Category Archives: General Microbiome

Microbiome digest, November 21, 2014

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Microbiome general

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives – Aibin Zhan, Hugh J. MacIsaac – Conservation Genetics

Human oral microbiome

Polymicrobial synergy and dysbiosis in inflammatory disease – Richard J. Lamonta, George Hajishengallis – Trends in Molecular Medicine

Human skin microbiome

* Dialogue between skin microbiota and immunity – Yasmine Belkaid, Julia A. Segre – Science

Human respiratory microbiome

Asthma 2014: from monoclonals to the microbiome – Peter G Gibson, Paul S Foster – The Lancet Respiratory Medicine

Human gut microbiome

Development of Fecal Microbiota Transplantation Suitable for Mainstream Medicine – Alexander Khoruts – Clinical Gastroenterology and Hepatology

The role of the gut and microbes in the pathogenesis of spondyloarthritis – Mark Asquith – Best Practice & Research Clinical Rheumatology

From lifetime to evolution: timescales of human gut microbiota adaptation – Sara Quercia – Frontiers in Microbiology

Animal and other models of microbiome research

Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin – Jian Sun – Frontiers in Microbiology

Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development – Guanxiang Liang – Molecular Immunology

Gut Microbial Colonization Orchestrates TLR2 Expression, Signaling and Epithelial Proliferation in the Small Intestinal Mucosa – Nives Hörmann – PLOS ONE

The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium – Souichiro Kato – Frontiers in Microbiology

Animal microbiome

Aerobic cloacal and pharyngeal bacterial flora in six species of free-living birds – J. Stenkat – Journal of Applied Microbiology

Plant microbiome

Expanding genomics of mycorrhizal symbiosis – Alan Kuo – Frontiers in Microbiology

Soil and sediment microbiome

* Impact of interspecific interactions on antimicrobial activity among soil bacteria – Olaf Tyc – Frontiers in Microbiology

* Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems – Gabriela Martínez de la Escalera – Molecular Ecology

Characterisation of the soil microbial community of cultivated and uncultivated vertisol in Australia under several management regimes – Karuna Shrestha – Agriculture, Ecosystems & Environment

Wastewater reuse in irrigation: A microbiological perspective on implications in soil fertility and human and environmental health – Cristina Becerra-Castro – Environment International

Kotuikan Formation assemblage: a diverse organic-walled microbiota in the Mesoproterozoic Anabar succession, northern Siberia – Natalya G. Vorob’eva – Precambrian Research

Water microbiome

Diurnal expression of SAR11 proteorhodopsin and 16S rRNA genes in coastal North Atlantic waters – Raphaël Lami, David L. Kirchman – Aquatic Microbial Ecology

Leaf-litter-associated fungi and bacteria along temporal and environmental gradients in boreal streams – Jenny Bergfur, Carina Sundberg – Aquatic Microbial Ecology

Seasonal variation in marine-snow-associated and ambient-water prokaryotic communities in the northern Adriatic Sea – Jana Vojvoda – Aquatic Microbial Ecology

Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile – Darren J. Parris – Frontiers in Microbiology

* Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean – Eva Mayol – Frontiers in Microbiology

Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand – Katrin Hug – Frontiers in Microbiology

Food microbiology

* Unpasteurised commercial boza as a source of microbial diversity – Andrea Osimani – International Journal of Food Microbiology

Metabolomics

* Prediction and quantification of bioactive microbiota metabolites in the mouse gut –
Gautham V. Sridharan – Nature Communications

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography–tandem mass spectrometry – Jun Han – Analytica Chimica Acta

Metagenomics / Bioinformatics

Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing – Rohit Ghai – Molecular Ecology

* BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities – Mahdi Shafiei – PLOS Computational Biology

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships – Maggie C. Y. Lau – Frontiers in Microbiology

Techniques

Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples – Michael J. Strong – PLOS Pathogens

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys – Frédéric Mahé – Journal of Eukaryotic Microbiology

More microbiology papers

The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes – Yann Lesecque – PLOS Genetics

Association between Footwear Use and Neglected Tropical Diseases: A Systematic Review and Meta-Analysis – Sara Tomczyk – PLOS Neglected Tropical Diseases

Impact of wash cycle time, temperature and detergent formulation on the hygiene effectiveness of domestic laundering – M. Honisch – Journal of Applied Microbiology

Microbes in the news

Contaminated samples point the finger at the wrong suspects – Dalmeet Chawla – Imperial College London

Analyzing COPD Patients’ Sputum And Microbiota Composition Might Improve Treatment – Isaura Santos – Lung Disease News

Willy Burgdorfer, Who Found Bacteria That Cause Lyme Disease, Is Dead at 89 – William Yardley – The New York Times

Plants talk to each other using an internet of fungus – Nic Fleming – BBC

Bacteria on Russian ‘sex satellite’ survive reentry – Alec Luhn – The Guardian

Body’s bacteria may keep our brains healthy – Elizabeth Pennisi – Science Magazine

Hand dryers ‘splatter’ users with bacteria, scientists warn – Sarah Knapton – Telegraph UK

Unique sense of ‘touch’ gives a prolific bacterium its ability to infect anything – Morgan Kelly – Princeton

Science, publishing and career

Gates Foundation announces world’s strongest policy on open access research – Richard Van Noorden – Nature News Blog

Bogus Journal Accepts Profanity-Laced Anti-Spam Paper – Jeffrey Beal – Scholarly Open Access

* Sh*t My Reviewers Say – Collecting the finest real specimens of reviewer comments since 1456

Ten Simple Rules to Achieve Conference Speaker Gender Balance – Jennifer L. Martin – PLOS ONE

Bik’s Picks

Shedding light on skin color – Ann Gibbons – Science

Flashback Friday: Does garlic protect against vampires? An experimental study – Seriously Science – Discover Magazine

The Secret Life of Passwords – Ian Urbina – New York Times

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Microbiome digest, November 17, 2014

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Microbiome in pregnancy and birth

16S rRNA Gene Sequencing, Multilocus Sequence Analysis, and Mass Spectrometry Identification of the Proposed New Species “Clostridium neonatale” – Philippe Bouvet – Journal of Clinical Microbiology

Human oral microbiome

Shaping the oral microbiota through intimate kissing – Remco Kort – Microbiome

Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults – Toru Takeshita – Scientific Reports

Periodontal and peri-implant microbiota in patients with healthy and inflamed periodontal and peri-implant tissues – Long-Fei Zhuang – Clinical Oral Implants Research

An in vivo comparison of internal bacterial colonization in two dental implant systems: Identification of a pathogenic reservoir – Joanne Mawhinney – Acta Odontologica Scandinavica

Oral pathogens in children with respiratory disease – Yumiko Endo – Pediatric Dental Journal

Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease – Marian Garcia-Nuñez – Journal of Clinical Microbiology

Human vaginal microbiome

Diversity of vaginal microbial communities and role of PAP smear in its detection – Neha Batra – International Journal of Current Microbiology and Applied Sciences

Human microbiome – other and general

The conjunctival microbiome in health and trachomatous disease: a case control study – Yanjiao Zhou – Genome Medicine

What is a host? Incorporating the Microbiota into the ‘Damage-Response Framework’ – Arturo Casadevall and Liise-anne Pirofski – Infection and Immunity

Plant microbiome

Plant–insect interactions under bacterial influence: ecological implications and underlying mechanisms – Akiko Sugio – Journal of Experimental Botany

Soils and sediments microbiome

Bacterial community composition and biogeochemical heterogeneity in PAH-contaminated riverbank sediments – Gloria P. Johnston, Laura G. Leff – Journal of Soils and Sediments

Diversity of acidophilic prokaryotes at two acid mine drainage sites in Turkey – Pınar Aytar – Environmental Science and Pollution Research

Ammonia-oxidizing archaea versus bacteria in two soil aquifer treatment systems – Kun Ding – Applied Microbiology and Biotechnology

Water microbiome

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir – Zhen Sun – Scientific Reports

454 Pyrosequencing reveals diversity of Bdellovibrio and like organisms in fresh and salt water – Nan Li – Antonie van Leeuwenhoek

Metabolomics

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

Immunology

Prevention and cure of rotavirus infection via TLR5/NLRC4–mediated production of IL-22 and IL-18 – Benyue Zhang – Science

Microbes in the news

Worm Defies Tradition, Stores Gut Bacteria in Gills Instead – Elizabeth Preston – Discover Magazine

Here’s How Many Bacteria Spread Through One Kiss – Mandy Oaklander – Time

How Bacteria In The Gut Help Fight Off Viruses – Michaeleen Doucleff – Goats and Soda – NPR

This could be the most important scientific breakthrough in our lifetimes – Bengt Saelensminde – MoneyWeek

Probing the Microbial Mysteries of Wine – Iratxe Zarraonaindia and Jack A. Gilbert – Microbe

Self-destructing drone is made of fungus, bacteria, and wasp spit – Lee Mathews – Geek.com

Bik’s Picks

Scientists Descend into Massive Crater in Yamal Peninsula in Siberia: Bermuda Triangle Mystery Solved? – Rhodi Lee – Tech Times

Lightning expected to increase by 50 percent with global warming – Science Daily

Sometimes a Shirt is More Than Just a Shirt.. – Isis the Scientist

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Microbiome digest, November 11, 2014

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Human oral microbiome

Physiological Adaptations of Key Oral Bacteria – C. W. Ian Douglas – Advances in Microbial Physiology

Human gut microbiome

Development and Survival of Th17 Cells within the Intestines: The Influence of Microbiome- and Diet-Derived Signals – Joseph H. Chewning – The Journal of Immunology

Gut Inflammation and Immunity: What Is the Role of the Human Gut Virome? – Alfredo Focà – Mediators of Inflammation

Animal microbiome

Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change – Karlette A. Fernandes – PLOS ONE

The Effect of Phytochemical Tannins-Containing Diet on Rumen Fermentation Characteristics and Microbial Diversity Dynamics in Goats Using 16S rDNA Amplicon Pyrosequencing – B. R. Min – Agriculture, Food & Analytical Bacteriology

Microbial diversity in forestomach and caecum contents of the greater long-tailed hamster Tscherskia triton (Rodentia: Cricetidae) – Akio Shinohara – Mammalian Biology – Zeitschrift für Säugetierkunde

The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection – Andrea J. Jani – PNAS USA

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk – Roberta M. O’Connor – PNAS USA

Arbuscular mycorrhizal fungi communities in a coral cay system (Morrocoy, Venezuela) and their relationships with environmental variables – M.M. Alguacil – Science of the Total Environment

Soil microbiome

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities – Jun-Min Li – Scientific Reports

Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples – Franziska B. Brandt – Systematic and Applied Microbiology

Seasonal influence of climate manipulation on microbial community structure and function in mountain soils – Jérémy Puissant – Soil Biology and Biochemistry

Effect of organic and conventional practices on carbon-substrate utilisation by the soil microbial community in a ‘Cripps Pink’/M7 apple orchard – Andre H Meyer – South African Journal of Plant and Soil

* The Soil Biota Composition along a Progressive Succession of Secondary Vegetation in a Karst Area – Jie Zhao – PLOS ONE

Effects of salinization and crude oil contamination on soil bacterial community structure in the Yellow River Delta region, China – Yong-chao Gao – Applied Soil Ecology

Water microbiome

Community dynamics of prokaryotic and eukaryotic microbes in an estuary reservoir – Zhen Sun – Scientific Reports

Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula – Camila N. Signori – Frontiers in Microbiology

Metagenomics

Assessment of quality control approaches for metagenomic data analysis – Qian Zhou – Scientific Reports

PaperClip: rapid multi-part DNA assembly from existing libraries – Maryia Trubitsyna – Nucleic Acids Research

Microbial phylogeny

* Assessing the global phylum level diversity within the bacterial domain: A review – Noha H. Youssef – Journal of Advanced Research

Science, publishing, career

Crosspost: Using Google Scholar in Scholarly Workflows – Jonathan Eisen – microBEnet

Hilarious: Overly honest references: “Should we cite the crappy Gabor paper here?” – RetractionWatch – (Note: paper has been removed – see a screenshot here)

Microbes in the news

* Bacteria Hysteria? Deadly bacteria normally found in toilets was discovered in the microwave of these students – The Journal.ie

Bik’s Picks

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication – Michael J. Montague – PNAS USA

UCSF develops site to make sense out of sugar science – Erin Allday – SFGate

Found: The Ideal Fatness for Elephant Seals – Elizabeth Preston – Discover

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Microbiome digest, November 10, 2014

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Pregnancy and birth microbiome

* Intestinal Microbiota is Different in Women with Preterm Birth: Results from Terminal Restriction Fragment Length Polymorphism Analysis – Arihiro Shiozaki – PLOS ONE

Ureaplasma species and Mycoplasma hominis in cervical fluid of pregnancies complicated by preterm prelabor rupture of membranes – Ivana Musilova – Journal of Maternal-Fetal and Neonatal Medicine

Human respiratory microbiome

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis – Sven D Willger – Microbiome

Human gut microbiome

* The human intestinal microbiome at extreme ages of life. Dietary intervention as a way to counteract alterations – Nuria Salazar – Frontiers in Genetics

Nanosilver-Mediated Change in Human Intestinal Microbiota – Pranab Das – Journal of Nanomedicine & Nanotechnology

Animal microbiome

Bacterial Diversity Dynamics Associated with Different Diets and Different Primer Pairs in the Rumen of Kankrej Cattle – Dipti W. Pitta – PLOS ONE

Think laterally: horizontal gene transfer from symbiotic microbes may extend the phenotype of marine sessile hosts– Sandie M. Degnan – Frontiers in Microbiology

* Temporal changes in the bacterial community of animal feces and their correlation with stable fly oviposition, larval development, and adult fitness – Thais A. Albuquerque and Ludek Zurek – Frontiers in Microbiology

Plant microbiome

Bacterial networks and co-occurrence relationships in the lettuce root microbiota – Massimiliano Cardinale – Environmental Microbiome

Fungicide Effects on Fungal Community Composition in the Wheat Phyllosphere – Ida Karlsson – PLOS ONE

* Spatial structuring of bacterial communities within individual Ginkgo biloba trees – Jonathan W. Leff – Environmental Microbiology

Soil microbiome

Printing Soil: A single-step, high throughput method to isolate microorganisms and near-neighbor microbial consortia from a complex environmental sample – Bradley R. Ringeisen – Methods in Ecology and Evolution

Microbial communities of frozen soils of the Tuimaada Valley in Central Sakha – T. I. Ivanova – Biology Bulletin

Metabolomics

Automatic Prediction of Polysaccharide Utilization Loci in Bacteroidetes Species –
Nicolas Terrapon – Bioinformatics

Microbial Ecology

* The importance of sample archiving in microbial ecology – S. Craig Cary & Noah Fierer – Nature Reviews Microbiology

“it is an unwritten rule that all freezers will rapidly become filled to capacity, no matter how many freezers are purchased”

Coincidental Loss of Bacterial Virulence in Multi-Enemy Microbial Communities – Ji Zhang – PLOS ONE

Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases – Ji Zhang – Ecology and Evolution

Bioinformatics

Toward a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing “PhyloH” as a novel phylogenetic diversity analysis tool – A Sandionigi – Molecular Ecology Resources

SRI International’s BioCyc Database Collection Expanded for Easy Access to Information about Microbes and Metabolic Pathways

Microbes in the news

* Will You Donate Your Poop To Science? – Christopher Robbins – Gothamist

Pediatric Research | Microbiome research exploding with new revelations – John Barnard – Dispatch

Line Dancing Bacteria on a Chip – UTwente.nl

* Researcher studies microbiome of the dead – Melissa Benmark – WKAR Michigan State University

Bik’s Picks

The Unbelievable Skepticism of the Amazing Randi – Adam Higginbotham – New York Times

Winners Announced For The World’s Richest Science Award: The $3 Million Breakthrough Prize – F.D. Flam – Forbes

* The Challenge of Teaching Science in Rural America – Alexandra Ossola – The Atlantic

Don’t swallow it: Six health myths you should ignore – New Scientist

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Microbiome digest, November 6, 2014

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I won’t have much time for the blog in the coming weeks (my paid job is more important!), so I won’t be doing much formatting – just giving you the links and titles. I hope that is OK!

Pregnancy and birth microbiome

Exploring preterm birth as a polymicrobial disease: An overview of the uterine microbiome – Matthew S. Payne and Sara Bayatibojakhi – Frontiers in Immunology
http://journal.frontiersin.org/Journal/120834/abstract

Genital tract microbial isolate in women with preterm pre-labour rupture of membranes in resource-constrained community setting – G. U. Eleje – Journal of Obstetrics & Gynaecology
http://informahealthcare.com/doi/abs/10.3109/01443615.2014.970145

The Same Microbiota and a Potentially Discriminant Metabolome in the Saliva of Omnivore, Ovo-Lacto-Vegetarian and Vegan Individuals – Francesca De Filippis – PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0112373

The oral microbiota of patients with recurrent aphthous stomatitis – Maria Bankvall – Journal of Oral Microbiology
http://www.journaloforalmicrobiology.net/index.php/jom/article/view/25739/36599

Human respiratory microbiome

Application of 16S rRNA metagenomics to analyze bacterial communities at a respiratory care centre in Taiwan – Chuan Yi Tang – Applied Microbiology and Biotechnology
http://link.springer.com/article/10.1007/s00253-014-6176-7/fulltext.html

Animal microbiome

This is not really a microbiome paper, but possibly relevant:
High-throughput sequencing of fecal DNA to identify insects consumed by wild Weddell’s saddleback tamarins (Saguinus weddelli, Cebidae, Primates) in Bolivia – E.K. Mallott – American Journal of Physical Anthropology
http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22654/abstract

Pyrosequencing reveals diverse fecal microbiota in Simmental calves during early development – Daniela Klein-Jöbstl – Frontiers in Microbiology
http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00622/abstract

Diet disparity among sympatric herbivorous cichlids in the same ecomorphs in Lake Tanganyika: amplicon pyrosequences on algal farms and stomach contents
Hiroki Hata – BMC Biology
http://www.biomedcentral.com/1741-7007/12/90/abstract

Plant microbiome

Tree communities rapidly alter soil microbial resistance and resilience to drought – David Rivest – Functional Ecology
http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.12364/abstract

Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by Illumina high-throughput sequencing
Wan-Ying Xie – Applied and Environmental Microbiology
http://aem.asm.org/content/early/2014/10/27/AEM.03191-14.abstract

Illumina Amplicon Sequencing of 16S rRNA Tag Reveals Bacterial Community Development in the Rhizosphere of Apple Nurseries at a Replant Disease Site and a New Planting Site – Jian Sun – PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0111744

Soil microbiome

Spatial distribution of microbial communities associated with dune landform in the Gurbantunggut Desert, China – Ruyin Liu – Journal of Microbiology
http://link.springer.com/article/10.1007/s12275-014-4075-3

Vegetation-associated impacts on Arctic tundra bacterial and micro-eukaryotic communities
Yu Shi – Applied and Environmental Microbiology
http://aem.asm.org/content/early/2014/10/27/AEM.03229-14.abstract

Microbes in the news

New interdisciplinary center at MIT to focus on the microbiome and human health – MIT news
http://newsoffice.mit.edu/2014/new-mit-center-microbiome-and-human-health-1106

New center aims to use gut microbiome discoveries to improve human nutrition – Washington University
http://news.wustl.edu/news/Pages/27647.aspx

Wastewater, wheat and table wipes: adventures in culture-independent microbiology
Jacob E Munro – Microbiology Australia
http://microbiology.publish.csiro.au/?paper=MA14061

Gut Microbiome Heritability – Tracy Vence – The Scientist
http://www.the-scientist.com/?articles.view/articleNo/41395/title/Gut-Microbiome-Heritability/

Great Ape Microbiomes – Tracy Vence – The Scientist
http://www.the-scientist.com/?articles.view/articleNo/41393/title/Great-Ape-Microbiomes/

Love your gut: Embrace healthy bacteria – Agnes Zhu – Eating Berkeley

Love your gut: Embrace healthy bacteria

Bik’s Picks

Searching for new branches on the tree of life – Tanja Woyke, Edward M. Rubin – Science
http://www.sciencemag.org/content/346/6210/698.short

GIF Shows The Inside Of The Entire Human Body, From Top To Bottom – Justine Alford – IFL Science
http://www.iflscience.com/health-and-medicine/gif-shows-entire-human-body-top-bottom

Microbiome Digest, November 4, 2014

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Tomorrow, Wednesday November 5, at 1:00pm USA-EST : Upcoming AMA (Ask Me Anything) in reddit/r/science: “Microbiota of the human gut” with my co-worker Les Dethlefsen. Ask him anything! You can submit questions, vote for the best questions, and the top questions will be answered by Les.

Human gut microbiome

* Rapid changes in the gut microbiome during human evolution – Andrew H. Moeller – PNAS USA

“To establish how the gut microbiome has changed since the diversification of human and ape species, we characterized the microbial assemblages residing within hundreds of wild chimpanzees, bonobos, and gorillas.”

and: Human Gut Bacteria Much Different Than Apes – Science 2.0

* Blastocystis Is Associated with Decrease of Fecal Microbiota Protective Bacteria: Comparative Analysis between Patients with Irritable Bowel Syndrome and Control Subjects – Céline Nourrisson – PLOS ONE

“Here, we first compared the prevalence of Blastocystis among 56 IBS patients (40 IBS with constipation (IBS-C), 9 IBS with diarrhea (IBS-D), 4 mixed IBS (IBS-M) and 3 unsubtyped IBS (IBS-U) according to the Rome III criteria) and 56 control (i.e. without any diagnosed chronic or acute gastrointestinal disorder) subjects. “

Animal models of microbiome research

* Bone Marrow Dendritic Cells from Mice with an Altered Microbiota Provide Interleukin 17A-Dependent Protection against Entamoeba histolytica Colitis – Stacey L. Burgess – mBio

“In studies utilizing a murine model, we demonstrated that colonization of the gut with the commensal Clostridia-related bacteria known as segmented filamentous bacteria (SFB) is protective during E. histolytica infection.”

Animal microbiome

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis – Ren-Mao Tian – mBio

“16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. “

Bioinformatics tools

Massive fungal biodiversity data re-annotation with multi-level clustering – Duong Vu – Scientific Reports

“An implementation of the algorithm allowed clustering of all 344,239 ITS (Internal Transcribed Spacer) fungal sequences from GenBank”

Viruses and phages

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applied to virus identification – Adriana Calderaro – Scientific Reports

“The results revealed MALDI-TOF MS to be an effective and inexpensive tool for the identification of the three poliovirus serotypes. “

More microbiology

Occurrence and expression of bacterial human virulence gene homologues in natural soil bacteria – Ditte A. Søborg – FEMS Microbial Ecology

“About 25% of the bacterial isolates contained virulence gene homologues representing toxin (hblA, cytK2), adhesin (fimH), regulator (phoQ) and resistance (yfbI) determinants in pathogenic bacteria.”

Science, publishing, and career

* Don’t Worry Your Pretty Little Heads – Rebecca Schuman – Slate

“I don’t understand how they wrote the paper or the op-ed they did while looking at the same results I see in their paper. … Where I come from,” she concludes, “we call that institutional bias.”

Bik’s Picks

Birds found using human musical scales for the first time – Virginia Morell – Science Blog

“The flutelike songs of the male hermit thrush (Catharus guttatus) are some of the most beautiful in the animal kingdom.”

Vaccine-resistant polio strain discovered – Science Daily

“The DNA sequence shows two mutations, unknown until now, of the proteins that form the “shell” (capsid) of the virus.”

The appliance of science: home experiments with your kids – Louise Holden – Irish Times

“Next week is Science Week, and one of the messages that McCarthy is hoping to put out there is that science is for everybody, not just those hoping to work in the sector. Helping your child to become science-literate is a great gift.”

The top 20 catchiest songs of all time, according to science – Michelle Starr – CNET

“A year-long survey by the Museum of Science and Industry in Manchester has revealed the top 10 most persistent earworms — with the Spice Girls topping the list.”

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Microbiome digest, November 3, 2014

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Human oral and vaginal microbiomes, rumen microbiome of impalas, sample handling and sponges, and two remarkable pieces in the New York Times.

Human oral microbiome

The association between the upper digestive tract microbiota by HOMIM and oral health in a population-based study in Linxian, China – Guoqin Yu – BMC Public Health

“Human Oral Microbe Identification Microarrays were used to test for the presence of 272 human oral bacterial species (97 genera) in upper digestive tract (UDT) samples collected from 659 participants. “

Pregnancy and birth microbiome

Poster: Comparison of the Vaginal Microbiomes of Pregnant Women of Four Ethnicities
and Identification of Taxa Associated with Urogenital Disease – Mendz GL – ECCMID Poster

“Principal component analysis suggested differences in the bacterial populations of healthy women and those with genital infections, with clustering of the latter along the Protobacteria axis “

Animal microbiome

Examination of the Rumen Bacteria and Methanogenic Archaea of Wild Impalas (Aepyceros melampus melampus) from Pongola, South Africa – Laura M. Cersosimo – Microbial Ecology

“In the present study, next-generation sequencing and real-time polymerase chain reaction were used to investigate the diversity and density of the bacteria and methanogenic archaea residing in the rumen of five adult male impalas”

Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges – Cristiane C. Hardoim – Frontiers in Microbiology

Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. “

Plant microbiome

Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce – Susanne Schreiter – FEMS Microbiology Ecology

“16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. “

Are heterotrophic and silica-rich eukaryotic microbes an important part of the lichen symbiosis? – David M Wilkinson – Mycology: An International Journal on Fungal Biology

“In this necessarily speculative paper we highlight areas for future research and how newer technologies may be useful for understanding the full suite of organisms involved in the lichen symbiosis.”

Soil microbiome

Selection on soil microbiomes reveals reproducible impacts on plant function – Kevin Panke-Buisse – ISME Journal

“Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment.”

Chemolithotrophy in the continental deep subsurface: Sanford Underground Research Facility (SURF), USA – Magdalena R. Osburn – Frontiers in Microbiology

“Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment.”

Bioinformatic tools

* Seeing the forest for the genes: Using metagenomics to infer the aggregated traits of microbial communities – Noah Fierer – Frontiers in Microbiology

“Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated.”

Metabolomics

Fructan supplementation of senior cats affects stool metabolite concentrations and fecal microbiota concentrations, but not nitrogen partitioning in excreta – K.A. Barry – Journal of Animal Science

“Fructan supplementation may benefit senior cats as it modulates stool odor-forming compounds and decreases some protein catabolites and pathogenic gut microbiota concentrations without affecting N retention.”

Proteomics

From the Banfield lab: Development of an enhanced metaproteomic approach for deepening the microbiome characterization in the human infant gut – Weili Xiong – Journal of Proteome Research

“….we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. “

More microbiology

Complementarity between targeted real-time specific PCR and conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious diseases – A.-S. Morel – European Journal of Clinical Microbiology & Infectious Diseases

“Herein, we report our experience in the diagnosis of infectious diseases over two years, during which 32,948 clinical samples from 18,056 patients were received from France and abroad.”

Microbes in the news

* There Is No ‘Healthy’ Microbiome – Ed Yong – New York Times

“The microbiome is complex, varied, ever changing and context-dependent — qualities that are the enemies of easy categorization.”

Study: Ice Man has traces of bacteria that undermined his health – BetaWired

“…they found evidence of the presence of Treponema denticola, an opportunistic pathogen implicated in the development of periodontal diseases. “

Science, publishing, and career

How Do Small Things Make a Big Difference? Activities to Teach about Human–Microbe Interactions – Chandana Jasti – The American Biology Teacher

“In these guided inquiry activities, students investigate human–microbe interactions as they work together to interpret and analyze authentic data from published articles and develop scientific models.”

2014 Life Sciences Salary Survey – Jyoti Madhusoodanan – The Scientist

“This year’s data reveal notable variation in compensation for life scientists working in different fields, sectors, and regions of the world.”

Academic Science Isn’t Sexist – Wendy M. Williams and Stephen J. Ceci – New York Times

“Our analyses show that women can and do prosper in math-based fields of science, if they choose to enter these fields in the first place.”

and two rebuttals:
Academic science is sexist: We do have a problem here – Emily Willingham
* The flawed and offensive logic of “Academic Science Isn’t Sexist” in the @nytimes – Jonathan Eisen – The Tree of Life

Bik’s Picks

Standing time and all-cause mortality in a large cohort of Australian adults – Hidde P. van der Ploeg – Preventive Medicine

“Increasing standing may hold promise for alleviating the health risks of prolonged sitting.”

A Face to Remember – Kerry Grens – The Scientist

“Once dominated by correlational studies, face-perception research is moving into the realm of experimentation—and gaining tremendous insight.”

* With a very cute picture: Rovers Disguised as Baby Penguins Can Quietly Infiltrate Penguin Colonies – Rachel Nuwer – Smithsonian

“Pursuing this hunch, they outfitted the rover with a big ball of fluff and a little penguin head and arms. ”

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Microbiome digest, 31 October 2014

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Happy Halloween! Today we have fungal communities in mammals, more on the TMAO story, some microbiome reviews, honey bee colonization, and microbophobia papers.

General human/mammalian microbiome

* Richness and diversity of mammalian fungal communities shape innate and adaptive immunity in health and disease – Lisa Rizzetto, Carlotta De Filippo and Duccio Cavalieri – European Journal of Immunology

“In this review, we describe the ecology and the human niches of our fungal “fellow travelers” in both health and disease, discriminating between passengers, colonizers, and pathogens based on the interaction of these fungi with the human immune system.”

Prognostic Value of Elevated Levels of Intestinal Microbe-Generated Metabolite Trimethylamine-N-Oxide in Patients With Heart Failure – Refining the Gut Hypothesis – W.H. Wilson Tang – Journal of the American College of Cardiology

“High TMAO levels were observed in patients with HF, and elevated TMAO levels portended higher long-term mortality risk independent of traditional risk factors and cardiorenal indexes.”

* Deciphering the human microbiome using next-generation sequencing data and bioinformatics approaches – Yihwan Kim – Methods

“This review examines computational methods that are valuable for the analysis of human microbiome, and highlights the results of several large-scale human microbiome studies.”

Human gut microbiome

Novel opportunities for the exploitation of host–microbiome interactions in the intestine – Ingmar JJ Claes – Current Opinion in Biotechnology

“New sequencing technologies have dramatically increased our knowledge on the composition of the human intestinal microbiota in health and disease. ”

Animal microbiome

* Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera – J. Elijah Powell – Applied and Environmental Microbiology

“Colonization patterns were evaluated using quantitative real-time PCR (qPCR) to assess community sizes and using deep sequencing of 16S rRNA gene amplicons to assess community composition.”

Soil microbiome 

Landscape-scale Variation in Pathogen-suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica – Kristen K. Becklund – Biotropica

“To estimate the potential for disease suppression among Streptomyces communities in tropical dry forests, we cultured soil-borne Streptomyces from plots in two forests in northwestern Costa Rica (Santa Rosa and Palo Verde)”

Microbes in the news

More scary than Halloween: this month in germophobia microbophobia – Jonathan Eisen – MicroBEnet

“It seems that any time a holiday comes around in the US, the press starts to ramp up the writing of stories about evil microbes that are lurking all around us. “

MSU and Detroit analyze tiny bacteria to investigate murders – Kate Wells – Michigan Rado

““Can we use these communities to identify whether a person is from a certain location or if they’ve been to a location?” asks Benbow”

Science and career

Satire: Sixth Person Dies As Another “Dance Your PhD” Video Goes Wrong – The Allium

“Principal Investigator, Professor Tom Morrow (61) slipped as he was mimicking a helix-turn-helix motif as part of a much larger transcription factor protein.”

10 Creative Careers That Rely on Science and Math – Alexandra Ossola – The Atlantic

“Knowledge of STEM subjects isn’t just essential for physicists or computer engineers. Fashion designers, zookeepers, and deep-sea divers also use it every day.”

Bik’s Picks

Lava Flow In Hawaii Spares Homes, But Threatens To Cut Off Community – Scott Neuman – NPR

“Officials in Hawaii are sending National Guard troops to the town of Pahoa on the Big Island, where a lava flow is creeping toward a main road, threatening to cut off the community.”

100-Year-Old Time Capsule Discovered – Clapway

“A 100-year old time capsule was found at Baltimore’s Washington Monument during a restoration project. And it seems officials are hesitant to even open it because of how old it is.”

Researchers: Science says girls’ sexualized Halloween costumes are scary – Rebecca C Bigler and Sarah McKenney – Dallas News

“Parents could also foster girls’ creativity by encouraging them to make their own costumes. “

And, related to the post above, make sure to read the hilarious comments here:
Delicious Women’s Phd Darling Sexy Costume – Amazon

“Sexy graduation gown is a micro mini with zip up front. Gold sash, hat, and diploma included”

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General microbiology and science digest, October 27, 2014

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A new Shiny R tool for microbial communities, virus-like pictures in human distal gut, interaction between oral bacteria, dancing your PhD, and X-ray movies of human joints in action.

Bioinformatics

* Seed: a user-friendly tool for exploring and visualizing microbial community data –
Daniel Beck – Bioinformatics

“Seed is written in R using the Shiny library. This provides access to powerful R based functions and libraries through a simple user interface. “

Viruses and phages

With cool pictures: Characterization of virus-like particles associated with the human faecal and caecal microbiota – Lesley Hoyles – Research in Microbiology

“Various methodologies for the recovery of VLPs from faeces were tested and optimized, including successful down-stream processing of such samples for the purpose of an in-depth electron microscopic analysis, pulsed-field gel electrophoresis and efficient DNA recovery.”

Transcriptomics / Proteomics / Metabolomics

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis – Yu Xia – Scientific Reports

“The metatranscriptomic recharacterization in the present study captured microbial enzymes at the unprecedented scale of 40,000 active genes belonged to 2,269 KEGG functions were identified.”

Proteomic and transcriptional analysis of interaction between oral microbiota Porphyromonas gingivalis and Streptococcus oralis – Kazuhiko Maeda – Journal of Proteome Research

“Here, using shotgun proteomics we examined the molecular basis of mixed-biofilm formation by P. gingivalis with Streptococcus oralis.”

Review: Toward the comprehensive understanding of the gut ecosystem via metabolomics-based integrated omics approach – Wanping Aw, Shinji Fukuda – Seminars in Immunopathology

“In this review, we discuss in detail the relationship between gut microbiota and its metabolites … in the host health and etiopathogenesis of various pathological states such as multiple sclerosis, autism, obesity, diabetes, and chronic kidney disease. “

More Microbiology

Biofilms: Five-Star Accommodations for the Aerobically Challenged – Robert A. Cramer – Current Biology

“A recent study finds that fungal biofilms are capable of supporting growth of anaerobic bacteria, suggesting that these fungi can promote bacterial growth in otherwise toxic environments.”

Microbes in the news

* Sorry, Your Gut Bacteria Are Not the Answer to All Your Health Problems – Gabrielle Canon – Mother Jones

“We’re told that tweaks to the microbiome can cure everything from allergies to Ebola. Not exactly, say experts. …despite the optimism, some researchers caution that much of what we hear about microbiome science isn’t always, well, science. “

* Orthopedic surgeon studies bear bacteria to aid bear attack victims – Healio

“Working with the Montana Fish, Wildlife & Parks, Iwersen has been collecting cultures of bacteria from the mouths of grizzly bears and correlating them with the types of bacteria found in the bear bites on patients. “

Mexican scientist investigates intestinal bacteria – BetaWired

“Recent findings of the investigator Xicotencatl Gracida Canales…at Harvard University in Cambridge, USA, suggest that in the absence of an intestinal shield, variations in bacterial metabolism can affect reproductive cells and cause infertility in an animal model called C. Elegans.”

Algae-Based Material Takes On Body Odor – Dana Dovey – NewsWeek

“A team of Swedish researchers from the KTH Royal Institute of Technology has found a way to eliminate the growth of this smell-inducing bacteria using one of nature’s best antimicrobials, algae.”

MoBE Postdoctoral Fellowship: From Source to Tap: Linking the Drinking Water Microbiome to Human Health – Sarah Haig – MicroBEnet

“We hypothesize that the microbial communities in municipally treated drinking water are a source of opportunistic pathogens, posing a risk to people with cystic fibrosis”

Science, publishing, career

Is NIH policy the best way to sex equality in studies? – Bethany Brookshire – Science News

“The end goal will be to make sure that NIH-funded scientists “balance male and female cells and animals in preclinical studies in all future [grant] applications” to the NIH.”

Some suggestions for having diverse speakers at meetings – Jonathan Eisen – The Tree of Life

“Some people were asking what one can do to improve gender diversity at meetings so I thought I would post this which I was meaning to do anyway “

‘Dance Your Ph.D.’ finalists announced – John Bohannon – Science

“Rather than reading a paper about it, why not watch a dance? A ballet and a modern dance on those very topics have made it into the finals of this year’s “Dance Your Ph.D.” contest.”

Bik’s Picks

Interactive world map of vaccine-preventable outbreaks – Council for Foreign Relations

“This interactive map visually plots global outbreaks of measles, mumps, whooping cough, polio, rubella, and other diseases that are easily preventable by inexpensive and effective vaccines.”

Dietary cocoa flavanols reverse age-related memory decline in mice – Science Daily

“Dietary cocoa flavanols —- naturally occurring bioactives found in cocoa —- reversed age-related memory decline in healthy older adults, according to a new study. Flavanols are also found naturally in tea leaves and in certain fruits and vegetables”

Amazing X-ray GIFs Show Joints In Motion – Lisa Winter – IFL Science

“Cameron Drake of San Francisco has created a collection of magnificent images showing joints in motion. He was aided by orthopedic physician Dr. Noah Weiss and the finished product is completely amazing. “

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Human microbiome digest, October 27, 2014

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Development of gut microbiome in infants, understanding oral microbiome through high-throughput sequencing, gut bacteria in deceased alcoholics, and bacteria after stroke.

Microbiome general

The symbiont side of symbiosis: do microbes really benefit? – Justine R. Garcia and Nicole M. Gerardo – Frontiers in Microbiology

“We evaluate these hypotheses based on available evidence, which indicate reduced competition and predation are not universal benefits for symbionts. “

Pregnancy and birth microbiome

Review: Diet and the development of the human intestinal microbiome – Noah Voreades – Frontiers in Microbiology

“This review focuses primarily on diet, as it is one of the most pivotal factors in the development of the human gut microbiome from infancy to the elderly.”

Human oral microbiome

Review: Application of high-throughput sequencing in understanding human oral microbiome related with health and disease – Hui Chen and Wen Jiang – Frontiers in Microbiology

“This review describes the application of high-throughput sequencing for characterization of oral microbiota and analyzing the changes of the microbiome in the states of health or disease.”

Human gut microbiome

Cellular and molecular pathways through which commensal bacteria modulate sensitization to dietary antigens – Taylor Feehley, Cathryn R Nagler – Current Opinion in Immunology

“This review will discuss the cellular and molecular pathways activated by commensal bacteria to protect against allergic sensitization.”

Microbial Therapy in Liver Disease: Probiotics Probe the Microbiome–Gut–Liver–Brain Axis – David W. Victor 3rd, Eamonn M.M. Quigley – Gastroenterology

“It is timely, therefore, that Dhiman et al should embark on an ambitious study, reported in this issue of Gastroenterology, designed to assess the efficacy of the probiotic cocktail, VSL#3, as secondary prophylaxis in patients with OHE.”

Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics – Sari Tuomisto – BMC Gastroenterology

“Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males”

Animal models of microbiome research

Age-related changes in intestinal permeability and gut microbiota after ischemic stroke – Joshua Crapser – Journal of Neuroimmunology

“This study aimed to elucidate the role of systemic factors, such as intestinal stress, underlying the poor outcomes of aging mice after stroke.”

Spatial and temporal colonization dynamics of segmented filamentous bacteria is influenced by gender, age and experimental infection with Helicobacter hepaticus in Swiss Webster mice – Zhongming Ge – Microbes and Infection

“Hh infection in both genders did not alter SFB levels in the jejunum and ileum, but increased SFB levels in the cecum and colon of males compared to the controls”

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