Category Archives: Techniques

January 28, 2015

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I will be traveling to visit family in the upcoming week, so there might not be a post every day. But I will do my best to keep y’all up to date with the microbiome literature. In today’s installment, there are articles about skin microbiome around abscesses, misclassifications of bacteria in Genbank, archaea and rice plant roots. Also, if you like chicken wings with Campylobacter, you should have put some sauce on it.

General microbiome

Crystal Ball: Human microbiota: ‘The philosophers have only interpreted the world in various ways. The point, however, is to change it’ – Harald Brüssow – Microbial Biotechnology

Human skin microbiome

The cutaneous microbiome in out-patients presenting acutely with skin abscesses – James M. Horton – Journal of Infectious Diseases

Animal and other models for microbiome research

In Vitro Investigation of the Effect of Oral Bacteria in the Surface Oxidation of Dental Implants – Sathyanarayanan Sridhar – Clinical Implant Dentistry and Related Research

Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice – Xiaofei Xu – PLOS ONE

Animal microbiome

New Light on the Systematics of Fungi Associated with Attine Ant Gardens and the Description of Escovopsis kreiselii sp. nov. – Lucas A. Meirelles – PLOS ONE

Plant microbiome

Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols– Sarah Croes – Environmental Microbiology

Colonization of rice roots with methanogenic archaea controls photosynthesis-derived methane emission – Judith Pump – Environmental Microbiology

Soil and rock microbiome

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

Water microbiome

Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling– Markus V. Lindh – Environmental Microbiology

Combined effects of zooplankton grazing and dispersal on the diversity and assembly mechanisms of bacterial metacommunities – Mercè Berga – Environmental Microbiology

Review: Marine Snow: A Brief Historical Sketch – Mary Silver – Limnology and Oceanography Bulletin

Food microbiology

Just in time for the Superbowl: The Antimicrobial Effect of Spice-Based Marinades against Campylobacter jejuni on Contaminated Fresh Broiler Wings – Gintarė Zakarienė – Journal of Food Science

Metagenomics

Strategies to Avoid Wrongly Labelled Genomes Using as Example the Detected Wrong Taxonomic Affiliation for Aeromonas Genomes in the GenBank Database – Roxana Beaz-Hidalgo – PLOS ONE

Metabolomics

Dominant components of the Thoroughbred metabolome characterised by 1H-nuclear magnetic resonance spectroscopy: A metabolite atlas of common biofluids – E. E. Escalona – Equine Veterinary Journal

New Techniques

DNA sequencing using ​polymerase substrate-binding kinetics – Michael John Robert Previte – Nature Communications

Single cell biotechnology to shed a light on biological ‘dark matter’ in nature – Wei E. Huang – Microbial Biotechnology

Ecology

Natural Variation in Preparation for Nutrient Depletion Reveals a Cost–Benefit Tradeoff – Jue Wang – PLOS Biology

Review: Is successional research nearing its climax? New approaches for understanding dynamic communities – Scott J. Meiners – Functional Ecology

Editorial: Beyond borders: investigating microbiome interactivity and diversity for advanced biocontrol technologies – Gabriele Berg – Microbial Biotechnology

Microbes in the news

Skin abscesses displayed distinct cutaneous microbiota – Healio

Stress during pregnancy related to infant gut microbiota – HealthCanal

Fatal peanut allergies could be cured by probiotic bacteria, say Australian doctors – Jonathan Pearlman – The Telegraph

UF researcher gets grant to study probiotics’ effects – Jeff Schweers – Gainesville

Science, publishing and career

Not your average technician: Research relies on unsung heroes working behind the scenes — and some of them have rather unusual jobs – Michael Hopkin – Nature

Career counselling: Pick a path – Neil Savage – Nature

Inclusivity: Mentor matters – Nature

FactChecking Science-based Claims – FactCheck.org
http://www.factcheck.org/2015/01/factchecking-science-based-claims/

Bik’s Picks

Did genetic links to modern maladies provide ancient benefits? – Science Daily

Skull discovery suggests location where humans first had sex with Neanderthals – The Guardian

Spiders Spin Electrically Charged Silk To Make It Sticky – Marissa Fessenden – Smithsonian

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January 27, 2015

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Human gut microbiome

Dysbiosis of Fungal Microbiota in the Intestinal Mucosa of Patients with Colorectal Adenomas – Chunguang Luan – Scientific Reports

Plant microbiome

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient – Bin Ma – Journal of Applied Microbiology

Nostopeptolide plays a governing role during cellular differentiation of the symbiotic cyanobacterium Nostoc punctiforme – Anton Liaimer – PNAS USA

Air microbiome

Antibiotics, Bacteria, and Antibiotic Resistance Genes: Aerial Transport from Cattle Feed Yards via Particulate Matter – Andrew D. McEachran – Environmental Health Perspectives

Techniques

Review: High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats – Jizhong Zhou – mBio

Bioinformatics

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline) – Murat Eren – Github

Why now is the time to learn R – David Smith – OpenSource

Other scientific papers of interest

Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses – Jennifer E. Cox – PNAS USA

Discussion: Mice are not men – H. Shaw Warren – PNAS USA
Reply to Warren et al. and Shay et al.: Commonalities across species do exist and are potentially important – Keizo Takao – PNAS USA

Microbes in the news

Dust From Factory Farms Carries Drugs, Poop Bacteria, and Antibiotic-Resistant Genes Far and Wide – Tom Philpott – Mother Jones

How does your gut garden grow? Feeding your intestinal bacteria in a positive way – Áilín Quinlan – Irish Independent

The expert’s view: Ted Dinan, Professor of Psychiatry at UCC, on microbiome and stool transplants – Irish Independent

Obama proposes sharp increase to fight drug-resistant bacteria – Amy R. Connolly – UPI

Antibiotics for travellers’ diarrhoea – super-bacteria as a souvenir – Päivi Lehtinen – University of Helsinki

Science, publishing, and career

Number of College Students Pursuing Science, Engineering Stagnates – Melissa Korn – Wall Street Journal

Baring it all: Some researchers believe that openness can promote constructive communication and enable science to move forward faster – Rachel Bernstein – Science Careers

Why women are ditching STEM careers-and how to change it – Vivian Giang – FastCompany

Science and art

“Blurred Bands”: 2015 Lab Grammys: 8 nominees for Lab Parody of the Year – Biotechniques.com

Science and Culture: Science on-screen and behind the scenes – Stephen Ornes – PNAS USA

Science And Art Need Each Other, And Here’s Why – Cheryl Eddy – io9.com

Winners of the British Heart Foundation’s annual Reflections of Research competition – Richard P Grant – The Guardian

Bik’s Picks

Science finds a new way to unboil an egg – Michelle Starr – CNET

Asteroid that flew past Earth has moon – Science Daily

The continental divide of 2014 temperature – Thomas Summer – Science News

Blizzard 2015: Science Experiments to Do With Snow – Alyssa Newcomb – ABC News

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January 26, 2015

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Human oral microbiome

* 16S rRNA gene-based metagenomic analysis identifies a novel bacterial co-prevalence pattern in dental caries – Sri Nisha Jagathrakshakan – European Journal of Dentistry

Human urinary tract microbiome

The microbiome of the urinary tract—a role beyond infection – Samantha A. Whiteside – Nature Reviews Urology

Human gut microbiome

* Association between specific mucosa-associated microbiota in Crohn’s disease at the time of resection and subsequent disease recurrence: A pilot study – Peter De Cruz – Journal of Gastroenterology and Hepatology

Enhanced vaccination effect against influenza by prebiotics in elderly patients receiving enteral nutrition – Hiroyasu Akatsu – Geriatrics & Gerontology International

Review: The small bowel microbiota – Carthage Moran – Current Opinion in Gastroenterology

Animal microbiome

Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay – Riazuddin Mohammed – Frontiers in Microbiology

Plant microbiome

Mycorrhizal networks and coexistence in species-rich orchid communities – Hans Jacquemyn – New Phytologist

A 3-year field investigation of impacts of Monsanto’s transgenic Bt-cotton NC 33B on rhizosphere microbial communities in northern China – Yan-Jun Zhang – Applied Soil Ecology

Ectomycorrhizal fungal maladaptation and growth reductions associated with assisted migration of Douglas-fir – J. Marty Kranabetter – New Phytologist

Review: Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism – Ariane C. Kemen – New Phytologist

Soil and sediment microbiome

Soil microbial community composition does not predominantly determine the variance of heterotrophic soil respiration across four subtropical forests – Hui Wei – Scientific Reports

Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses – Fabio Stagnari – Frontiers in Microbiology

Microbial diversity in a Venezuelan orthoquartzite cave is dominated by the Chloroflexi (Class Ktedonobacterales) and Thaumarchaeota Group I.1c – Hazel A. Barton – Frontiers in Microbiology

Diversity of Soil Microbial Communities Formed by Different Light Penetrations in Forests (article in Korean) – Jun Ho Park – DBpia

Bacterial community composition of sediments from a milkfish Chanos chanos Forsskål farm – Sheila Mae S Santander-de Leon – Aquaculture Research

Bacterial diversity and fatty acid composition of hypersaline cyanobacterial mats from an inland desert wadi – Raeid M.M. Abed – Journal of Arid Environments

Study of the succession of microbial communities for sulfur cycle response to ecological factors change in sediment of sewage system – Yanchen Liu – Environmental Science and Pollution Research

Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link – Pablo Souza-Alonso – Journal of Environmental Science and Health, Part B: Pesticides, Food Contaminants, and Agricultural Wastes

Fire alters vegetation and soil microbial community in alpine meadow – Changting Wang – Land Degradation & Development

Long-term oil contamination increases deterministic assembly processes in soil microbes – Yuting Liang – Ecological Applications

Reduced vertical stratification of soil bacterial community structure and composition is associated with Bromus tectorum invasion of sagebrush steppe – Carolyn F. Weber – Journal of Arid Environments

Water microbiome

Temporal dynamics of active Archaea in oxygen-depleted zones of two deep lakes – Mylène Hugon – Environmental Microbiology Reports

Prokaryotic and diazotrophic population dynamics within a large oligotrophic inverse estuary – L. F. Messer – Aquatic Microbial Ecology

Assessing impact of acid mine drainage on benthic macroinvertebrates: can functional diversity metrics be used as indicators? – Fengzhi He – Journal of Freshwater Ecology

Microbial community of the deep-sea brine Lake Kryos seawater–brine interface is active below the chaotropicity limit of life as revealed by recovery of mRNA – Michail M. Yakimov – Environmental Microbiology

Microbiome of the built environment
Aeromonas biofilm on stainless steel: efficiency of commonly used disinfectants – Sara Craveiro – International Journal of Food Science & Technology

Fungi and the like

An improved high throughput sequencing method for studying oomycete communities – Rumakanta Sapkota, Mogens Nicolaisen – Journal of Microbiological Methods

Metagenomics and bioinformatics

VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data – Cedric C Laczny – Microbiome

GrammR: Graphical Representation and Modeling of Count Data with Application in Metagenomics – Deepak Nag Ayyala, Shili Lin – Bioinformatics

Exploiting topic modeling to boost metagenomic reads binning – Ruichang Zhang – BMC Bioinformatics

Metagenomics shows low energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene dissemination from domestic wastewater – Beate Christgen – Environmental Science & Technology

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes – Mikihiko Kawai – Environmental Microbiology Reports

Techniques

Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities – Patrick K. H. Lee – Environmental Science & Technology

Infection and Immunity

Dissemination of a Highly Virulent Pathogen: Tracking The Early Events That Define Infection – Rodrigo J. Gonzalez – PLOS Pathogens

Hypotheses: Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space – Gerardo Suzán – Ecology and Evolution

Bacteria in the news

Immune System Promotes Digestive Health by Fostering Community of “Good” Gut Bacteria – University of Utah – LabManager

Breastmilk drug could fight resistant bacteria – The Local

Zombie bacteria in tuberculosis – Medical Express

Conversation Between “Good” Bacteria and Immune System Is Key to Digestive Health – Healthcare Utah

 

How Gut Bacteria Affect Brain Health – Sleep Review Magazine

Inflammatory Bowel Diseases Linked to Viruses – John Wilson – Utah People’s Post

Inflammatory bowel disease blamed on viruses – Regie Green – SMN Weekly

Oral Health Hack: Chewing Gum Removes Up To 100M Bacteria In 10 Minutes, Similar To Flossing – Lizette Borreli – Medical Daily

Understanding ‘Plant Microbiome’ Can Improve Farming And Plant Health – Elizabeth Bent – Science 2.0

Science Digested: A new mold species discovered on salami – Benjamin Wolfe – Microbial Foods

* Tricking Soil Bacteria to Grow in Lab: Discovering a Class of Antibiotics to Combat Drug-Resistant Bacteria – Kendra Witt – Daily Nexus

Bacteria Hysteria

How often do you change your pajamas? – Ali Berman – Mother Nature Network

Bik’s Picks

Wake no more – What if you could sleep 50 hours straight and still never feel truly awake? Welcome to the bizarre, distressing, and totally exhausting world of the hypersomniac – Virginia Hughes – Medium.com

Learning to Talk Like a Woman: For many transgender people, achieving a feminine voice can be difficult – Shivam Saini – The Atlantic

Is it OK to eat snow? Short answer: Yes, as long it’s fresh and white – Lydia Ramsey – Popular Science

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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 13, 2015

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Human oral microbiome

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

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

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

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

Animal models of microbiome research

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

Animal microbiome

Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors – Carmit Cohen – The ISME Journal

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

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

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

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

Soil microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Water microbiome

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

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

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

Metagenomics

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

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

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

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

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

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

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

Metabolomics

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

Techniques

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

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

Microbes in the news

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

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

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

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

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

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

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

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

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

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

Science, publishing and career

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

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

Bik’s Picks

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

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

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

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January 8, 2015

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Human gut microbiome

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation – T. W. Cullen – Science

Review: Ancient human microbiomes – Christina Warinner – Journal of Human Evolution

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

Animal models of microbiome research

Opposite effects of anthelmintic treatment on microbial infection at individual versus population scales – Vanessa O. Ezenwa, Anna E. Jolles – Science

Plant microbiome

Engineering the plant rhizosphere – Yanxia Zhang – Current Opinion in Biotechnology

Soil and sediment microbiome

Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment (Kartchner Caverns, AZ, USA) (video) – Lin Zhang – JOVE

Sedimentology and Sequence Stratigraphy of the Late Precambrian Carbonates of the Mbuji-Mayi Supergroup in the Sankuru-Mbuji-Mayi-Lomami-Lovoy Basin (Democratic Republic of the Congo) – Franck Delpomdor – Geology and Resource Potential of the Congo Basin

Soil biology for resilient, healthy soil – R. Michael Lehman – Journal of Soil and Water Conservation

Techniques

Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform – Yoon-Seong Jeon – Journal of Microbiology

Microbes in the news

Gut bacteria, prebiotics and the link between helping stress, anxiety and depression – Clio Corn – Independent

What’s lurking in your microbiome? Possibly, a cure for disease – Jon Gertner – FastCompany

Could gut bacteria that help us digest beer and bread fight disease, too? – Phys.org

Delivery Mode Alters Newborn’s First Bacterial Exposure How microbiome develops after birth could affect later-life immunity – Bridget M. Kuehn – Gastroenterology and Endoscopy News

CAMI Hosts Community Challenge for Assessing Metagenomes – Joint Genome Institute

Consumer-Funded Test Finds 11 of 12 Pet Foods Contaminated – James Andrews – Food Safety News

Science, publishing, career

My metamorphosis – Elizabeth A. Marchio – Science

A multi-journal partnership to highlight joint first-authors of manuscripts – M Bishr Omary – Gut

Introductory Comments for the Scientific Ethics Theme – Beth A. Fischer – ASM Journal of Microbiology and Biology Education

Exaggerated science reporting – who’s to blame? – NewsWorks

Bik’s Picks

Monkeys can learn to see themselves in the mirror – Science Daily

Poker program Cepheus is unbeatable, claim scientists – The Guardian

Super-insulated clothing could eliminate need for indoor heating – Lisa Zyga – Phys.org

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January 6, 2015

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Human gut microbiome

The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy – Giovanni Cammarota – Pharmacology & Therapeutics

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

Human respiratory microbiome

Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR – Sophie Edouard – Journal of Clinical Microbiology

Animal models of microbiome research

Effects of dietary mono- and multiprobiotic strains on growth performance, gut bacteria and body composition of Javanese carp (Puntius gonionotus, Bleeker 1850) – S.K. Allameh – Aquaculture Nutrition

Animal microbiome

Harlequin ladybird: Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics – Débora P. Paula – Molecular Ecology Resources

Protist microbiome

Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera) – Masashi Tsuchiya – The Journal of Eukaryotic Microbiology

Plant microbiome

Synergists and antagonists in the rhizosphere modulate microbial communities and growth of Quercus robur L. – Fuensanta Caravaca – Soil Biology and Biochemistry

Soil microbiome

Examination of biotic and abiotic controls of soil bacterial diversity under perennial shrubs in xeric soils – Naama Berg – CATENA

Two Metagenomes from Late Pleistocene Northeast Siberian Permafrost – Kirill Krivushin – Genome Announcements

Extractable N and microbial community structure respond to grassland restoration regardless of historical context and soil composition – Sara Jo M. Dickens – AoB Plants

Methane dynamics in an alpine fen: A field based study on methanogenic and methanotrophic microbial communities – Alessandro G. Franchini – FEMS Microbiology Ecology

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients – Hamed Azarbad – FEMS Microbial Ecology

Effect of biostimulation, temperature and salinity on respiration activities and bacterial community composition in an oil polluted desert soil – Raeid M.M. Abed – International Biodeterioration & Biodegradation

High-throughput sequencing shows inconsistent results with a microscope-based analysis of the soil prokaryotic community – Masayuki Ushio – Soil Biology and Biochemistry

Water microbiome

Oil-derived marine aggregates – hot spots of polysaccharide degradation by specialized bacterial communities – Carol Arnosti – Deep Sea Research Part II: Topical Studies in Oceanography

Bioreactor and wastewater microbiomes

Overall functional gene diversity of microbial communities in three full-scale activated sludge bioreactors – Yu Xia – Applied Microbiology and Biotechnology

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw – Christopher W Simmons – Biotechnology for Biofuels

Techniques

Protocols for Metagenomic Library Generation and Analysis in Petroleum Hydrocarbon Microbe Systems – Stephanie M. Moormann – Springer Protocols Handbooks 2014

Science, publishing and career

Assessing Research Productivity: A new way of evaluating academics’ research output using easily obtained data – Ushma S. Neill – The Scientist

How many scientific papers are not original? – Michael Lesk – PNAS USA

Know Your PIO: Scientists and public information officers share several common goals. Here’s how to collaborate effectively – Tracy Vence – The Scientist

Microbes in the news

Signs of mother’s diet, birth delivery mode in human milk microbiome – EA Quinn – Genetic Literacy Project

Celebrate your fat – it’s fighting off infection – Clare Wilson – New Scientist

Common cold really is triggered by chilly weather, Yale scientists find – Sarah Knapton – The Telegraph

Picturing Infection: whole-animal, light-based imaging of infected small mammals – Kelly Rae Chi – The Scientist

Bik’s Picks

New evidence on the origin of carnivorous plants – Thomas J. Givnish – PNAS USA

Inching toward the 3D genome – Elizabeth Pennisi – Science

Chopsticks or spoon: The impact of eating methods on eating rate and glycemic response in healthy adults – Lijuan Sun – Physiology & Behavior

Anti-Vaxxers Are Idolizing the Amish, Inexplicably – Olga Khazan – The Atlantic

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December 23, 2014

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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 19, 2014

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Pregnancy and Birth

Lots of abstracts (mostly from the group of Kjersti Aagaard) from the 35th Annual Meeting of the Society for Maternal-Fetal Medicine — The Pregnancy Meeting in the American Journal of Obstetrics and Gynecology

13: Association of preterm birth with alterations in the microbiome and linkage to host mtDNA variants – Kjersti Aagaard

57: Alterations in the intestinal microbiome of infants are associated with breastfeeding practice – Derrick Chu

78: Distinct alterations in the placental microbiome among spontaneous preterm births – Kjersti Aagaard

79: Metagenomics of a population-based prospective cohort reveals no discernable impact of mode of delivery (MOD) on the infant microbiome by 6 weeks of age – Derrick Chu

122: The microbiome of the placenta is altered among subjects with severe chorioamnionitis & spontaneous preterm birth – Amanda Prince

282: Chorioamnionitis induced by intramniotic injection of IL1, LPS or Ureaplasma parvum is associated with an altered microbiome in a primate model of inflammatory preterm birth (PTB) – Amanda Prince

283: Amniotic fluid microbiome community and inflammation in women with second trimester cervical changes – Amanda Roman

342: Poor maternal nutrition is associated with alterations in the maternal and neonatal microbiome communities – Kathleen Antony

650: Characterization of the vaginal microbiome following preterm premature rupture of membranes (PPROM) – Janet Hill

709: Race, latency, and fetal membrane microbiota diversity in preterm premature rupture of membranes – Sarahn Wheeler

Human oral microbiome

* Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa – Li J – BMC Microbiology

Human respiratory microbiome

* The adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition – Cremers AJ – Microbiome Journal

Human gut microbiome

* The gut microbiota of Colombians differs from that of Americans, Europeans and Asians – Escobar JS – BMC Microbiology

Gut Microbiota: Its Role in Hepatic Encephalopathy – Rahul Rai – Journal of Clinical and Experimental Hepatology

The fungal microbiota of de-novo paediatric inflammatory bowel disease – I. Mukhopadhya – Microbes and Infection

Human vaginal microbiome

Colonization of the upper genital tract by vaginal bacterial species in non-pregnant women  – Caroline M. Mitchell – American Journal of Obstetrics and Gynecology

Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments – Dorothée Duluc – Genome Medicine

Animal models

Microbially Driven TLR5-Dependent Signaling Governs Distal Malignant Progression through Tumor-Promoting Inflammation – Melanie R. Rutkowski – Cancer Cell

Intestinal microbiota diversity and expression of pattern recognition receptors in newly weaned piglets – Xin Tao – Anaerobe

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

The effects of Lactobacillus acidophilus as feed supplement on skin mucosal immune parameters, intestinal microbiota, stress resistance and growth performance of black swordtail (Xiphophorus helleri) – Seyed Hossein Hoseinifar – Fish & Shellfish Immunology

Animal microbiome

Investigation of a new acetogen isolated from an enrichment of the tammar wallaby forestomach – Gagen EJ – BMC Microbiology

Metagenomics, bioinformatics

Determining the quality and complexityof next-generation sequencing data without
a reference genome – Seyed Yahya Anvar – Genome Biology

Techniques

Tracking down the sources of experimental contamination in microbiome studies – Sophie Weiss – Genome Biology

More microbiology

Single cell genomics of bacterial pathogens: outlook for infectious disease research – Jeffrey S McLean and Roger S Lasken – Genome Medicine

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens – Maha R Farhat – Genome Medicine

Environmental enteropathy and malnutrition: do we know enough to intervene? – William A Petri – BMC Medicine

Microbes in the news

Mix of Bacteria in Gut May Depend More on Diet than Genes – Microbiota, Microbiome Change Quickly, UCSF Researchers Find – Jeffrey Norris – UCSF

Protection of the mouse gut by mucus depends on microbes – Phys.org

Life would go on if all bacteria disappeared (but it would totally suck) – Rachel Feltman – Washington Post

New technology using bacteria from dung helps coffee farmers to purify water – Oliver Balch – The Guardian

Science, publishing, career

Dragging scientific publishing into the 21st century – Razib Khan – Genome Biology

Training for peer review: why we need it and how to get there – David Moher – Biome BioMedCentral

Along with the privilege of authorship come important responsibilities – David Moher – BMC Medicine

Crashing the Old Boys’ Science Club – Yamina Berchiche – Live Science

Bik’s Picks

‘People Can Be Afraid of Anything’ – There are plenty of people afraid of whales who will never even see one. How I learned about, and tried to conquer, my own cetaphobia – Kate Horowitz – The Atlantic

Playlist: Science! – NPR/TED staff – NPR

Birds sensed severe storms and fled before tornado outbreak – Science Daily

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December 17, 2014

Posted on by

A late digest today – I have been busy writing a paper and cooking for our lab’s annual holiday potluck party tomorrow. But here we go:

Human gut microbiome

Complex host genetics influence the microbiome in inflammatory bowel disease – Dan Knights – Genome Medicine

Microbiota and the human nature: know thyself – Harald Brüssow – Environmental Microbiology

Animal and bioreactor models of microbiome

Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model – Julie A.K. McDonald – Journal of Microbiological Methods

A novel method to characterize bacterial communities affected by carbon source and electricity generation in microbial fuel cells using stable isotope probing and Illumina sequencing – Yang Song – Journal of Microbiological Methods

Animal microbiome
Crab: Linking regional variation of epibiotic bacterial diversity and trophic ecology in a new species of Kiwaidae (Decapoda, Anomura) from East Scotia Ridge (Antarctica) hydrothermal vents – Katrin Zwirglmaier – MicrobiologyOpen

Soil microbiome

Minireview: The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria – Joseph Nesme and Pascal Simonet – Environmental Microbiology

The soil microbial community predicts the importance of plant traits in plant–soil feedback – Po-Ju Ke – New Phytologist

Metagenomics

Tle distribution and diversity in metagenomic datasets reveal niche specialization – Frank Egan – Environmental Microbiology Reports

Techniques

Application of a single-colony coculture technique to the isolation of unculturable gut bacteria – Yoshiki Tanaka – Microbiology and Immunology

A novel universal DNA labeling and amplification system for rapid microarray-based detection of 117 antibiotic resistance genes in Gram-positive bacteria – Christian Strauss – Journal of Microbiological Methods

Microbial Ecology

Microbial biogeography: the end of the ubiquitous dispersal hypothesis? – Christopher J. van der Gast – Environmental Microbiology

Bacteria can mobilize nematode-trapping fungi to kill nematodes – Xin Wang – Nature Communications

Microfluidic single-cell analysis links boundary environments and individual microbial phenotypes – Christian Dusny and Andreas Schmid – Environmental Microbiology

Microbes in the News

Microbiome may have shaped early human populations – Phys.org

Commensal bacteria were critical shapers of early human populations – Phys.org

Microbes played a significant role in human evolution, study says – Chuck Bednar – RedOrbit

The microbes we eat: Study investigates bacteria in different diets – Nathan Gray – NutraIngredients

Researchers source stool samples to study gut bacteria – Nicole Kwan – FOX News

Bacterial biofilms are associated with colon cancer, imaging technique reveals – Science Daily

Do Autoimmune Diseases Begin in the Gut? – Stephen Paget – Medscape

People may inherit ‘gut’ bacteria that cause Crohn’s disease and ulcerative colitis – MedicalXpress

* 2015 will be the year of the Microbiome (and 28 other predictions) – Fortune

#BacteriaHysteria: The hidden dangers lurking in your kitchen: Chopping boards harbour 200% more faecal bacteria than toilet seats and potatoes and leeks can give you food poisoning – Lizzie Parry – Daily Mail Online

Scientists Debate If It’s OK To Make Viruses More Dangerous In The Lab – Nell Greenfieldboyce – NPR Shots Health News

Science, publishing, and career

12 Unimpressed Comments From Peer Reviewers – Kristy Hamilton – IFL Science (for more entertaining quotes in Environmental Microbiology, see here)

Journalists to Catalog Retractions: Staff of the blog Retraction Watch will create a database of papers retracted from the scientific literature – Kerry Grens – The Scientist

Here’s What Happens When Female MIT PhDs Do a Reddit AMA About Computer Science – Lauren Landry – BostInno

How to be a science girl in a Barbie world – Eve Andrews – Grist.org

For Sale: “Your Name Here” in a Prestigious Science Journal – Charles Seife – Scientific American

These Beautiful Women in Science Art Prints Feature Rad As Heck Ladies – Sam Maggs – The Mary Sue

Bik’s Picks

Happy Holidays from the Corals! – Ocean Portal – Smithsonian

Science’s good, bad, ugly year – Tom Siegfried – Science News

Meet Bill Nye, The Anti-Science Guy – Robert Tracinski – The Federalist

10 Cutest Animals in Science in 2014 – Megan Gannon – Live Science

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