Posted on January 19, 2015 by eliesbik

Thanks for all the encouraging comments here and per email! This blog appears to fill an important niche in the coverage of scientific microbiome research, in a wide range of hosts and environmental sources, so I will continue writing this. But please spread the word – 100 viewers per day is nice, but more is better!

As one of the commenters suggested, I will try to mark Reviews as such, so they are easier to find (or skip).

Here we go with a new post. It’s Monday, so there is a lot to cover.

Human oral microbiome

Herpesvirus in the oral cavity of children with leukaemia and its impact on the oral bacterial community profile – Tacíria M Bezerra – Journal of Clinical Pathology

Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron – Pamela Vazquez-Gutierrez – BMC Microbiology

Review: Tuning the Brain-Gut Axis in Health and Disease – Rainbo Hultman – Current Stem Cell Reports

Microbiome of pregnancy and birth

Clinical chorioamnionitis at term I: microbiology of the amniotic cavity using cultivation and molecular techniques – Roberto Romero – Journal of Perinatal Medicine

Review: Relationship between periodontal diseases and preterm birth: Recent epidemiological and biological data – Moneet Walia, Navdeep Saini – International Journal of Applied and Basic Medical Research

Review: Viral Infections During Pregnancy – Michelle Silasi – American Journal of Reproductive Immunology

Review: Stress and the Commensal Microbiota: Importance in parturition and infant neurodevelopment – Tamar L. Gur – Frontiers in Psychiatry

Animal models of microbiome research

Commensal microbiota influence systemic autoimmune responses – Jens T Van Praet – The EMBO Journal

Modulation of the Intestinal Microbiota Is Associated with Lower Plasma Cholesterol and Weight Gain in Hamsters Fed Chardonnay Grape Seed Flour – Hyunsook Kim – J. Agric. Food Chem

Dysbiotic bacteria translocate in progressive SIV infection – Z Klase – Mucosal Immunology

Animal microbiome

Comparison of the gut microbiomes of 12 bony fish and 3 shark species – Carrie E. Givens – Marine Ecology Progress Series

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation – Jian Xue – Genome Biology

Review: Towards an integrated understanding of the consequences of fungus domestication on the fungus-growing termite gut microbiota – Michael Poulsen – Environmental Microbiology

Plant microbiome

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root associated fungi mirrors plant succession in two glacial chronosequences – Marie Davey – Environmental Microbiology

Book: Beneficial Plant-Bacterial Interactions – Bernard R. Glick

Soil and sediment microbiome

Soil Bacterial Communities are Shaped by Temporal and Environmental Filtering: Evidence from a Long-Term Chronosequence – Zachary Freedman and Donald R. Zak – Environmental Microbiology

Abstract: Garlic mustard and its effects on soil microbial communities in a sandy pine forest in central Illinois – Alexander B Faulkner – Proceedings, 19th Central Hardwood Forest Conference; 2014 March

Bacterial community composition at anodes of microbial fuel cells for paddy soils: the effects of soil properties – Ning Wang – Journal of Soils and Sediments

Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Soil-Borne Microbiome: Linking Diversity to Function – Lucas W. Mendes – Microbial Ecology

Phytoextraction of nickel and rhizosphere microbial communities under mono- or multispecies hyperaccumulator plant cover in a serpentine soil – Marie Rue – Australian Journal of Botany

Methane-derived carbon flow through microbial communities in arctic lake sediments – Ruo He – Environmental Microbiology

Review: Potential applications of soil microbial ecology and next-generation sequencing in criminal investigations – Sheree J. Finley – Applied Soil Ecology

Water microbiome

Book (open access): Subseafloor Biosphere Linked to Hydrothermal Systems
Some chapters of interest:
– Intra-Field Variation of Prokaryotic Communities On and Below the Seafloor in the Back-Arc Hydrothermal System of the Southern Mariana Trough – Shingo Kato
– Microbial Cell Densities, Community Structures, and Growth in the Hydrothermal Plumes of Subduction Hydrothermal Systems – Michinari Sunamura, Katsunori Yanagawa
– Comparative Investigation of Microbial Communities Associated with Hydrothermal Activities in the Okinawa Trough – Ken Takai, Satoshi Nakagawa
– Quantification of Microbial Communities in Hydrothermal Vent Habitats of the Southern Mariana Trough and the Mid-Okinawa Trough – Katsunori Yanagawa

Microbiome of the built environment

Review: From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome – Brent Stephens – Indoor Air

Food microbiology

Diversity of Lactic Acid Bacteria Isolated from Brazilian Water Buffalo Mozzarella Cheese – Luana Faria Silva – Journal of Food Science

Metagenomics

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data – Xutao Deng – Nucleic Acids Research

Review: Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics – Charlotte J. Houldcroft and Judith Breuer – Frontiers in Microbiology

Metabolomics, transcriptomics, and proteomics

Effects of high fructose and salt feeding on systematic metabonome probed via 1H NMR spectroscopy – Yongxia Yang – Magnetic Resonance in Chemistry

Also see above: Adaptation of soil microbial community structure and function to chronic metal contamination at an abandoned Pb-Zn mine – Lur Epelde – FEMS Microbiology Ecology

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome – Florence Privé – Applied Microbiology and Biotechnology

Review: Proteomics of hosts and pathogens in cystic fibrosis – Karthik Shantharam Kamath – Proteomics – Clinical Applications

Bioinformatics

Book chapter: e-DNA Meta-Barcoding: From NGS Raw Data to Taxonomic Profiling – Fosso Bruno – RNA Bioinformatics / Methods in Molecular Biology

Book chapter: Deciphering Metatranscriptomic Data – Evguenia Kopylova – RNA Bioinformatics / Methods in Molecular Biology

Amplification and sequencing techniques

Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples – Marta Pawluczyk – Analytical and Bioanalytical Chemistry

Probiotics

Consecutive oral administration of Bifidobacterium longum MM-2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model – Tomohiro Kawahara – Microbiology and Immunology

Microbes in the news

* One Scientist’s Race To Help Microbes Help You – Katherine Harmon Courage – NPR Shots

Researchers reveal link between the microbiome of young mice and later onset of autoimmune disease – News Medical

Podcast: Do Gut Bacteria Tell Us What To Eat? – Beth Anne Austein / The Food Guys – Montana Public Radio

The Fungus in Your Cheese Is Having Weird Sex – Rose Eveleth – Smithsonian.com

Disturbed gut microbiome linked to Parkinson’s disease – News Medical

#BacteriaHysteria

Honoring last week’s Law Enforcement Appreciation Day: Sheriff’s Office gets bacteria cleanse – Richard Goad – Cleveland Banner

Science, publishing, and career

7 Tips for Women at Science Conferences – Hilda Bastian – PLOS Blogs

Bik’s Picks

Do 80% of Americans not know there’s DNA in food? – Ben Lillie blog

Researchers Who Provided Key Evidence For Gluten Sensitivity Have Now Thoroughly Shown That It Doesn’t Exist – Jennifer Welsh – Business Insider

This whale might be old, but it does not look too happy (or it is swimming upside down?)
The Secret To Living 200 Years? Ask A Whale – Paul Rodgers – Forbes.com

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January 16, 2015

Posted on January 16, 2015 by eliesbik

(edited: MicrobiomeNews has been around for a year, but I had not seen it until today)

I just found out about MicrobiomeNews, run by MoBio Laboratories. It seems to cover the same articles I have been blogging about.

So here is a question for you, dear readers: Should I stop running this blog MicrobiomeDigest and let MoBio do the work? With only ~100 visitors a day, I am not sure if my efforts (3-4 hours a day) are worth it. After a couple of months of growth, I seem to have reached a plateau, and it is just not serving the large audience I had hoped to attract.

Any suggestions for improvement or increasing the visibility of my blog are very welcome, at eliesbik * stanford dot edu! But, at least today, here is a new installment.

Pregnancy and birth

Prematurity and Perinatal Antibiotics: A Tale of Two Factors Influencing Development of the Neonatal Gut Microbiota – Daniel B. DiGiulio – The Journal of Pediatrics

Intestinal dysbiosis: an emerging cause of pregnancy complications? – Dongxin Zhang – Medical Hypotheses

Human gut microbiome

The role of the gut microbiome in the healthy adult status – Valeria D’Argenio, Francesco Salvatore – Clinica Chimica Acta

What’s One Phosphate between Friends (and Foe)? – Charles L. Bevins, Andreas J. Bäumler – Cell Host & Microbe

Acarbose treatment affects the serum levels of inflammatory cytokines and the gut content of bifidobacteria in Chinese patients with type 2 diabetes mellitus – Benli Su – Journal of Diabetes

Human urine microbiome

Search for Microorganisms in Men with Urologic Chronic Pelvic Pain Syndrome: A Culture-Independent Analysis in the MAPP Research Network – J. Curtis Nickel – The Journal of Urology

Animal models of microbiome research

Commensal microbes and interferon-λ determine persistence of enteric murine norovirus infection – Megan T. Baldridge – Science

Interferon-λ cures persistent murine norovirus infection in the absence of adaptive immunity – Timothy J. Nice – Science

Adult Hippocampal Neurogenesis is Regulated by the Microbiome – Ebere S. Ogbonnaya – Biological Psychiatry

Animal microbiome

Sweet talking your partner – Christina Tobin Kåhrström – Nature Reviews Microbiology

Soil microbiome

Metagenomic Sequence of saline desert Microbiota from Wild Ass Sanctuary, Little Rann of Kutch, Gujarat, India – Patel Rajesh – Genomics Data

Phages and viruses

Temperate bacteriophages collected by outer membrane vesicles in Komagataeibacter intermedius – Alla Kharina – Journal of Basic Microbiology

Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution – Mart Krupovic & Eugene V. Koonin – Nature Reviews Microbiology

Archaea

Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota – Céline Petitjean – Genome Biology and Evolution

Metagenomics

What is a resistance gene? Ranking risk in resistomes – José L. Martínez – Nature Reviews Microbiology

Metabolomics

Intestinal Microbiota-Derived Metabolomic Blood Plasma Markers for Prior Radiation Injury – Pilib Ó Broin – International Journal of Radiation Oncology*Biology*Physics

Metabolic dependence of phytoplankton species richness – A. M. Segura – Global Ecology and Biogeography

Microbes in the news

How The Body Maintains A Healthy Balance Of ‘Friendly’ Gut Bacteria – Carolyn Gregoire – Huffington Post

Cracked! Researchers Nearing Completion of Genetic Map of Grapevine Disease – James Duren – Snooth.com

A. vaginae, G. vaginalis linked to preterm birth, miscarriage – Healio

3Bar Biologics developing beneficial bacteria for farmers’ fields – Carrie Ghose – BizJournals

Brain Food: The Human Microbiome (podcast with Greg Caporaso) – Bonnie Stevens – KNAU Northern Arizona University

Analyzing the Gut Microbiome to Help Detect Colorectal Cancer – National Cancer Institute

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – Research and Markets

New tech keeps bacteria from sticking to surfaces – Krishna Ramanujan – R&D Magazine

Your Phone Contains Personal Contacts… And Lots of Bacteria – Jenna Iacurci – Nature World News

Science, publishing and career

By a former student in our lab: Protecting genetic privacy may be bad for your health – Akshay Maheshwari – SF Gate

A European postdoc for the family – Michelle Gabriele Sandrian – Science

Expectations of brilliance underlie gender distributions across academic disciplines – Sarah-Jane Leslie – Science

Bik’s Picks

What’s the Secret to Getting Kids to Eat Veggies? Let Them Play First! – Shannon Hall – Live Science

HiRISE camera spots long-lost space probe on Mars – Science Daily

Satire: Epidemiologists Warn of Emerging Deadly Pandemic of Selfie-sticks – The Allium

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January 15, 2015

Posted on January 15, 2015 by eliesbik

Human respiratory microbiome

Aging and the microbiome: implications for asthma in the elderly? – Sanjay H Chotirmall, and Conor M Burke – Expert Review of Respiratory Medicine

Human oral microbiome

Code blue: Acinetobacter baumannii, a nosocomial pathogen with a role in the oral cavity –
A.M. Richards – Molecular Oral Microbiology

Inhibitory effect of Lactobacillus salivarius on Streptococcus mutans biofilm formation – C.-C. Wu – Molecular Oral Microbiology

Animal models of microbiome research

Murine Gut Microbiota—Diet Trumps Genes – Jens Walter – Cell Host & Microbe

Animal microbiome

Effects of dietary synbiotic on growth, survival, lactobacillus bacterial count, blood indices and immunity of beluga (Huso huso Linnaeus, 1754) juvenile – R. Akrami – Aquaculture Nutrition

Plant microbiome

Short-term impact of two liquid organic fertilizers on Solanum lycopersicum L. rhizosphere Eubacteria and Archaea diversity – L. Canfora – Applied Soil Ecology

A review on weeds as source of novel plant growth promoting microbes for crop improvement – C. Sarathambal – Journal of Applied and Natural Science

Different mycorrhizal fungal strains determine plant community response to nitrogen and water availability – Laura B. Martínez – Journal of Plant Nutrition and Soil Science

Soil microbiome

Effects of wildfires on flora, fauna and physico-chemical properties of soil-An overview –
Manoj Kumar Jhariy* and Abhishek Raj – Journal of Applied and Natural Science

Cellulolytic potential under environmental changes in microbial communities from grassland litter – Renaud Berlemont – Frontiers in Microbiology

Water microbiome

Insights into environmental controls on microbial communities in a continental serpentinite aquifer using a microcosm-based approach – Melitza Crespo-Medina – Frontiers in Microbiology

Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India – Devanita Ghosh – Frontiers in Microbiology

Food microbiology

Isolation and Identification of Lactic Acid Bacteria in Winter Salad (Local Pickle) during Fermentation Using 16S rRNA Gene Sequence Analysis – Mansour Saeedi – Journal of Food Safety

Metagenomics

Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State – Melanie R. Mormile – Frontiers in Microbiology

Bioinformatics

The yearly Database Issue of Nucleic Acids Research is out. Just a selection:
– rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development – Steven F. Stoddard
– Update on RefSeq microbial genomes resources – Tatiana Tatusova

Scientific Meeting 2014 “NGS Data after the Gold Rush” Meeting, Norwich, UK – EMBnet.journal. Selection of 2 abstracts:
– Analyzing RNA-Seq data with RNASeqGUI – Claudia Angelini, Francesco Russo – EMBnet.journal
– NGS data management and analysis for hundreds of projects: Experiences from Sweden – Ola Spjuth – EMBnet.journal
Microbial Ecology

Perspective: Impact of spatial distribution on the development of mutualism in microbes – Ákos T. Kovács – Frontiers in Microbiology

Bacteria in the news

Cataloguing 10 million human gut microbial genes – Tim Sandle – Pharmamicroresources

Arctic bacteria could make life-saving drugs – Samantha Bresnahan – KSPR

Iron Overload Disease Causes Rapid Growth of Potentially Deadly Bacteria, UCLA Study Finds – Infection Control Today

The Microbiome Diet: Evolving Past Paleo – Raphael Kellman

Is Naya Rivera right about her ‘showering too often’ theory? – Hope Gillette – Voxxi

Science, publishing and career

Want To Be In STEM? Here Are The 10 Best Metro Areas – Hank Campbell – Science 2.0

Gender gap: Women welcome in ‘hard working’ fields, but ‘genius’ fields are male-dominated, study finds – Rachel Feltman – Washington Post

Bik’s Picks

Prolonging lifespan: Researchers create ‘Methuselah fly’ by selecting best cells – Science Daily

Proteins found in the brain may help speed up flu recovery while you sleep – Lydia Ramsey – Popular Science

What the history of dogs tells us about civilization in the Americas – Elahe Izadi – Washington Post

Earth’s magnetic field guides sea turtles home – Julia Rosen – Science News

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January 14, 2015

Posted on January 14, 2015 by eliesbik

Human gut microbiome

Review: Fusobacterium and Escherichia: models of colorectal cancer driven by microbiota and the utility of microbiota in colorectal cancer screening – Andrea Leung – Expert Review of Gastroenterology & Hepatology

Animal microbiome

Passage of Wolbachia pipientis through Mutant Drosophila melanogaster Induces Phenotypic and Genomic Changes – Irene L. G. Newton and Kathy B. Sheehan – Applied and Environmental Microbiology

Water microbiome

Alternative Fecal Indicators and Their Empirical Relationships with Enteric Viruses, Salmonella enterica, and Pseudomonas aeruginosa in Surface Waters of a Tropical Urban Catchment – L. Liang – Applied and Environmental Microbiology

Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean – Alyson E. Santoro – PNAS USA

More microbiology

Innate sensing of microbial products promotes wound-induced skin cancer – Esther Hoste – Nature Communications

Identifying strains that contribute to complex diseases through the study of microbial inheritance – Jeremiah J. Faith – PNAS USA

Long-term phenotypic evolution of bacteria – Germán Plata – Nature

Co-infection alters population dynamics of infectious disease – Hanna Susi – Nature Communications

Ferment in the family tree – Nathaniel J. Dominy – PNAS USA

Infection and Host response

Profiling lymphocyte interactions at the single-cell level by microfluidic cell pairing – Burak Dura – Nature Communications

B-cell repertoire responses to varicella-zoster vaccination in human identical twins
Chen Wang – PNAS USA

Metabolomics

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi – Ralph A. Cacho – Frontiers in Microbiology

The chemistry of negotiation: Rhythmic, glycan-driven acidification in a symbiotic conversation – Julia A. Schwartzman – PNAS USA

Microbes in the news

I love this title! Featuring Margaret McFall-Ngai: Microbiology: Here’s looking at you, squid – Ed Yong – Nature

How Bread, Beer, and Soy Sauce Changed the Human Microbiome – Francie Diep – Popular Science

Early human microbiome studies may aid modern nutrition science – Nathan Gray – Nutraingredients

Understanding the personalities of bacteria – Phys.org

2014: The Year of the Virus – Joan B. Rose – Huffington Post

Have viruses made us smarter? ‘Junk’ virus genes in our DNA may have helped our brain cells evolve – By Victoria Woollaston – Daily Mail

With Vedanta Deal, Johnson & Johnson Marks Big-Pharma Milestone in the Microbiome – Alex Lash – Xconomy

Scientists developing Teflon for bacteria – Amanda Schupak – CBS News

Understanding the personalities of bacteria – Phys.org

#BacteriaHysteria – beautiful, not filthy! Smartphone bacteria ‘prints’ show how filthy your mobile really is – Rob Waugh – Metro

Science, publishing and career

A generation at risk: Young investigators and the future of the biomedical workforce – Ronald J. Daniels – PNAS USA

Work–life balance: Lab life with kids – Kendall Powell – Nature

Bik’s Picks

‘I can haz genomes’: cats claw their way into genetics – Canine dominance bows to tabby chic as cat sequencing takes off – Ewen Callaway – Nature
and
Out of the bag: The preference for either cats or dogs affects science more than you might think– Nature

Geographically varying associations between personality and life satisfaction in the London metropolitan area – Markus Jokela – PNAS USA

Very important science: Watch a chainsaw made with shark teeth slice through salmon – Francie Diep – Popular Science

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January 13, 2015

Posted on January 13, 2015 by eliesbik

Human oral microbiome

The Biofilm Community: Rebels with a Cause – A. Wilson Aruni – Current Oral Health Reports

Human respiratory microbiome

Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age – J C Stearns – The ISME Journal

Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection – Sophie E. Darch – Scientific Reports

Human gut microbiome

Effect of Exclusive Enteral Nutrition on the Microbiota of Children With Newly Diagnosed Crohn’s Disease – Nadeem O. Kaakoush – Clinical and Translational Gastroenterology

The intestinal microbiota: its role in health and disease – Luc Biedermann, Gerhard Rogler – European Journal of Pediatrics

Geographical patterns of the standing and active human gut microbiome in health and IBD – Ateequr Rehman – Gut

Severity of atopic disease inversely correlates with intestinal microbiota diversity and butyrate-producing bacteria – L. Nylund – Allergy

The influence of the microbiota on the immune response to transplantation – Bartman, Caroline – Current Opinion in Organ Transplantation

Animal models of microbiome research

The enduring importance of animal models in understanding periodontal disease – George Hajishengallis – Virulence

Animal microbiome

Molecular analysis of cecal and tracheal microbiome of heat-stressed broilers supplemented with prebiotic and probiotic – Muhammad U. Sohail – Avian Pathology

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies – Karen E Sullam – The ISME Journal

Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes – Daniel F. R. Cleary – Antonie van Leeuwenhoek

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community – Pim Bongaerts – Scientific Reports

Soil microbiome

Exploring the dynamics of bacterial community composition in soil: the pan-bacteriome approach – Giovanni Bacci – Antonie van Leeuwenhoek

Role of RNase on microbial community analysis in the rice and wheat plants soil by 16S rDNA-DGGE – Md. Mizanur Rahman – Journal of Crop Science and Biotechnology

Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils – Jing Li – Frontiers in Microbiology

Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil – Gaidi Ren – Frontiers in Microbiology

Soil bacterial and fungal communities respond differently to various isothiocyanates added for biofumigation – Ping Hu – Frontiers in Microbiology

Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage – Björn Breidenbach and Ralf Conrad – Frontiers in Microbiology

Biogeography and biophysicochemical traits link N2O emissions, N2O emission potential and microbial communities across New Zealand pasture soils – Sergio E. Morales – Soil Biology and Biochemistry

Formation of iron-rich shelled structures (IRSS) by microbial communities – David C. Fernández-Remolar – Journal of Geophysical Research: Biogeosciences

Effects of alkyl-imidazolium ionic liquid [Omim]Cl on the functional diversity of soil microbial communities – Pengpeng Guo – Environmental Science and Pollution Research

Cyanobacteria drive community composition and functionality in rock-soil interface communities – Angel Valverde – Molecular Ecology

Separation of soil microbial community structure by aggregate size to a large extent under agricultural practices during early pedogenesis of a Mollisol – Na Li – Applied Soil Ecology

Microbial community structure of anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454-pyrosequencing – Zhen Zhou – Chemical Engineering Journal

Conservation tillage positively influences the microflora and microfauna in the black soil of Northeast China – Shixiu Zhang – Soil and Tillage Research

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity – Zach Aanderud – Frontiers in Microbiology

Water microbiome

Drinking water microbiology — from measurement to management – Caitlin R Proctor, Frederik Hammes – Current Opinion in Biotechnology

Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time – Guus Roeselers – Environmental Microbiology

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge – Håkon Dahle – The ISME Journal
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2014247a.html

Metagenomics

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics – Tomàs Llorens-Marès – The ISME Journal

Environmental Metagenomics: The Data Assembly and Data Analysis Perspectives – Vinay Kumar – Journal of The Institution of Engineers (India): Series A

Metagenome assembly through clustering of next-generation sequencing data using protein sequences – Mikang Sim, Jaebum Kim – Journal of Microbiological Methods

Metagenomic Insights into the Effects of Fructo-oligosaccharides (FOS) on the Composition of Fecal Microbiota in Mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

Diagnosis of Neuroinvasive Astrovirus Infection in an Immunocompromised Adult With Encephalitis by Unbiased Next-Generation Sequencing – Samia N. Naccache – Clinical Infectious Diseases

Unbiased Next-Generation Sequencing and New Pathogen Discovery: Undeniable Advantages and Still-Existing Drawbacks – Arianna Calistri and Giorgio Palù – Clinical Infectious Diseases

Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA – Anisha Dayaram – Infection, Genetics and Evolution

Metabolomics

Multi -omics and metabolic modelling pipelines: challenges and tools for systems microbiology – Marco Fondi and Pietro Liò – BioRxiv

Techniques

Accounting for uncertainty in DNA sequencing data – Jason A. O’Rawe – Trends in Genetics

More microbes
3D-Printed Microfluidic Device for the Detection of Pathogenic Bacteria Using Size-based Separation in Helical Channel with Trapezoid Cross-Section – Wonjae Lee – Scientific Reports

Microbes in the news

UCSD hires star biologist Rob Knight – Gary Robbins – UT San Diego

Drug developed out of microbiome studies advances in phase I trial – Stephanie M. Lee – SF Gate
and
Second Genome’s gut check uncovers a possible drug for bowel disease – Ron Leuty – San Francisco Business Times

The Megabiome – It’s not micro anymore – Megabiome.net

Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome… (with Jessica Richman and Jonathan Eisen) – Tim Ferriss Show – Four Hour Workweek

Mounting Research Shows Gut-Brain Connection – Traci Pedersen – Psych Central

Microbiota organization influences colorectal cancers – Nicola Garrett – Family Practice News

“MyNewGut”: New project explores role of gut microbiota in preventing diet- and brain-related diseases – News-Medical.net

Joint Pain, From the Gut – David Kohn – The Atlantic

A Lamp Whose Light Comes From Bioluminescent Bacteria – Liz Stinson – Wired.com

Pieter Dorrestein Recognized by Pharmacology Society – Heather Buschman – UC San Diego

Science, publishing and career

Post publication peer review comes of age – Emma Stoye – Chemistry World

What Tech Conferences Need to Stop for Women to Contribute More – Kellyn Pot’Vin-Gorman – LinkedIn

Bik’s Picks

Because our lab is close: Jeepers! New Look at ‘Creeping’ San Andreas Fault
by Becky Oskin – LiveScience
http://www.livescience.com/49435-san-andreas-fault-less-creepy.html

These scientists raised bot fly larvae in their own bodies — on purpose – Rachel Feltman – The Washington Post

Today in Adorable Science: Disney Has Created a L’il Turtle Robot to Draw Doodles in the Sand – Carolyn Cox – The Mary Sue

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Science – Career – Publishing

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