Author Archives: eliesbik

June 6, 2015

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A new paper on the microbiome of the human nose, several gut microbiome reviews,  microbiomes of soils and extreme environments, microbiome models and a cool poster about defining OTU. Happy Saturday!

Human oral microbiome

Antimicrobial Effect of a Single Dose of Amoxicillin on the Oral Microbiota – Cecilia Larsson Wexell – Clinical Implant Dentistry and Related Research

Human respiratory microbiome

Staphylococcus aureus and the ecology of the nasal microbiome – Cindy M. Liu – Science Advances

Human gut microbiome

Review: Interactions between Diet, Bile Acid Metabolism, Gut Microbiota, and Inflammatory Bowel Diseases – Devkota S – Digestive Diseases

Review: Gut Microbiota, Cirrhosis, and Alcohol Regulate Bile Acid Metabolism in the Gut – Ridlon J.M – Digestive Diseases

Review: Relationship between Obesity, Gut Microbiome and Hepatocellular Carcinoma Development – Hara E. – Digestive Diseases

Animal models of microbiome research

Absence of the intestinal microbiota exacerbates hepatobiliary disease in a murine model of primary sclerosing cholangitis – James H. Tabibian – Hepatology

Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice – Yan Y. Lam – Obesity

Animal microbiome

Gut-Associated Bacteria of Dendroctonus valens and their Involvement in Verbenone Production – Letian Xu – Microbial Ecology

Feeding of β-1,3/1,6-glucan increases the diversity of the intestinal microflora of carp (Cyprinus carpio) – V. Jung-Schroers – Aquaculture Nutrition

Changes in coral reef communities across a natural gradient in seawater pH – Hannah C. Barkley – Science Advances

Plant root, soil and sediment microbiome

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential – Alessandra Salvioli – ISME Journal

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes – Margarita Lopez-Fernandez – Microbial Ecology

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity – Eric Capo – Microbial Ecology

Water microbiome

Phytoplankton community structure in relation to vertical stratification along a north-south gradient in the Northeast Atlantic Ocean – Kristina D. A. Mojica – Limnology and Oceanography

Extremophile microbiome

Supratidal Extremophiles—Cyanobacterial Diversity in the Rock Pools of the Croatian Adria – Maria Brandes – Microbial Ecology

Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment – Elena González-Toril – Microbial Ecology

Metagenomics and bioinformatics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities – Markus Majaneva

Microbiome models, on computers and in lab dishes, see progress – Jop de Vrieze – Nature Medicine

Don’t miss this cool poster: OTU robustness, reproducibility and ecological consistency in the demarcation of operational taxonomic units – Thomas SB Schmidt

Microbes in the news

Nasal Microbiome Study Examines Influence of Host Genetics, Types of Bacterial Communities – Genome Web

The fastest-growing biome on Earth is in our homes. Forget your kids and pets. Your house’s biodiversity hotspots shelter tons of microorganisms – Mary Jo DiLonardo

Socialising Baboons and Gut Microbes – deSciphered: summarising research with simple graphics

Exploring the Link Between Gut Microbes and Diabetes – Betul Hatipoglu

Kaiser Permanente Fresno uses ‘zapper’ to get rid of deadly bacteria – ABC30

This Man Believes Mushrooms Can Solve Virtually All of Humanity’s Problems: next probiotic? – Munchies

Bik’s Picks

Eating placenta ‘does not benefit health’: There is no scientific evidence that eating the placenta after childbirth can protect women against depression and boost energy, US research suggests –  – BBC News

Ancient Shark Fossil Found in Texas – Deborah Grace – Pioneer News

Video: Robots Falling Down at DARPA Robotics Challenge – IEEE Spectrum – Youtube

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June 5, 2015

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A new test that reveals past viral infections using one drop of blood, subgingival microbiota in HIV-infected adults, and influencing horse behavior through diet.

Human oral microbiome

The oral mucosal and salivary microbial community of Behçet’s syndrome and recurrent aphthous stomatitis – Seoudi N – J Oral Microbiology

Subgingival bacterial community profiles in HIV-infected Brazilian adults with chronic periodontitis – D. C. Ferreira – Journal of Periodontal Research

Human bladder microbiome

Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference – Deborah Horwitz – Journal of Infection

Human gut microbiome

Use of T-RFLP and seven restriction enzymes to compare the faecal microbiota of obese and lean Japanese healthy men – T. Kobayashi – Beneficial Microbes

The Gut Microbiome and Childhood Obesity: Connecting the Dots – An interview with Mueller Noel Theodore – Childhood Obesity

Review: Metagenomics of the Human Intestinal tract: From who is there to what is done there – Antonietta Cultrone – Current Opinion in Food Science

Editorial: On the Gut Microbiome-Brain Axis and Altruism – Theoharis C. Theoharides – Clinical Therapeutics

Review: Potential Etiologic Factors of Microbiome Disruption in Autism – Timothy Buie – Clinical Therapeutics

Conference abstract: Dietary supplementation with a type 3 resistant starch induces butyrate producing bacteria within the gut microbiota of human volunteers – J. Kelly – Appetite

Review: Immunogenetic control of the intestinal microbiota – Eric Marietta – Immunology

Book chapter: Fecal Microbiota Transplantation for Clostridium Difficile Infection: A Systematic Review of the Evidence – Dimitri Drekonja – Department of Veterans Affairs

Review: Gut bacteria and cancer – Susan E. Erdman – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Review: The Gut Microbiota and Type 1 Diabetes – Elke Gülden – Clinical Immunology

Animal models of microbiome research

Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis – Baokun He – Scientific Reports

Antibiotics promote inflammation through the translocation of native commensal colonic bacteria – Kathryn A Knoop – Gut

Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats – S.U. Wetzels – Journal of Dairy Science

Programming rumen bacterial communities in newborn Merino lambs – I. De Barbieri – Small Ruminant Research

Changes of the hindgut microbiota due to high-starch diet can be associated with behavioral stress response in horses – Alexandra Destrez – Physiology & Behavior

Animal microbiome

Bats: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies – Mario Carrillo-Araujo – Frontiers in Microbiology

Squirrels: An Invasive Mammal (the Gray Squirrel, Sciurus carolinensis) Commonly Hosts Diverse and Atypical Genotypes of the Zoonotic Pathogen Borrelia burgdorferi Sensu Lato
Caroline Millins – Applied and Environmental Microbiology

Fish: High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species – Marlène Chiarello

Snakes: Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake – Timothy J. Colston – PLOS ONE

Insects: Leaf-Cutter Ant Fungus Gardens Are Biphasic Mixed Microbial Bioreactors That Convert Plant Biomass to Polyols with Biotechnological Applications – Alexandre F. Somera – Applied and Environmental Microbiology

Nematodes: Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts – Kristen E. Murfin – mBio

Coral: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella – D. Tye Pettay – PNAS

Plant root and soil microbiome

Linking jasmonic acid signalling, root exudates and rhizosphere microbiomes – Lilia C Carvalhais – Molecular Plant-Microbe Interactions

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils – David A. Lipson – Environmental Microbiology Reports

Two decades of warming increases diversity of a potentially lignolytic bacterial community  – Grace Pold – Frontiers in Microbiology

Water microbiome

Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems – Afef Najjari – Applied and Environmental Microbiology

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre – Kristina M. Fontanez – Frontiers in Microbiology

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center – Karthik Anantharaman – The ISME Journal

Built environment microbiome

Inflammatory potential in relation to the microbial content of settled dust samples collected from moisture-damaged and reference schools: results of HITEA study – K. Huttunen

Pyrosequencing analysis of bacterial diversity in dental unit waterlines – Damien Costa – Water Research

Viruses and phages

Comprehensive serological profiling of human populations using a synthetic human virome – George J. Xu – Science

Metagenomics and 16S rRNA sequencing

Viewpoint: Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0 – Olivier Pible and Jean Armengaud – Proteomics

Opinion: Confusion about the species richness of human gut microbiota – E. Avershina, K. Rudi – Beneficial Microbes

Metabolomics

Microbial secondary metabolites in homes in association with moisture damage and asthma – P. V. Kirjavainen – Indoor Air

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum “Latescibacteria” (WS3) – Noha H. Youssef – PLOS ONE

Bioinformatics

BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes – Frank Pennekamp – Ecology and Evolution

Techniques

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH – Bangzhou Zhang – Applied and Environmental Microbiology

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems – Yan Yan – Applied and Environmental Microbiology

Microbes in the news

How Many Viruses Have Infected You? – Nell GreenfieldBoyce – NPR

A Lifetime of Viruses: Scientists devise an antibody-based test that can generate a person’s complete “viral history” with just one drop of blood. – Amanda B. Keener – The Scientist

Single Test for All Virus Exposure Opens Doors for Researchers – Denise Grady – New York Times

Shielded Microbes Could Spread Life Far Beyond Earth – Elizabeth Howell – Discovery

Unregulated faecal transplants could squander gut-bug promise – New Scientist

Antibiotics affect piglets’ immune system – All About Feed

Good, good, good, good bacteria – Elisabeth Winkler – Sustainable Food Trust

#ASM2015: Many Skin Bacteria Are Dead or Inactive, Study Finds – Health.com

Invasive microbe protects corals from global warming, but at a cost – A’ndrea Elyse Messer, Penn State – Steam Register

Bik’s Picks

India is building millions of toilets. Getting people to use them is a bigger task. – Rama Lakshmi – Washington Post

There Is No Global Warming Hiatus After All – Sarah Zielinski – Smithsonian

New ‘Hellboy’ Dinosaur Unveiled In Scientific Paper With A Romantic Twist – Hilary Hanson – The Huffington Post

Two Newfound Marsupials Do It to Death – Laura Geggel – Discovery

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Evaluation of MicrobiomeDigest – feedback welcome

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It’s been a year since I started this blog (Happy Anniversary, MD!), so this seems like a good time to reflect on the past and get some feedback on this blog.

I started this WordPress blog in May 2014 as a service to everyone in the microbiome field who spend too much time scanning the latest literature, or (like me) not enough time. “If I have to spend hours every day reading all my eTOC alerts and Google Scholar findings, I might as well post all the relevant papers on a blog and save other people some time, ” I thought, and several of my coworkers agreed. So I bought the domain name and hosted the blog on my hubbie’s server, with the intention to make this a completely free blog. For always.

After a slow start in May 2014, the number of views steadily went up. I tried to advertise on Twitter and by sending emails to other labs in our field.  Jonathan Eisen from UC Davis has been incredibly helpful in getting the word out as well. So far, March 2015 has been the best month for MicrobiomeDigest, with 3,355 visitors and 8,184 views (spammers and my own visits are not counted by WordPress). On a busy day, I get about 200 visitors and 400 views.

Screen Shot 2015-06-04 at 02.49PM, Jun 04

The average visitor will click on 2 links, with links from Nature, Wiley, and ScienceDirect being the most popular. Please note that I cannot see the identity of the viewers (that would be creepy), just the number of clicks and the country of origin.

The vast majority of the MD visitors are from the US, followed by Canada, the UK, Germany, Denmark, and Australia. In the map from March 2015 (the busiest month so far, see graph above), you can see that MD has been viewed from pretty much every corner of the world.

Screen Shot 2015-06-04 at 02.58PM, Jun 04

However, after a good start, it appears as if the blog’s readership has reached a plateau, and might even been going down. This makes me wonder if there is room for improvement. I’m sure there is! There have to be more than 200 people in the world who are interested in microbiome papers, so I was hoping to get some feedback on how to improve my blog and increase the readership. It takes me about 3-4 hours a day to scan all the latest literature and news articles and compile the results into this daily blog and I can only justify this big effort if the readership is large enough.

So here we go, dear reader: I’d like some feedback, please. Here are some questions that I hope you all can think about. Please post your comments below this post or email them to eliesbik at stanford dot edu. You don’t have to answer all of them, but I’l love to get some feedback. Thanks a lot!

  • Is the frequency of the blog (once a day on each work day) good?
  • Is the length of each blog post good, or too long? Should I split the up into different parts, as I did in the beginning?
  • Do you like the breadth of the topics, or should I focus more on e.g. human microbiome (no more soil/water/air microbiome), top journals only, scientific papers only (no more popular press articles), microbiome only (no more general science, publishing/career/Bik’s Picks)? Or should I even include more microbiology papers?
  • How can I improve the number of visitors, especially from non-US countries?
  • For Tweeps who follow me on @MicrobiomDigest on Twitter: is the number of tweets good, too many, too few? Too much overlap with this blog?
  • Any other suggestions, also about more automated ways of posting here, would be more than welcome.

Thanks all! And please do tell others about MicrobiomeDigest if you like it. If the readership keeps on going down, I will have to consider stopping this service and focus on my (real!) job.

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June 4, 2015

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Smoking changes microbial shifts in mouse gut, root microbiome in sugarcane, microbial life after a volcanic eruption, and disturbing developments in the olive bacterial infection situation in Italy.

Human oral microbiome

Phage-bacteria interaction network in human oral microbiome – Jinfeng Wang – Environmental Microbiology

Models of microbiome research

Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology – Lihong Guo – PNAS USA

Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut – Liesbeth Allais – Environmental Microbiology

Use of Germ-Free Animal Models in Microbiota-Related Research – Maha Al-Asmakh – Journal of Microbiology and Biotechnology

Animal microbiome

Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments – Manuel Kleiner – Environmental Microbiology

Rodent reservoirs of future zoonotic diseases – Barbara A. Han – PNAS

Plant root and soil microbiome

Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism – Gijsbert D. A. Werner – PNAS

Inner Mongolian steppe arbuscular mycorrhizal fungal communities respond more strongly to water availability than to nitrogen fertilization – Xiaoliang Li – Environmental Microbiology

The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application – Yun Kit Yeoh – Environmental Microbiology

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska – Lydia H. Zeglin – Environmental Microbiology

Water microbiome

Light availability affects stream biofilm bacterial community composition and function, but not diversity – Karoline Wagner – Environmental Microbiology

Bioreactor microbiome

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics – Rose S. Kantor – Environmental Microbiology

Metagenomics

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages – Laura A. Hug – – Environmental Microbiology

Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph – Carolina Grob – Environmental Microbiology

Extrachromosomal circular DNA is common in yeast – Henrik D. Møller – PNAS

More microbes

A noisy linear map underlies oscillations in cell size and gene expression in bacteria –
Yu Tanouchi – Nature

The Matrix Reloaded: How Sensing the Extracellular Matrix Synchronizes Bacterial Communities – Nitai Steinberg and Ilana Kolodkin-Gal – Journal of Bacteriology

Measuring ruggedness in fitness landscapes – Jeremy Van Cleve – PNAS

Microbes in the news

Microbiology: Gut Bacteria cooperate when life gets tough – Université du Luxembourg – Alpha Galileo

Does treating koala chlamydia hurt their gut microbes? – Rachel Feltman – Washington Post

Xylella bacteria increasingly affecting olive trees in Southern Europe – Wageningen UR

Italian scientists vilified in wake of olive-tree deaths: Police investigate researchers’ role in devastating bacterial epidemic – Alison Abbott – Nature

Chemists weigh intact virus mixture with mass spectrometer – Science Daily

Swapping Symbionts Enabled Mediterranean Lichen to Conquer the Arctic – Jennifer Frazer – Scientific American

Researchers explain mechanism that makes their mouthwash so effective against tooth decay – Medical Xpress

Microbes and money

Human Microbiome Market – Global Industry Analysis and Forecast to 2020, by Persistence Market Research – MedGadget

Science, publishing, and career

Retracted gay-marriage study debated at misconduct meet-up: Over rum cocktails at the World Conference on Research Integrity, experts discussed what can be learnt from the fallout of a flawed political-science paper – Richard van Noorden – Nature

Bik’s Picks

Scientists use new ‘tool sled’ to collect sea sponges that have potential to combat various diseases – Science Daily

Groundbreaking study to test metabolism of dugongs to see how much food they need to survive – ABC Australia

Seven new species of miniature frogs discovered (and they’re adorable) – Rachel Feltman – Washington Post

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June 3, 2015

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Microbiomes of seahorses, diet and human stool, gut microbes influencing CNS, lichen-associated bacteria, sequencing beer, and news from #ASM2015.

Human gut microbiome

Fecal Microbiota in Healthy Subjects Following Omnivore, Vegetarian and Vegan Diets: Culturable Populations and rRNA DGGE Profiling – Ilario Ferrocino – PLOS ONE

Animal models of microbiome research

Host microbiota constantly control maturation and function of microglia in the CNS – Daniel Erny – Nature Neuroscience

Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community, Composition, and Diversity in Yanbian Yellow Cattle – Xiang Z. Li – PLOS ONE

Animal microbiome

A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province – Chenyan Shi – PLOS ONE

Comparison of the Intestinal Bacterial Flora in Healthy and Intestinal-diseased Seahorses Hippocampus trimaculatus, Hippocampus erectus, and Hippocampus spinosissimus – Feng Li – Journal of the World Aquaculture Society

Plant and soil microbiome

Analysis of the Peltigera membranacea metagenome indicates that lichen-associated bacteria are involved in phosphate solubilization – Margrét Auður Sigurbjörnsdóttir – Microbiology

Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration – Ramasamy Krishnamoorthy – PLOS ONE

Built environment microbiome

Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes – Rachel I. Adams – PLOS ONE

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing – Wuttichai Mhuantong – PLOS ONE

Metagenomic Insights into the Bioaerosols in the Indoor and Outdoor Environments of Childcare Facilities – Su-Kyoung Shin – PLOS ONE

Food microbiology

PCR-DGGE assessment of the bacterial diversity in Spanish-style green table-olive fermentations – Helena Lucena-Padrós – International Journal of Food Microbiology

Microbial ecology

Perspectives on the context-dependency of stream community responses to contaminants – William H. Clements – Freshwater Biology

Metacommunity speciation models and their implications for diversification theory – Nicolas Hubert – Ecology Letters

The complex relationship between microbial growth rate and yield and its implications for ecosystem processes – David A. Lipson – Frontiers in Microbiology

Techniques

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects – Danyta I. Tedjo – PLOS ONE

Microbes in the news

Sequence your beer: BeerDeCoded: the 1,000 beer genomes

#ASM2015 – Soil microbes ally with plants to fight disease and tolerate stress – Phys.org

#ASM2015 video: A Critical Role of the Plant Microbiome for Immunocompetency – ASM

#ASM2015: Share a Bathroom With Other People? Here’s Something You May or May Not Want to Know About Your Toothbrush – Liz Klimas – The Blaze

All About Flora: How Important Gut Health Really Is. Don’t be grossed out – those little guys living in your guts are your friends – Lacie Glover – US News
Ancient algae found deep in tropical glacier – Biology News

Microbes, biodiversity and the benefits of getting dirty – David Suzuki – National Observer

Former COD Theater Major Researches Microbiology in South Africa – Mitchell11 – Chicago Tribune

Interview with Jessica Richman of uBiome – Tracy Mac – The Power of Poop

Bacteria study may curb antibiotics use – Jeremy Watson – The Times

Could remnants of the earliest life be preserved in volcanic glass? Controversy about microbial “biotextures” – Shalini Saxena – ArsTechnica

Science, publishing, and career

Why we should help people understand our scientific literature – R. W. Abrams – Conservation Biology

Announcing mSystems™: a new ASM open-access journal launching in early 2016 with Jack Gilbert as Founding Editor in Chief – ASM

Scientists Behaving Badly (On Social Media) – Brett Buttliere – PLOS Blogs

Publons and the American Society for Microbiology announce pilot partnership – ASM

Helpful websites for women scientists interested in fellowships, scholarships and funding opportunities – ASM

Bik’s Picks

Chimps Can’t Cook, But Maybe They’d Like To – Michael D. Lemonick – National Geographic

20-year-old invents ingenious system to rid ocean of trash – Olivia Solon – Mirror

Sea lions injured in chlorine attack return to ocean (video) – Chicago Tribune

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June 2, 2015

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General human microbiome

The human microbiome in hematopoiesis and hematological disorders – Veronica E. Manzo and Ami S. Bhatt – Blood

Special issue of Microbial Ecology in Health and Disease: Editorial: We all need friends – Jørgen Valeur

Early Factors Leading to Later Obesity: Interactions of the Microbiome, Epigenome, and Nutrition – Lilly Chang, Josef Neu – Current Problems in Pediatric and Adolescent Health Care

Microbiome of pregnancy and birth

Opportunities to assess factors contributing to the development of the intestinal microbiota in infants living in developing countries – Dennis Lang – Microbial Ecology in Health and Disease

Review: Factors affecting infant gut microbiota and possible consequences for health
Merete Eggesbø – Microbial Ecology in Health and Disease

Human gut microbiome

Draft Genome Sequences of 24 Microbial Strains Assembled from Direct Sequencing from 4 Stool Samples – Patricio Jeraldo – Genome Announcements

Book Chapter: Physiology of Digestion and Absorption: The Functional Interdependence Between Food and the Gut – Stephen J. D. O’Keefe – The Principles and Practice of Nutritional Support

Review: With a little help from my enteric microbial friends – Ben Berkhout – Frontiers in Medicine

Editorial: AI-2 to the rescue against antibiotic-induced intestinal dysbiosis? – Zhongke Sun – Trends in Microbiology

Microbiome models

Evidence from Animal Models: Is a Restricted or Conventional Intestinal Microbiota Composition Predisposing to Risk for High-LET Radiation Injury? – Irene Maier – Radiation Research

Rumen Microbiome from Steers Differing in Feed Efficiency – Phillip R. Myer – PLOS ONE

Changes in the composition of intestinal fungi and their role in mice with dextran sulfate sodium-induced colitis – Xinyun Qiu – Scientific Reports

Microbiota prevents cholesterol loss from the body by regulating host gene expression in mice – Chun-Yan Zhong – Scientific Reports

Animal microbiome

Early-life establishment of the swine gut microbiome and impact on host phenotypes – Núria Mach – Environmental Microbiology Reports

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges – Ilia Burgsdorf – mBio

Plant microbiome

Antagonistic interactions between endophytic cultivable bacterial communities isolated from the medicinal plant Echinacea purpurea – Isabel Maida – Environmental Microbiology

Soil microbiome

Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra – Congcong Shen – Frontiers in Microbiology

Carcass mass has little influence on the structure of gravesoil microbial communities – Sophie Weiss – International Journal of Legal Medicine

Impact of different cropping conditions and tillage practices on the soil fungal abundance of a Phaeozem luvico – Romina P. Gomez – Spanish Journal of Agricultural Research

Biological activity and microbial genetic diversity of bare-fallow and grassland soils – Anna Kot – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Masters Thesis: Assessing soil microbial tolerance to salt – Arpita Maheshwari – Lund University

Water microbiome

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring – Karolina Ininbergs – AMBIO

Characterizing microbial communities dedicated for conversion of coal to methane in situ and ex situ – Ji Zhang – International Journal of Coal Geology

Dynamics of the bacterial and archaeal communities in the northern South China Sea revealed by 454 pyrosequencing of the 16S rRNA gene – Xia Xiaomin – Deep Sea Research Part II: Topical Studies in Oceanography

Editorial: Microbial symbiosis of marine sessile hosts- diversity and function – Suhelen Egan – Frontiers in Microbiology

Review: Biodiversity, community structure and function of biofilms in stream ecosystems – Katharina Besemer – Research in Microbiology

Built environment microbiome

pecunia non olet? Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach – Saakshi Jalali – PLOS ONE

Phages and viruses

Dark matter of the biosphere: The amazing world of bacteriophage diversity – Graham F. Hatfull – Journal of Virology

Bioinformatics and metagenomics

VirSorter: mining viral signal from microbial genomic data – Simon Roux – PeerJ

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction – David Laehnemann – Briefings in Bioinformatics

FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples – Jongin Lee – Journal of Microbiological Methods

PuzzleCluster: A Novel Unsupervised Clustering Algorithm for Binning DNA Fragments in Metagenomics – Current Bioinformatics

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi – Leho Tedersoo – MycoKeys

ANCOM: Analysis of composition of microbiomes: a novel method for studying microbial composition – Siddhartha Mandal – Microbial Ecology in Health and Disease

Transcriptomics and Metabolomics

MetabNet: an R package for metabolic association analysis of high-resolution metabolomics data – Karan Uppal – Frontiers in Bioengineering and Biotechnology

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism – Anna Edlund – ISME Journal

Review: Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders – Derrick F. MacFabe – Microbial Ecology in Health and Disease

Techniques

Co-extraction of DNA and PLFA from soil samples – Sheridan Brewer – Journal of Microbial Methods

Microbial ecology

Editorial: Flexible gene pools: hard to interpret the diversity often observed in microbial communities – Michael M. Desai – Science

Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche – Michael J. Rosen – Science

Microbes in the news

Good craft beer can be spoiled by bacteria – Phys.org / American Society for Microbiology

Treating Koala STDs May also Quash Their Essential Gut Microbes – Katherine Harmon Courage – Scientific American

New study: Gut bacteria cooperate when life gets tough – EurekAlert

Metabolic activity and health of the skin microbiome – Medical Xpress / American Society for Microbiology

Is our first line of defense sleeping on the job? – Science Daily / American Society for Microbiology

Growing Up In an UnSterile World –The Importance of a Healthy Gut Through the Lifespan – Sarah Lobisco – Dr. Lobisco

Citizen Scientists Send Microbes Into Space – Science 2.0

Methanogens: Earth organisms survive under low-pressure Martian conditions – Science Daily

Why is the H-pylori bacteria developing a liking for Mumbai police? – Santosh Andhale – DNA India

Book review: The great microbial beauty – Vittorio Capozzi – Trends in Microbiology

Science, publishing, and career

Plagiarism is the most common cause of retractions in BioMed Central journals:
Retractions Often Due to Plagiarism: Study – Kerry Grens – The Scientist

Bik’s Picks: not-microbial science

Giant Sawfish Have Virgin Births, Rewrite Biology Textbooks – Charles Q. Choi – Live Science

These newly discovered marsupials basically sex each other to death – Elahe Izadi – Washington Post

Seals Help Scientists Probe Remote Seas – Discovery

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Another June 1, 2015

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Here’s the second update of today, completing the backlog because of my travels. 

Human skin microbiome

The Cutaneous Microbiome in Outpatients Presenting With Acute Skin Abscesses – James M. Horton – Journal of Infectious Diseases

Book chapter: Skin Microbiota and Attractiveness to Mosquitoes – Niels O. Verhulst, Willem Takken – Encyclopedia of Metagenomics

Human gut microbiome

High prevalence of cannabis use among Aka foragers of the Congo Basin and its possible relationship to helminthiasis – Casey J. Roulette – American Journal of Human Biology

Hospitalization Type Predicts Risk of Subsequent Severe Sepsis – Hallie C Prescott – American Journal of Respiratory and Critical Care Medicine

Review: Harnessing the Microbiome to Enhance Cancer Immunotherapy – Michelle H. Nelson – Journal of Immunology Research

Review: The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity – Randy S. Longman – Current Opinion in Rheumatology

Review: The intestinal microbiome in spondyloarthritis – Tejpal Gill – Current Opinion in Rheumatology

Microbiome models

Thesis: Alterations in the Fecal Microbiome of Healthy Horses in Response to Antibiotic Treatment – Rachel Sarah Liepman – Ohio State University

Thesis: Effects of Maternal Dietary Yeast Supplementation on Foal Growth and Microbial
Diversity of the Hindgut in Quarter Horse Mares and Their Offspring – Elizabeth Rebecca Share – Ohio State University

Soil, plant root, and rock microbiome

Fungal invasion of the rhizosphere microbiome – Emilie Chapelle – ISME Journal

Shifts in the phylogenetic structure of arbuscular mycorrhizal fungi in response to experimental nitrogen and carbon dioxide additions – Rebecca C. Mueller – Oecologia

Archean (3.33 Ga) microbe-sediment systems were diverse and flourished in a hydrothermal context – Frances Westall – Geology

Crop rotational diversity enhances belowground communities and functions in an agroecosystem – L. K. Tiemann – Ecology Letters

Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers – Abdullah M. Al-Sadi – Journal of Applied Microbiology

Water microbiome

Aquifer community structure in dependence of lithostratigraphy in groundwater – Andrea Beyer – Environmental Science and Pollution Research

Microbial diversity in the deep-sea sediments of Iheya North and Iheya Ridge, Okinawa Trough – Jian Zhang – Microbiological Research

Urbanisation and earthquake disturbance influence microbial nutrient limitation in streams – Emma R. Moffett – Freshwater Biology

On the use of the serial dilution culture method to enumerate viable phytoplankton in natural communities of plankton subjected to ballast water treatment – John J. Cullen, Hugh L. MacIntyre – Journal of Applied Phycology

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics – Rendy Ruvindy – ISME Journal

Carbon export efficiency and phytoplankton community composition in the Atlantic sector of the Arctic Ocean – Frédéric A. C. Le Moigne – Journal of Geophysical Research – Oceans

Extremophile microbiome

Photoadaptation to the polar night by phytoplankton in a permanently ice-covered Antarctic lake – Morgan-Kiss R. M.- Limnology and Oceanography

Biodegradation: Updating the concepts of control for microbial clean-up in contaminated aquifers – Rainer Udo Meckenstock – Environmental Science & Technology

Bioreactor microbiome

Multi-system Nernst–Michaelis–Menten model applied to bioanodes formed from sewage sludge – Mickaël Rimboud – Bioresource Technology

Community shifts in a well-operating agricultural biogas plant: how process variations are handled by the microbiome – Susanne Theuerl – Applied Microbiology and Biotechnology

Review: Tolerance engineering in bacteria for the production of advanced biofuels and chemicals – Aindrila Mukhopadhyay – Trends in Microbiology

Viruses and phages

When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities – Luis P. Villarreal, Guenther Witzany – Journal of Molecular Evolution

Metagenomics and bioinformatics

Large-scale Machine Learning for Metagenomics Sequence Classification – Kévin Vervier – ArXiv

Review: Metagenomics as a tool for the investigation of uncultured microorganisms – N. V. Ravin – Russian Journal of Genetics

Metabolomics

Metabolic dynamics analysis by massive data integration: application to tsunami-affected field soils in Japan – Tatsuki Ogura – ACS Chemical Biology

Review: Defining the Metabolome: Size, Flux, and Regulation – Nicola Zamboni – Molecular Cell

Techniques

Review: High-Throughput Sequencing Technologies – Jason A. Reuter – Molecular Cell

Microbes in the news

One Week Change In My Microbiome – Richard Sprague – uBiome blog

Unconscious use of ‘medical marijuana? ‘ Hunter-gatherer cannabis use linked to fewer internal parasites – Science Daily

Touchy Feely: Physical contact helps determine who’s present among baboons’ gut bacteria – Kerry Grens – The Scientist

Mysteries of cat, human health revealed through microbiome – Meredith Knight – Genetic Literacy Project

Gut check: Does a hospital stay set patients up for sepsis by disrupting the body’s microbiome? – Kara Gavin – University of Michigan

Immunotherapy: Target the Gut in Patients with Multiple Sclerosis – Linda G. Hughes – HCP Live

Q&A With Pavan Bhargava of Johns Hopkins University School of Medicine: Studying the Microbiome in Treatment of Multiple Sclerosis – Adam Hochron – HCP Live

Contact Lenses Can Change the Ocular Microbiome – Amanda B. Keener – The Scientist

Microbiome and money

Synthetic Biologics to Host Microbiome Analyst & Investor Meeting – Market Watch

Science, publishing, and career

Scientists Who Cheat – The Editorial Board – New York Times

Michael LaCour Probably Fabricated a Document About Research Integrity – Jesse Singal – New York Magazine

Bik’s Picks

What’s Old Is New Again: Revolutionary new methods for extracting, purifying, and sequencing ever-more-ancient DNA have opened an unprecedented window into the history of life on Earth – Bob Grant – The Scientist

See The Tiny Origami Robot That’s Going Viral — Folds Itself, Walks, Swims, And Dissolves [Video] – Inquisitr

Quick to laugh or smile? It may be in your genes – Science Daily

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June 1, 2015

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Still catching up from my trip abroad – lots of new papers to share, so I will do two blog posts today.

General microbiome

Elucidating microbial codes to distinguish individuals – Allyson L. Byrd and Julia A. Segre – PNAS

Human oral microbiome

Periodontal status and pathogenic bacteria after gastric bypass: a cohort study – Sílvia Helena de Carvalho Sales-Peres – Journal of Clinical Periodontology

Inflammation-associated microbiota in pediatric eosinophilic esophagitis – Alain J Benitez – Microbiome

Global transcription of CRISPR loci in the human oral cavity – Andrew G Lum – BMC Genomics

Oral and Gastric Helicobacter Pylori: Effects and Associations – Nélio Veiga – PLOS ONE

Book Chapter: Obesity and Periodontal Disease – Simon D. Tran – Environmental Metagenomics

Human gut microbiome

Investigation of the Association Between the Fecal Microbiota and Breast Cancer in Postmenopausal Women: a Population-Based Case-Control Pilot Study – James J. Goedert – Journal of the National Cancer Institute

Review: The art of targeting gut microbiota for tackling human obesity – Marisol Aguirre, Koen Venema – Genes and Nutrition

Review article: dietary fibre–microbiota interactions – H. L. Simpson and B. J. Campbell – Alimentary Pharmacology & Therapeutics

Animal and other microbiome models

Evolutionary transition in symbiotic syndromes enabled diversification of phytophagous insects on an imbalanced diet – Sailendharan Sudakaran – ISME Journal

Fecal Microbial Transplant After Ileocolic Resection Reduces Ileitis but Restores Colitis in IL-102/2 Mice – Troy Perry – IBD Journal

Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity – Injae Hwang – The FASEB Journal

Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains – Michael S. Gilmore – PNAS

Human Microbiota-Associated Swine: Current Progress and Future Opportunities – Mei Wang and Sharon M. Donovan – ILAR Journal

Animal microbiome

Marked seasonal variation in the wild mouse gut microbiota – Corinne F Maurice – ISME Journal

Evolution of host specialization in gut microbes: the bee gut as a model – Waidan K Kwong – Gut Microbes

Soil microbiome

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China – Yuguang Zhang – Microbial Biotechnology

High resolution dynamics of microbial communities during dissimilatory selenate reduction in an anoxic soil – Ronald Ragudo Navarro – Environmental Science & Technology

Study and assessment of microbial communities in natural and commercial bioleaching – Arevik Vardanyan – Minerals Engineering

Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient – S. Hortal – Soil Biology and Biochemistry

Evaluation of soil microbial communities as influenced by crude oil pollution – Eucharia Oluchi Nwaichi and Magdalena Frac – African Journal of Biotechnology

Water microbiome

Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management – William Van Bonn – Zoo Biology

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations – Sergio Pulido-Tamayo – Nucleic Acids Research

Manganese and iron as structuring parameters of microbial communities in Arctic marine sediments from the Baffin Bay – Camelia Algora – FEMS Microbial Ecology

Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level – Mounira Smati – Microbiology Open

Manganese cycling microbial communities inside deep-sea manganese nodules – Marco Blöthe – Environmental Science & Technology

Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands – Pengfei Li – Water

Thesis: Evaluating changes in diversity and functional gene abundance of denitrifying microbe communities and nutrient concentrations in runoff following the implementation of low-grade weirs in agricultural drainage systems – Beth Baker – Mississippi State University/ Gradworks

Bioreactor microbiome

Lipid hydrolysis products affect the composition of infant gut microbial communities in vitro – Rikke G. Nejrup – British Journal of Nutrition

Effect of phospholipid on pyrite oxidation and microbial communities under simulated acid mine drainage (AMD) conditions – Andro-Marc Pierre-Louis – Environmental Science & Technology

Antibiotic resistome and its association with bacterial communities during sewage sludge composting – Jianqiang Su – Environmental Science & Technology

Food microbiology

Microbiota dynamics associated with environmental conditions and potential roles of cellulolytic communities in traditional Chinese cereal starter solid-state fermentation – Pan Li- Applied and Environmental Microbiology

Bioinformatics and metagenomics

Note: not metagenomics but Single Locus Sequencing / OTU defining: MICCA: a complete and accurate software for taxonomic profiling of metagenomic data – Davide Albanese – Scientific Reports

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data: GotCloud – Goo Jun – Genome Research

GITIRBio: A Semantic and Distributed Service OrientedArchitecture for Bioinformatics Pipeline – Luis F. Castillo – Journal of Integrative Bioinformatics

mmnet: an R package for metagenomics systems biology analysis: community-level metabolic network reconstruction – Yang Cao – BioMed Research International

Techniques

How to evaluate PCR assays for the detection of low-level DNA – Frederik Banch Clausen – APMIS
http://onlinelibrary.wiley.com/doi/10.1111/apm.12405/full

A Novel Microbial Source Tracking Microarray for Pathogen Detection and Fecal Source Identification in Environmental Systems – Xiang Li – Environmental Science & Technology

Functional Foods

Programmable probiotics for detection of cancer in urine – Tal Danino – Science Translational Medicine

Microbes in the news

Alterations to the eye microbiome of contact lens wearers may increase infections – Medical News Today

U.S. defense chief monitoring military anthrax investigation – Reuters

Deadly Bacteria Now a Proven Cancer Detector? – Samantha Solomon – Wall Street Daily’

Gut Bacteria Impacts Toddlers’ Behavior, Particularly Boys – Traci Pederson – PsychCentral

Cervicovaginal Bacteria May Increase the risk of HIV Acquisition in Women – University of Kwazulu – Natal

DNA Genotek’s microbiome collection and stabilization blog: Microbiome learnings from the Weizmann Institute – Cindy MacCullough – DNA Genotek

Scientists probe mysterious wave of antelope deaths – Rory Galloway – BBC News

Bacteria may cause Type 2 diabetes – University of Iowa Now

Should we care about fungi? The mycobiome: an emerging field of the human microbiome research – Human Microbiome Club

Hardy bacteria thrive under hot desert rocks – Nola Taylor Redd – Phys.org

Colon Cancer Diagnosis With Lumninescent Bacteria: Modified Probiotics Can Successfully Detect Tumors In Liver – Colon Cancer News Today

Scientists Find Link Between Ocean Bacteria and Atmosphere – Simon Yu – UCSD Guardian

Woman goes blind after cat licks her and transmits rare bacteria that could affect the brain, eyes, heart, and internal organs – Daily Mail

Science, career, and publishing

This poor advice blog post was retracted from Science today, but the internet never forgets.

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May 29, 2015

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General microbiome

Perspective: The trendy microbes – VK Viswanathan – Gut Microbes

Review: Use of the Microbiome in the Practice of Epidemiology: A Primer on -Omic Technologies – Betsy Foxman – American Journal of Epidemiology

Review: Biological warfare: Microorganisms as drivers of host–parasite interactions – Nolwenn M. Dheilly – Infection, Genetics and Evolution

Microbiome of pregnancy and birth

Bacterial communities in neonatal feces are similar to mothers’ placentae – X-D Dong – Canadian Journal of Infectious Diseases and Medical Microbiology

Human oral microbiome

Maturation of Oral Microbiota in Children with or without Dental Caries – Pernilla Lif Holgerson – PLOS ONE

Exploring the variation of oral microbiota in supragingival plaque during and after head-and-neck radiotherapy using pyrosequencing – Li Gao – Archives of Oral Biology

Human genital microbiome

Sensitive Detection of Thirteen Bacterial Vaginosis-Associated Agents Using Multiplex Polymerase Chain Reaction – Natália Malaguti – BioMed Research International

Human gut microbiome

Esophageal Microbiome in Eosinophilic Esophagitis – J. Kirk Harris – PLOS ONE

Pyrosequencing Analysis Reveals Changes in Intestinal Microbiota of Healthy Adults Who Received a Daily Dose of Immunomodulatory Probiotic Strains – Julio Plaza-Díaz – Nutrients

Fecal menaquinone profiles of overweight adults are associated with gut microbiota composition during a gut microbiota–targeted dietary intervention – J Philip Karl – American Journal of Clinical Nutrition

Pouch Inflammation is Associated with a Decrease in Specific Bacterial Taxa – Leah Reshef – Gastroenterology

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Acute cholecystitis associated with infection of Enterobacteriaceae from gut microbiota – Jianjun Liu – Clinical Microbiology and Infection

Letter to the Editor: Mediterranean diet: the missing link between gut microbiota and inflammatory diseases – M Bifulco – European Journal of Clinical Nutrition

Editorial: Fecal Microbiota Transplantation for Ulcerative Colitis: Not Just Yet – Ari M. Grinspan – Gastroenterology

Perspective: Rifaximin, gut microbes and mucosal inflammation: unraveling a complex relationship – Jun Gao – Gut Microbes

Review: Apples and Cardiovascular Health—Is the Gut Microbiota a Core Consideration? – Athanasios Koutsos  – Nutrients

Animal models of microbiome research

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats – Agnieszka Mika – PLOS ONE

Gut microbiota inhibit Asbt-dependent intestinal bile acid reabsorption via Gata4 – Carolien Out – Journal of Hepatology

Animal microbiome

RUMINANT NUTRITION SYMPOSIUM: The impact of the rumen microbiome on nutrition, health, and production – R.A. Kohn – Journal of Animal Science
How to use data on the rumen microbiome to improve our understanding of ruminant nutrition – J.L. Firkins – Journal of Animal Science

Production attributes of Merino sheep genetically divergent for wool growth are reflected in differing rumen microbiotas – I. De Barbieri – Livestock Science

The camel faecal metagenome under different systems of management: phylogenetic and gene-centric Approach – Suchitra S. Dande – Livestock Science

Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences – Cornelia Roder – Molecular Ecology

Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines – Dirkjan Schokker – BMC Genomics

Soil microbiome

Biodegradation kinetic rates of diesel-contaminated sandy soil samples by two different microbial consortia – Alejandro Ledezma-Villanueva – Annals of Microbiology

Temperature sensitivity of soil bacterial community along contrasting warming gradient – Jinfeng Wu – Applied Soil Ecology

Water microbiome

Heavy metals and TPH effects on microbial abundance and diversity in two estuarine areas of the southern-central coast of São Paulo State, Brazil – Aline Bartelochi Pinto – Marine Pollution Bulletin

Food microbiology

Microbial food safety: Potential of DNA extraction methods for use in diagnostic metagenomics – Mathilde H. Josefsen – Journal of Microbiological Methods

Metagenomics

Alarmingly high segregation frequencies of quinolone resistance alleles within human and animal microbiomes are not explained by direct clinical antibiotic exposure – Wesley Field – Genome Biology and Evolution

Bioinformatics

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – PeerJ PrePrints

Microbes in the news

The germ at the scene of the crime – Viviane Richter – Cosmos

Researchers combat bias in next-generation DNA sequencing – Eric Beidel – Phys.org

Microbiome research heralds new era of medical diagnosis – Aaron Krumins – Extreme Tech

Community Microbiomes: Chatting Cat Scat with Kittybiome’s Holly Ganz – Scott Edmunds – BioMedCentral Blog

Pheromones produced by gut bacteria found to kill resistant variants of its own kind – Bob Yirka – Phys.org

500 protesters chant in Santa Barbara as bacteria munch the oil spill – Chriss W. Street – Breitbart

Science, publishing, and career

Career Advice From an Oldish Not-Quite Geezer: You can’t count on your publications and awards to take care of you – Robert J. Sternberg – Chronicle

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May 28, 2015

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Catching up after a couple of days in Paris…

General microbiome

Metagenomics meets time series analysis: unraveling microbial community dynamics – Karoline Faust – Current Opinion in Microbiology

What’s Bugging you and your Diet? – Bryn L Yeomans and Nicholas T Bello – Journal of Food and Nutritional Disorders

Pregnancy and birth microbiome

Comparison of Bacterial Composition in Blood and Placentas Using Conventional and Molecular Methods – Tingtao Chen – Clinical Microbiology: Open Access

Gut microbiome composition is associated with temperament during early childhood – Lisa M. Christian – Brain, Behavior, and Immunity

Human genital microbiome

Cervical Microbiota in Women with Preterm Prelabor Rupture of Membranes – Marian Kacerovsky – PLOS ONE

Re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – C Griffin – BJOG: An International Journal of Obstetrics & Gynaecology
Author’s reply re: The vaginal microbiome, vaginal anti-microbial defence mechanisms and the clinical challenge of reducing infection-related preterm birth – SS Witkin – BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Human seroreactivity to gut microbiota antigens – Benjamin S. Christmann – Journal of Allergy and Clinical Immunology

Models of microbiome research

A Role for Gut Microbiota and the Metabolite-Sensing Receptor GPR43 in a Murine Model of Gout – Angélica T. Vieira – Arthritis & Rheumatology

Tumor Grafting Induces Changes of Gut Microbiota in Athymic Nude Mice in the Presence and Absence of Medicinal Gynostemma Saponins – Lei Chen – PLOS ONE

Dynamic vaginal microbiota in pigtail macaques is associated with menstrual cycle and inflammation (MUC9P.753) – Nichole Klatt – The Journal of Immunology

Animal microbiome

Pyrosequencing Characterization of the Microbiota from Atlantic Intertidal Marine Sponges Reveals High Microbial Diversity and the Lack of Co-Occurrence Patterns – Anoop Alex – PLOS ONE

Characterization of the Bacterial Microflora on the Skin of Boreal toads, Anaxyrus (Bufo) boreas boreas, and Columbia Spotted Frogs, Rana luteiventris, in Grand Teton National Park, Wyoming USA – A.M. Hillis – International Journal of Microbiology Research

Soil microbiome

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities – Jordan G. Okie – The Royal Society – Proceedings B

Book: The Soils of Antarctica – James G. Bockheim

Thesis: Role of Viruses Infecting Bacteria in Subsurface Sediments and Groundwater – Donald Pan – University of Nebraska-Lincoln

Water microbiome

Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria – S. A. Amin – Nature

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor – R. Danovaro – Aquatic Microbial Ecology

Bioreactor microbiome

Ecological Media Reveal Community Structure Shifts in a Municipal Wastewater Treatment Train – Bergmann RC – Bioremediation & Biodegradation

Extremophile microbiome

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species – Nur A. Hassan – PNAS

Book: The Soils of Antarctica – James G. Bockheim

Techniques

New Perspectives on Microbial Community Distortion after Whole-Genome Amplification – Alexander J. Probst – PLOS ONE

Human Bacterial and Fungal Amplicon Collection and Processing for Sequencing – Julia Oh – Bio-Protocol

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches – Stefan J. Green – PLOS ONE

Microbial Ecology

Community quorum sensing signalling and quenching: microbial granular biofilm assembly – Chuan Hao Tan – NPJ Biofilms and Microbiomes

Theoretical analysis of the cost of antagonistic activity for aquatic bacteria in oligotrophic environments – Eneas Aguirre-von-Wobeser – Frontiers in Microbiology

More microbiology

Instrumentation: The mystery of the microscope in mud – Brian J. Ford – Nature

Antibiotic alternatives rev up bacterial arms race: From predatory microbes to toxic metals, nature is inspiring new ways to treat infections – Sara Reardon – Nature

Bioinformatics and Metagenomics

obitools: a unix-inspired software package for DNA metabarcoding – Frédéric Boyer – Molecular Ecology Resources

GenoLIB: a database of biological parts derived from a library of common plasmid features – Neil R. Adames – Nucleic Acids Research

PhD Thesis: Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale – Jeffrey A. Daily – Washington State University

Book Chapter: Lessons Learned from Simulated Metagenomic Datasets – Germán Bonilla-Rosso – Encyclopedia of Metagenomics

Review: Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology – Lisa Ufarté – Frontiers in Microbiology

Microbes in the news

The microbial world at our feet – Richard Burn – Society for General Microbiology

‘Bacteria Whisperer’ Bonnie Bassler reveals the secret lives of bacteria in Vancouver – CBC News

Google Ventures: These eight life sciences techs are the most promising – and worthy of investment – Meghana Keshavan – MedCityNews

Fast food versus the African diet, the bacteria battle waged in your gut – Carina Storrs – CNN

Toddler temperament could be influenced by different types of gut bacteria – Science Daily

Is Your Nervous System Being Hacked by Bacteria in Your Gut? – Gaia Vince – Gizmodo

Bacteria appears to help bats fight deadly white-nose syndrome – Mary Beth Griggs – Popular Science

Invisible helpers of the sea: Marine bacteria boost growth of tiny ocean algae – Phys.org

Some like it hot: Extremophile bacteria could be key to solving nuclear problems – Seaes Manchester

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