Category Archives: General Microbiome

January 23, 2015

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Several papers on the effect of functional foods on the microbiome, fecal bacteria of the blue tit, and finding an old vial of bacteria.

Human gut microbiome

Toll-like receptor 5 in obesity: The role of gut microbiota and adipose tissue inflammation – Satu Pekkala – Obesity

Gut microbial and short-chain fatty acid profiles in adults with chronic constipation before and after treatment with lubiprostone – Dae-Wook Kang – Anaerobe

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

Review: The influence of diet on the gut microbiota and its consequences for health – Joël Doré, Hervé Blottière – Current Opinion in Biotechnology

Animal and other models of microbiome research

Effects of Probiotic Enterococcus faecium NCIMB 11181 Administration on Swine Fecal Microbiota Diversity and Composition using Barcoded Pyrosequencing – Edward Alain B. Pajarillo – Animal Feed Science and Technology

Influences of structures of galactooligosaccharides and fructooligosaccharides on the fermentation in vitro by human intestinal microbiota – Wei Li – Journal of Functional Foods

Differential effects of probiotics, prebiotics, and synbiotics on gut microbiota and gene expression in rats – Gunaranjan Paturi – Journal of Functional Foods

Animal microbiome

Phylogenetic diversity and biological activity of culturable Actinobacteria isolated from freshwater fish gut microbiota – Mansooreh Jami – Microbiological Research

Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus – Clare McW. H. Benskin – Ecology and Evolution

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 20, 2015

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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

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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 7, 2015

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Human skin microbiome

Commensal–dendritic-cell interaction specifies a unique protective skin immune signature – Shruti Naik – Nature

Human gut microbiome

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism – Fiona Cuskin – Nature

Animal models of microbiome research

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile – Charlie G. Buffie – Nature

Animal microbiome

Antibiotics in ingested human blood affect the mosquito microbiota and capacity to transmit malaria – Mathilde Gendrin – Nature Communications

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R. M. Polónia – Molecular Ecology

Plant microbiome

Plant-Plant-Microbe Mechanisms Involved in Soil-Borne Disease Suppression on a Maize and Pepper Intercropping System – Min Yang – PLOS ONE

Water microbiome

Adapt or Die on the Highway To Hell: Metagenomic Insights into Altered Genomes of Firmicutes from the Deep Biosphere – Brandon Briggs, Frederick Colwell – AGU Fall Meeting San Francisco

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles – Kate Wall – Microbiology Open

Bioinformatics

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences – Anirban Dutta – PLOS ONE

Probiotics

Isolation and Characterization of Faecalibacterium prausnitzii from Calves and Piglets – Carla Foditsch – PLOS ONE

Antibiotics

A new antibiotic kills pathogens without detectable resistance – Losee L. Ling – Nature

Phages and viruses

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions – Arun M. Nanda – Journal of Bacteriology

More microbes

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota – Jean-Christophe Lagier – Clinical Microbiology Reviews

Current and Past Strategies for Bacterial Culture in Clinical Microbiology – Jean-Christophe Lagier – Clinical Microbiology Reviews

Microbes in the news

How bacteria control their size – Diana Lutz – Washington University in St. Louis

Nestlé Health Science Invests $65M in Microbiome Therapy Startup – Drug Discovery and Development
Deep bacteria may evolve even without passing genes on – Colin Barras – New Scientist

Enough with the cleaning – it’s time we stopped giving bacteria such a hard time – Emer Sexton – Irish Examiner

Skin microbes trigger specific immune responses – Science Daily

Beer, bread yeast-eating bacteria aid human health – Science Daily

Science, publishing, career

Outreach: Speak up for science – Virginia Gewin – Nature

Science at risk as young researchers increasingly denied research grants – Phys.org

Science, in the Words of Alan Alda – Jessica Lahey – The Atlantic

University or University of Life? Neither provides workers with necessary people skills – Science Daily

English Is the Language of Science. That’s lousy luck for scientists in most of the world – Boer Deng – Slate.com

Bik’s Picks

Forget the selfish gene: Evolution of life is driven by the selfish ribosome, research suggests – Science Daily

Search for the First True Alien Earth Heats Up – Mike Wall – Space.com

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January 5, 2015

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Happy New Year!

Human oral microbiome

Salivaomics – David T.W. Wong – The Journal of the American Dental Association

Human respiratory microbiome

The Bergen COPD microbiome study (MicroCOPD): rationale, design, and initial experiences – Rune Grønseth – European Clinical Respiratory Journal

Human skin microbiome

Interactions between host factors and the skin microbiome – Adam SanMiguel, Elizabeth A. Grice – Cellular and Molecular Life Sciences

Molecular Characterization of the Skin Fungal Microbiota in Patients with Seborrheic Dermatitis – Akiomi Tanaka – Clinical & Experimental Dermatology Research

Human gut microbiome

Microbiota-Mediated Inflammation and Antimicrobial Defense in the Intestine – Silvia Caballero and Eric G. Pamer – Annual Review of Immunology

* Role of the intestinal microbiota and fecal transplantation in inflammatory bowel diseases – Jie Liang – Journal of Digestive Diseases

Special Issue: Faecal transplantation and infectious diseases practitioners – D. Raoult – Clinical Microbiology and Infection

Human Clostridium difficile infection: Inhibition of NHE3 and microbiota profile – Melinda A Engevik – American Journal of Physiology – Gastrointestinal and Liver Physiology

Gut Fungal Microbiota: The Yin and Yang of Inflammatory Bowel Disease –
Richard, Mathias L. – Inflammatory Bowel Diseases

Gut-Microbiota and Mental Health: Current and Future Perspectives –
Ajit Kumar Thakur – Journal of Pharmacology & Clinical Toxicology

Microbiota, Biofilms and Helicobacter Pylori in the Diseases of Gastroduodenal Zone – G.Sh. Isaeva , V.B. Ziatdinov – Kazan Medical Journal

Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers – Kristin Schmidt – Psychopharmacology

The Human Microbiome, Ecological Ontology, and the Challenges of Community – Gregory W. Schneider and Russell Winslow – Perspectives in Biology and Medicine

Microbiome of pregnancy and birth

* Temporal dynamics of the very premature infant gut dominant microbiota – Fabien Aujoulat – BMC Biology

The Preterm Placental Microbiome Varies in Association with Excess Maternal Gestational Weight Gain – Kathleen M. Antony – American Journal of Obstetrics and Gynecology

* Study in 2 million children: Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal models

Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques – Kai-tao Hu – International Journal of Infectious Diseases

Investigating the long-term effect of subchronic phencyclidine-treatment on novel object recognition and the association between the gut microbiota and behavior in this animal model of schizophrenia – B. Pyndt Jørgensen – Physiology & Behavior

Red Ginseng and Semen Coicis can improve the structure of gut microbiota and relieve the symptoms of ulcerative colitis – Mingzhang Guo – Journal of Ethnopharmacology

Animal microbiome

Stability of the Gorilla Microbiome Despite SIV Infection – Andrew H. Moeller – Molecular Ecology

Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota – Guillaume Carissimo – PNAS USA

* Microbiota shifts in the surface mucopolysaccharide layer of corals transferred from natural to aquaria settings – Zoe A. Pratte – Journal of Invertebrate Pathology

Sponging up metals: Bacteria associated with the marine sponge Spongia officinalis – Cléa Bauvais – Marine Environment Research

Plant microbiome

Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development – Laura B. Martínez-García – New Phytologist

* A Model to Explain Plant Growth Promotion Traits: A Multivariate Analysis of 2,211 Bacterial Isolates – Pedro Beschoren da Costa – PLOS ONE

The application of Arabidopsis thaliana in studying tripartite interactions among plants, beneficial fungal endophytes and biotrophic plant-parasitic nematodes – Alfonso Martinuz – Planta

Differences in thallus chemistry are related to species-specific effects of biocrust-forming lichens on soil nutrients and microbial communities – Manuel Delgado-Baquerizo – Functional Ecology

Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress – Nidhi Bharti – Microbial Ecology

Promoting effect of Fusarium oxysporum [f.sp. strigae] on abundance of nitrifying prokaryotes in a maize rhizosphere across soil types – Mary K. Musyoki – Biological Control

Preferential allocation, physio-evolutionary feedbacks, and the stability and environmental patterns of mutualism between plants and their root symbionts – James D. Bever – New Phytologist

Fungi in the future: interannual variation and effects of atmospheric change on arbuscular mycorrhizal fungal communities – T. E. Anne Cotton – New Phytologist

Soil and sediment microbiome

Prevalence of Antibiotic Resistance Genes and Bacterial Pathogens in Long-Term Manured Greenhouse Soils As Revealed by Metagenomic Survey – Hua Fang – Environmental Science & Technology

Water Content Differences Have Stronger Effects than Plant Functional Groups on Soil Bacteria in a Steppe Ecosystem – Ximei Zhang – PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0115798

A Novel Sister Clade to the Enterobacteria Microviruses (family Microviridae) Identified in Methane Seep Sediments – Sam Bryson – Environmental Microbiology

Dynamics of Plant Nutrients, Utilization and Uptake, and Soil Microbial Community in Crops Under Ambient and Elevated Carbon Dioxide – Shardendu K. Singh – Nutrient Use Efficiency: from Basics to Advances

Water microbiome

Physical controls of variability in North Atlantic phytoplankton communities – Andrew D. Barton – Limnology and Oceanography

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

Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities – Francisco J. R. C. Coelho – Global Change Biology

The Food Web of Boiling Springs Lake Appears Dominated by the Heterolobosean Tetramitus thermacidophilus Strain BSL – William H.H. Reeder IV – Journal of Eukaryotic Microbiology

Microbiome of digesters and wastewater

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters – David Wilkins – Applied and Environmental Microbiology

Association of Biodiversity with the Rates of Micropollutant Biotransformations among Full-Scale Wastewater Treatment Plant Communities – David R. Johnson – Applied and Environmental Microbiology

Microbial Community Structure and Diversity in an Integrated System of Anaerobic-Aerobic Reactors and a Constructed Wetland for the Treatment of Tannery Wastewater in Modjo, Ethiopia – Adey Feleke Desta – PLOS ONE

Enhancement of sludge granulation in anaerobic acetogenesis by addition of nitrate and microbial community analysis – Yang Li – Biochemical Engineering Journal

Microbiome of the built environment

* Indoor Fungi: Companions and Contaminants – A. Nevalainen – Indoor Air

Food microbiology

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method – M. Takahashi – Journal of Applied Microbiology

Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina – Patricia Elizaquível – International Journal of Food Microbiology

Metagenomics

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not – Jessica Hedge, Daniel J. Wilson – mBio

Reply to “Expanding the Conversation on High-Throughput Virome Sequencing Standards To Include Consideration of Microbial Contamination Sources” – Jason T. Ladner – mBio

Metabolomics

Response of Peripheral Rhythms to the Timing of Food Intake – Megumi Hatori, Satchidananda Panda – Methods in Enzymology

Techniques

The near-quantitative sampling of genomic DNA from various food-borne Eubacteria – Peter Irwin – BMC Microbiology

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system – Patrick D. Schloss preprint

Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems – Jarrad T. Hampton-Marcell – Springer Protocols Handbooks

Protocols for Handling, Storing, and Cultivating Oil Sands Tailings Ponds Materials for Microbial and Molecular Biological Study – J. M. Foght – Springer Protocols Handbooks

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples (video) – Yan Wei Lim – JOVE

Microbes in the news

Book: Principals of Microbial Diversity – James W. Brown – ASM Press

Bacteria hold clues to our health – Heather Kelly – CNN

11+ things everyone needs to know about microbes – Jonathan Eisen – MicrobeNet

How to Build a Healthy Microbiome, Before, During, and After Birth – Kelly Brogan – Mercola.com

Mining the microbiome: How the microbes that share our bodies could help prevent cancer – Leigh MacMillan – Vanderbilt-Ingram

The Surprising Link Between Gut Bacteria And Anxiety – Carolyn Gregoire – Huffington Post

Stress, Depression, & The Bacteria In Your Gut – Video with Professor John F. Cryan – Richard Zwolinski – PsychCentral

Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus – Jonathan Eisen – The Tree of Life

Gut Microbiome Rebounds After Colonoscopy Bowel Preparation – Lara C. Pullen – Medscape

Elevator buttons at hospitals have more bacteria than the toilets – Nicole Oran – MedCityNews

Can Mars be terraformed with bacteria? The Cyano Knights think so! Scott Sutherland – The Weather Network

Cholera’s Method of Killing Identified – Jim Algar – Tech Times

Science, publishing and career

A Stronger Post-Publication Culture Is Needed for Better Science – Hilda Bastian – PLOS Medicine

Advocating for women in hiring decisions – Dr. Mellivora – Tenure She Wrote

Science and art

Stylish Silk Scarves, Dyed With Bacteria – Liz Stinson – Wired.com

Bik’s Picks

The global distribution of diet breadth in insect herbivores – Matthew L. Forister – PNAS USA

‘Bad luck’ of random mutations plays predominant role in cancer, study shows – Science Daily

Experimental Diet Pill Tricks Body into Thinking It Ate – Bahar Gholipour – Live Science

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December 30, 2014

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Human oral microbiome

Mucosal Microbiome in Patients with Recurrent Aphthous Stomatitis – K. Hijazi – Journal of Dental Research

Human respiratory microbiome

Impact of saline irrigation and topical corticosteroids on the postsurgical sinonasal microbiota – Cindy M. Liu – International Forum of Allergy & Rhinology

Human gut microbiome

The Gastrointestinal Microbiota and Colorectal Cancer – Temitope O. Keku – American Journal of Physiology – Gastrointestinal and Liver Physiology

The Impact of Diet and Lifestyle on Gut Microbiota and Human Health – Michael A. Conlon and Anthony R. Bird – Nutrients

Understanding How Commensal Obligate Anaerobic Bacteria Regulate Immune Functions in the Large Intestine – Eva Maier – Nutrients

Animal microbiome
Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna – Saranya Peerakietkhajorn – Environmental Microbiology Reports

Antibiotic activity and microbial community of the temperate sponge, Haliclona sp. – A. Hoppers – Journal of Applied Microbiology

Plant microbiome

Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar – Shinjini Mukherjee – Molecular Ecology

Fungal Endophytes of Alpinia officinarum Rhizomes: Insights on Diversity and Variation across Growth Years, Growth Sites, and the Inner Active Chemical Concentration – Li Shubin – PLOS ONE

Endophytic microbial community in two transgenic maize genotypes and in their
near-isogenic non-transgenic maize genotype – Débora Alves Ferreira da Silva – BMC Microbiology

Soil, sediment, sludge, litter microbiome

Site properties have a stronger influence than fire severity on ectomycorrhizal fungi and associated N-cycling bacteria in regenerating post-beetle-killed lodgepole pine forests – Nabla M. Kennedy – Folia Microbiologica

Influence of Azo Dye Concentration on Activated Sludge Bacterial Community in the Presence of Functionalized Polyurethane Foam – Hong Lu – Applied Biochemistry and Biotechnology

The Potential of Antibiotic Alternatives for Enriching Beneficial Microbiota in Litter – Adriana A. Pedroso – SOJ Microbiology & Infectious Diseases

Water microbiome

Bacterial Community Composition in Three Freshwater Reservoirs of Different Alkalinity and Trophic Status – Marc Llirós – PLOS ONE

Bioinformatics
* Programming tools: Adventures with R – A guide to the popular, free statistics and visualization software that gives scientists control of their own data analysis – Sylvia Tippmann – Nature

Metabolomics, Proteomics

Symbiosis, dysbiosis, and rebiosis — The value of metaproteomics in human microbiome monitoring – Lei Mao and Jacqueline Franke – Proteomics

Viruses and Phages

Virus evolution towards limited dependence on the non-essential functions of the host: the bacteriophage SPP1 case – Virginija Cvirkaite-Krupovic – Journal of Virology

Microbial Ecology

Review: Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects – Jani Heino – Freshwater Biology

Microbes in the news

Is the Bacteria in Our Gut the Key to Our Health? (Podcast with Ed Yong, Jack Gilbert, Jonathan Eisen, Margaret McFall-Ngai starts at 9 min) – To The Point – Barbara Bogaev – KCRW

9 Amazing and Gross Things Scientists Discovered About Microbes This Year – Greg Miller – Wired.com

The Right Chemistry: Exposure to bacteria can help keep us healthy – Joe Schwarcz – Montreal Gazette

Scientists Discover How Mouth Microbes Cause Gum Disease – Randall Mayes – Design & Trend

Microbiologists cultivate “microbial dark matter” – Eric Hopton – RedOrbit

Science, Publishing, and Career

Open Access 2014: A Year that Data Cracked Through Secrecy and Myth – Hilda Bastian- PLOS Blogs

Bik’s Picks

Watch raindrops make asteroid-like collisions (slo-mo video) – Popular Science

An ‘Otter-This-World’ Christmas! – Total cuteness courtesy of the Monterey Bay Aquarium – Susan C. Schena – Patch.com

Go Outside Tonight and Take a Look at Comet Lovejoy in the Sky – Dan Van Winkle – The Mary Sue

46 Important Things Science Taught Us In 2014 – It was a big year for robot penguins, snake penises, and space exploration. Sadly not all at the same time – Kelly Oakes – BuzzFeed

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December 26, 2014

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Pregnancy and birth

* Early Childhood Gut Microbiomes Show Strong Geographic Differences Among Subjects at High Risk for Type 1 Diabetes – Kaisa M. Kemppainen – Diabetes Care

Human skin microbiome

* Spatial variations in the microbial community structure and diversity of the human foot is associated with the production of odorous volatiles – Deborah Stevens – FEMS Microbiology Ecology

Human respiratory microbiome

Microbiota profiling of bronchial fluids of elderly patients with pulmonary carcinoma – Naoko Ishida – Journal of Oral Biosciences

Human gut microbiome

* Microbial culturomics: paradigm shift in the human gut microbiome study – J.-C. Lagier
Clinical Microbiology and Infection

Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: Safety, feasibility, and efficacy trial results – Bota Cui – Journal of Gastroenterology and Hepatology

Culturomics: a new approach to study the human microbiome – G. Greub – Clinical Microbiology and Infection

The influence of the human microbiome and probiotics on cardiovascular health – Race Ettinger – Gut Microbes

Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility – Charlie T Seto – Microbiome

Animal microbiome

Use of metagenomic high-throughput sequencing technology and robust bioinformatics to assess the microbiome of cattle, their environments, and beef products to determine the degree of antimicrobial resistance – X. Yang – Meat Science

News in livestock research – use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Birds: Bacteria and the evolution of honest signals. The case of ornamental throat feathers in spotless starlings – Magdalena Ruiz-Rodríguez – Functional Ecology

Silverleaf whitefly: Diversity of symbiotic bacteria associated with Bemisia tabaci (Homoptera: Aleyrodidae) in cassava mosaic disease pandemic areas of Tanzania – L.S. Tajebe – Annals of Applied Biology

Physicochemical conditions, metabolites, and community structure of the bacterial microbiota in the gut of wood-feeding cockroaches (Blaberidae: Panesthiinae) – Eugen Bauer – FEMS Microbiology Ecology

Sea urchin larvae decipher the epiphytic bacterial community composition when selecting sites for attachment and metamorphosis – Shaun J. Nielsen – FEMS Microbiology Ecology

Plant microbiome

Land-use intensity and host plant identity interactively shape communities of arbuscular mycorrhizal fungi in roots of grassland plants – Kriszta Vályi – New Phytologist

Temporal patterns of orchid mycorrhizal fungi in meadows and forests as revealed by 454 pyrosequencing – Jane Oja – New Phytologist

Review: Exploring interactions of plant microbiomes – Fernando Dini Andreote – Scienta Agricola

Drying effects on archaeal community composition and methanogenesis in bromeliad tanks – Franziska B. Brandt – FEMS Microbiology Ecology

The effect of psychrotrophic bacteria isolated from the root zone of winter wheat on selected biotic and abiotic factors – Sebastian Wojciech Przemieniecki – Journal of Plant Protection Research

Soil microbiome

Influence of exogenous organic matter on prokaryotic and eukaryotic microbiota in an agricultural soil. A multidisciplinary approach – Daniela Pezzolla – Soil Biology and Biochemistry

Soil bacteria hold the key to root cluster formation – Byron B. Lamont – New Phytologist

Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula – Igor S. Pessi – FEMS Microbiology Ecology

The effect of storage on microbial activity and bacterial community structure of drained and flooded paddy soil – Juan Wang – Journal of Soils and Sediments

Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils – Andrew Long – FEMS Microbiology Ecology

Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments – Gordon Webster – FEMS Microbiology Ecology

Water microbiome

Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia) – Alexey S Rozanov – BMC Genomics

Food microbiology

Cheese rind microbial communities: diversity, composition and origin – Françoise Irlinger – FEMS Microbiology Letters

Microbiome and immunology

The role of IL-10 in microbiome-associated immune modulation and disease tolerance – Benoît Levast – Cytokine

TL1A regulates TCRγδ+ intraepithelial lymphocytes and gut microbial composition – Peter Tougaard – European Journal of Immunology

Microbiome components with probiotic or other interesting properties

Miniaturized Cultivation of Microbiota for Antimalarial Drug Discovery – Carrie Waterman – Medicinal Research Reviews

Antagonism against fish pathogens by cellular components and verification of probiotic properties in autochthonous bacteria isolated from the gut of an Indian major carp, Catla catla (Hamilton) – Anjan Mukherjee and Koushik Ghosh – Aquaculture Research

Probiotic strains introduced through live feed and rearing water have low colonizing success in developing Atlantic cod larvae – Jorunn Skjermo – Aquaculture

Metabolomics

Introducing the USA Plant, Algae and Microbial Metabolomics Research Coordination Network (PAMM-NET) – Lloyd W. Sumner – Metabolomics

Towards the Fecal Metabolome Derived from Moderate Red Wine Intake – Ana Jiménez-Girón – Metabolites

Bioinformatics

Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data – Koskinen Kaisa – Journal of Computational Biology

Microbes in the news

Is 2015 the Year We All Sequence Our Microbiomes?– The Atlantic

Do new natural products lurk in genes of bacteria? – Kevin Stacey-Brown – Futurity

Discovery holds promise for decoding elusive bacteria – Business Standard

Experimental Drugs Target Bacteria’s Social Network – Carl Zimmer – Scientific American

Did Microbes Shape the Human Life Span? – Tia Ghose – LiveScience

Does the Gut Microbiome Play a Role in Autoimmune Disease? – Amy Nett – ChrisKresser.com

Bik’s Picks

To Raise Science Scores, Colleges Look Beyond the Lecture – Richard Perez-Pena – New York Times

Tsunami Science: Advances Since the 2004 Indian Ocean Tragedy – Becky Oskin – Live Science

Rudimentary egg and sperm cells made from stem cells – David Cyranoski – Nature

Who Patented ‘My Favorite Things’? – Robinson Meyer – The Atlantic

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December 23, 2014

Posted on by

Microbiome publications are definitely not taking a winter break, so here is your holiday update. Merry Christmas to those who celebrate!

Human oral microbiome

Serum IgG Antibody Levels to Periodontal Microbiota Are Associated with Incident Alzheimer Disease – James M. Noble – PLOS ONE

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle – Xuesong He – PNAS USA

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant
and periodontal sites – Simone Schaumann – BMC Oral Health

Human respiratory microbiome

The Microbial Community of the Cystic Fibrosis Airway Is Disrupted in Early Life – Julie Renwick – PLOS ONE

Human gut or general microbiome
Effects of bowel cleansing on the intestinal microbiota – Jonna Jalanka – Gut

The Microbiome of Aging and Age-Related Disease – 2014 Meeting Abstracts

Microbial community pattern detection in human body habitats via ensemble clustering framework – Peng Yang – ArXiv.org

Cancer and the microbiome: potential applications as new tumor biomarker – Khan Shahanavaj – Expert Review of Anticancer Therapy

Influence of Intestinal Microbiota on Body Weight Gain: a Narrative Review of the Literature – Camila S. Cardinelli – Obesity Surgery

Animal models of microbiome research

Host genetics and diet, but not immunoglobulin A expression, converge to shape
compositional features of the gut microbiome in an advanced intercross population
of mice – Larry J Leamy – Genome Biology

Animal microbiome

Microbiomes, plausible players or not in alteration of host behaviour – David G. Biron – Frontiers in Microbiology

The Howler Monkey as a Model for Exploring Host-Gut Microbiota Interactions in Primates – Katherine R. Amato, Nicoletta Righini – Howler Monkeys

The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra) – Katherine R. Amato – Microbial Ecology

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota – T.D.J. Bello González – Beneficial Microbes

Effects of dietary supplementation of a commercial prebiotic Previda® on survival, growth, immune responses and gut microbiota of Pacific white shrimp, Litopenaeus vannamei – J.D. Anuta – Aquaculture Nutrition

Metagenomic-Based Study of the Phylogenetic and Functional Gene Diversity in Galápagos Land and Marine Iguanas – Pei-Ying Hong – Microbial Ecology

Plant microbiome

The plant microbiome at work – Klaus Schlaeppi and Davide Bulgarelli – Molecular Plant-Microbe Interactions

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology

The Sesquiterpene Biosynthesis and Vessel-Occlusion Formation in Stems of Aquilaria sinensis (Lour.) Gilg Trees Induced by Wounding Treatments without Variation of Microbial Communities – Zheng Zhang – International Journal of Molecular Sciences

Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists – Jürgen Köhl – Biological Control

Soil and sediment microbiome

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland – Raeid M. M. Abed – PLOS ONE

Do climate factors govern soil microbial community composition and biomass at a regional scale? – L. Ma – Biogeosciences Discuss

Water microbiome

Early succession of micro-periphyton communities in kelp bed and barren ground ecological systems – Roberto A. Uribe – Marine Ecology

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China – Shang Wang – Scientific Reports

Effects of warming on microbial communities in the coastal waters of temperate and subtropical zones in the Northern Hemisphere, with a focus on Gammaproteobacteria
Dao Thi Anh Tuyet – Journal of Oceanography

Colonization in the photic zone and subsequent changes during sinking determines bacterial community composition in marine snow – Stefan Thiele – Applied and Environmental Microbiology

Diversity, Distribution and Hydrocarbon Biodegradation Capabilities of Microbial Communities in Oil-Contaminated Cyanobacterial Mats from a Constructed Wetland
Raeid M. M. Abed – PLOS ONE

Bioreactor microbiology

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures – Shaobo Liang – Bioresource Technology

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates – Damian E. Helbling – Water Research

Metagenomics

Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India – Johan Bengtsson-Palme – Frontiers in Microbiology

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity – Michelle Davison – Photosynthesis Research

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms – Martial Marbouty – eLIFE

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing – Alexander W. Eastman and Ze-Chun Yuan – Frontiers in Microbiology

Metabolomics and transcriptomics

Terpene synthases are widely distributed in bacteria – Yuuki Yamada – PNAS USA

Scaling microbial biomass, metabolism and resource supply – Robert L. Sinsabaugh – Biogeochemistry

Metatranscriptomics of N2-fixing cyanobacteria in the Amazon River plume – Jason A Hilton – ISME Journal

Mining Soil Metagenomes to Better Understand the Evolution of Natural Product Structural Diversity: Pentangular Polyphenols as a Case Study – Hahk-Soo Kang and Sean F. Brady – Journal of the American Chemical Society

Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale – Darrell W. Cockburn – Molecular Microbiology

Techniques

Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory – Yolanda Blanco – PLOS ONE

Rapid species-level identification of vaginal and oral lactobacilli using MALDI-TOF MS analysis and 16S rDNA sequencing – Annette Carola Anderson – BMC Microbiology

Probiotics

Probiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis – Susana Delgado – Frontiers in Microbiology

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – E. Saussereau – Clinical Microbiology and Infection

More Microbiology

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria – Mesrop Ayrapetyan – Trends in Microbiology

Bacterial microcompartments and the modular construction of microbial metabolism – Cheryl A. Kerfeldemail, Onur Erbilgin – Trends in Microbiology

The impact of triclosan on the spread of antibiotic resistance in the environment – Daniel E. Carey – Frontiers in Microbiology

Microbes in the news

At Last, I Meet My Microbes – Katherine Harmon Courage – NPR Shots

This Is Your Microbiome: Katherine Harmon Courage at NPR is taking a tour through her microbiome and that of her husband, mother, and dog, as she recounts in a four-part series – Genome Web

Big Idea 2015: Medicine, Wellbeing, and the Microbiome – Deepak Chopra – LinkedIn

When Threatened By Worms, Bacteria Summon Killer Fungi – Ed Yong – National Geographic

Parkinson’s disease linked to gut bacteria – Tim Sandle – Digital Journal

Bacteria in 550-million-year-old fossils provide new clues about fossil formation – Science Codex

Yellowstone Thermal Pools Colored by Pollution – Patrick J Kiger – Discovery

Floating Toilets That Clean Themselves Grow On A Lake – Nsikan Akpan – NPR Goats and Soda

Bettendorf wrestling coach’s invention tackles germs and bacteria on sporting mats and floors – Dennis Moran – QC Online

People on Craigslist Want to Give You Bacteria for Free – Natalie Kitroeff – BusinessWeek

Science, publishing, career

Patterns of text reuse in a scientific corpus – Daniel T. Citron and Paul Ginsparg – PNAS USA

The Anti-Plagiarism Machine: An analysis of hundreds of thousands of scientific papers finds text re-use is rampant, but it isn’t always malicious – Adrienne Lafrance – The Atlantic

“You Are Welcome Here”: Small Stickers Make a Big Difference for LGBTQ Scientists – Kyle Frischkorn – Scientific American

Science and Art

Incredible Bacteria-Laced Fabric Combines Art, Biology And Fashion – Priscilla Frank – Huffington Post
Bik’s Picks

Evolutionary perspectives on human height variation – Gert Stulp and Louise Barrett – Biological Reviews

What the ‘marshmallow test’ can teach you about your kids – Chuck Hadad – CNN

7 of the Ocean’s Strangest Creatures, Including a Fish With a Flashlight – Matt Simon – Wired

Modern genetics confirm ancient relationship between fins and hands – Science Daily

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December 18, 2014

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Human gut microbiome

* Metagenomic Analysis of Viruses in Feces from Unsolved Outbreaks of Gastroenteritis in Humans – Nicole E. Moore – Journal of Clinical Microbiology

Altered faecal and mucosal microbial composition in post-infectious irritable bowel syndrome patients correlates with mucosal lymphocyte phenotypes and psychological distress – J. Sundin – Alimentary Pharmacology & Therapeutics

Animal models of microbiome research

* The composition of the gut microbiota shapes the colon mucus barrier – Hedvig E Jakobsson – EMBO Reports

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota – Rachel N. Carmody – Cell Host & Microbe

Animal microbiome

Fish: The Gastrointestinal Phage Communities of the Cultivated Freshwater Fishes – Yang He – FEMS Microbiology Letters

Mussel: Algae Consumption and Nitrate Removal in a Raw Water Transport System by Limnoperna fortunei and its Associated Microorganisms – Ruijian Zhang – Water Environment Research

Plant microbiome

Meeting report: A snapshot of molecular plant–microbe interaction research – Sebastian Wittulsky – New Phytologist

Plant–microbe interactions change along a tallgrass prairie restoration chronosequence – Anna J. Herzberger – Restoration Ecology

Water microbiome

The influence of iron and siderophores on eukaryotic phytoplankton growth rates and community composition in the Ross Sea – Adam B. Kustka – Marine Chemistry

Food microbiology

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products – Mathieu Almeida – BMC Genomics

Metabolomics

Identification and characterization of intestinal lactobacilli strains capable of degrading immunotoxic peptides present in gluten – R.M. Duar – Journal of Applied Microbiology

Microbes in the news

Behind The Scenes At The Lab That Fingerprints Microbiomes – Katherine Harmon Courage – NPR Shots Health News

Complex genome-microbiome link may influence risk for IBD – Healio

Patients don’t understand risks of unnecessary antibiotics, study shows – Science Daily

The Microbiota Crisis: How the Herbicide Glyphosate is Killing Microbiomes – Martin Michener – Health Impact News

Bik’s Picks

Asian Glow May Indicate Lower Pain Tolerance – Stephani Sutherland – Scientific American

What was the Worst #ScienceFail of 2014? (Op-Ed) – Aaron Huertas – LiveScience

Breakthrough of the year 2014 – Science

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Microbiome digest, December 8, 2014

Posted on by

Human microbiome general

The human microbiome: opportunities and challenges for clinical care – Geraint B. Rogers – Internal Medicine Journal

Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes – Raphael D Isokpehi – Microbiology Insights

Human oral microbiome

* High resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis – Szymon P. Szafranski – Applied and Environmental Microbiology

Human gut microbiome

Crosstalk at the mucosal border: importance of the gut microenvironment in IBS – Lena Öhman – Nature Reviews Gastroenterology & Hepatology

Antimicrobial resistance characteristics and fitness of Gram negative faecal bacteria from volunteers treated with minocycline or amoxicillin – Miranda Kirchner – Frontiers in Microbiology

Decrease in lactobacilli in the intestinal microbiota of celiac children with a gluten-free diet, and selection of potentially probiotic strains – María J. Lorenzo Pisarello – Canadian Journal of Microbiology

Safety assessment of genetically modified rice expressing human serum albumin from urine metabonomics and fecal bacterial profile – Xiaozhe Qi – Food and Chemical Toxicology

Pregnancy and birth microbiome

Placental Microbiome and Its Role in Preterm Birth – Bin Cao – NeoReviews

High A. vaginae and G. vaginalis vaginal loads are associated with preterm birth – Florence Bretelle – Clinical Infectious Diseases

Cesarean Section and Chronic Immune Disorders – Astrid Sevelsted – Pediatrics

Animal and other models of microbiome research

Intestinal epithelial ​MyD88 is a sensor switching host metabolism towards obesity according to nutritional status – Amandine Everard – Nature Communications

Bugs and Food: A Recipe for Cancer? – Christina L. Ohland, Christian Jobin – Cell Metabolism

The current provided by oxygen-reducing microbial cathodes is related to the composition of their bacterial community – Mickaël Rimboud – Bioelectrochemistry

Animal microbiome

The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment – Ana R.M. Polónia – Molecular Ecology

Plant microbiome

* The role of bacteria and mycorrhiza in plant sulfur supply – Jacinta M. Gahan and Achim Schmalenberger – Frontiers in Plant Science

Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation – Sunil Mundra – New Phytologist

Soil and sediment microbiome

Impacts of altered precipitation regimes on soil communities and biogeochemistry in arid and semi-arid ecosystems – Uffe N. Nielsen – Global Change Biology

* Effects of tree identity dominate over tree diversity on the soil microbial community structure – Andrea Scheibe – Soil Biology and Biochemistry

Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness – Candace L. Piper – Journal of Ecology

The interactive effects of elevated ozone and wheat cultivars on soil microbial community composition and metabolic diversity – Xuelian Bao – Applied Soil Ecology

Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers – Claire Passarelli – Estuarine, Coastal and Shelf Science

Pharmaceuticals in the environment: Biodegradation and effects on natural microbial communities. A Review – Anna Barra Caracciolo – Journal of Pharmaceutical and Biomedical Analysis

Water microbiome

Successional Change in Microbial Communities of Benthic Phormidium-Dominated Biofilms – Katie A. Brasell – Microbial Ecology

Microbiome of the built environment

Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms – D. Hospodsky – Indoor Air

Food microbiology

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay – Huipeng Liang – Journal of the Science of Food and Agriculture

Phages and viruses

Emerging methods to study bacteriophage infection at the single-cell level – Vinh T. Dang and Matthew B. Sullivan – Frontiers in Microbiology

Metabolomics

* The Community Ecology of Microbial Molecules – Robert A. Quinn, Theodore Alexandrov – Journal of Chemical Ecology

Ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for rapid analysis of the metabolites of morroniside produced by human intestinal bacteria – Min Zhao – Journal of Chromatography B

Small-intestinal or colonic microbiota as a potential amino acid source in animals – Werner G. Bergen – Amino Acids

Techniques

Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia – A.D. Samarajeewa – Journal of Microbiological Methods

Microbes in the news

Now We Know Some Creepy Things About How Penicillin Destroys Bacteria – Esther Inglis-Arkell – IO9

Arctic bacteria converts mercury – Kristian Sjøgren – ScienceNordic

Should I Eat Greek Yogurt? – Mandy Oaklander – Time

CSU team examines dairy-cattle microorganisms to improve food safety – Kristen Browning-Blas – Bovine Vet Online

Glyphosate used with GMO crops under attack for disrupting microbiome: Science or a gut feeling? – David Warmflash – Genetic Literacy Project

#BacteriaHysteria: Why it’s time to detox your desk: Average worker comes into contact with more than 10 MILLION disease-causing bacteria lurking on their keyboard, phone and mouse – Lizzie Parry – Daily Mail

Bik’s Picks

The Yearbook: Our list of newsmakers this year – Manasi Vaidya & Shraddha Chakradhar – Nature Medicine

Notable advances 2014 – Amanda Keener – Nature Medicine

Let’s face it, for robots, falling down is easy. But how do you teach them to land safely? – Maki Naro – Popular Science

Force-feeding a human to a snake is not science (and is also super dumb) – Rachel Feltman – Washington Post

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