Category Archives: More Microbes

August 6, 2015

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Obesity in Korean adolescents, banana rhizosphere, rare taxa and Deepwater Horizon spill, leaking septic tanks, and visualization of ‘omics data.

Events

BioMicroWorld 2015: International Conference on Environmental, Industrial and Applied Microbiology, 28-30 October 2015, Barcelona, Spain – Has a workshop called: “Modelling bacterial dynamics using the R software”

Human oral and gut microbiome

Oral and faecal microbiota in volunteers with hypertension in a double blind, randomised placebo controlled trial with probiotics and fermented bilberries – Jie Xu – Journal of Functional Foods

Obesity Alters the Microbial Community Profile in Korean Adolescents – Hae-Jin Hu – PLOS ONE

Microbiome models

Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity – Blanda Di Luccia – PLOS ONE

Plants, roots, and soil microbiome

Manipulating the banana rhizosphere microbiome for biological control of Panama disease – Chao Xue – Scientific Reports

Review: Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity – Barbara Reinhold-Hurek – Annual Review of Phytopathology

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants – Rashi Gupta – PLOS ONE

Effect of genetically modified rice producing resveratrol on the soil microbial communities – Soo-In Sohn – Journal of the Korean Society for Applied Biological Chemistry

Water microbiome

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume – Sara Kleindienst – The ISME Journal

Linking fecal bacteria in rivers to landscape, geochemical, and hydrologic factors and sources at the basin scale – Marc P. Verhougstraete – PNAS

Toolbox approaches using molecular markers and 16S rDNA amplicon datasets for the identification of fecal pollution in surface water – W. Ahmed – Applied and Environmental Microbiology

Bioinformatics

Anvi’o: An advanced analysis and visualization platform for ‘omics data – A. Murat Eren – Peer J

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads – Binbin Lai – BMC Bioinformatics

MiRKAT peeks at associations between the microbiome and disease – —JM Kocarnik – Fred Hutch

Fungi and microbiomes

Noisy neighbourhoods: quorum sensing in fungal polymicrobial infections – Emily F. Dixon – Cellular Microbiology

Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences – Adrian Langarica-Fuentes – Microbiology

More microbes

Review: Next-generation sequencing for pathogen detection and identification – Kenneth G. Frey – Methods in Microbiology

Microbes in the news

University of Missouri hosts open house at DNA sequencing center – Megan Favignano – Columbia Tribune

Detective work traces bacteria in Michigan rivers back to leaky septic tanks – Rebecca Williams – Michigan Radio

Bacteria that may cause spotty liver disease in chickens identified – Farmers Weekly

Bik’s Picks

World’s first ant map launched in Hong Kong:geographic locations of nearly 15,000 types of ant – Business Insider

Seeds That Defied Romans, Pirates, and Nazis – Robert Krulwich – National Geographic

The dark side of the moon sails across Earth in new NASA video – Deborah Netburn – Los Angeles Times

 

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August 4, 2015

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Diet-induced metabolic changes, rhythmicity of mouse gut microbiome, the microbiome of Lake Michigan, and chicken skin virome.

General microbiome

Antibiotics, microbiota and health: are there dangers hiding in plain sight? – A. Clinton White Jr – Current Opinion in Infectious Diseases

Short Course in the Microbiome: Meeting Dispatch – Kimberly Falana – Journal of Circulating Biomarkers

Pregnancy and birth microbiome

Influence of Intrapartum Antibiotic Prophylaxis for Group B Streptococcus on Gut Microbiota in the First Month of Life – Corvaglia, Luigi – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome – Saeed Shoaie – Cell Metabolism

Effect of daily intake of pomegranate juice on fecal microbiota and feces metabolites from healthy volunteers – Juana I. Mosele – Molecular Nutrition & Food Research

Gut microbiota richness promotes its stability upon increased dietary fiber intake in healthy adults – Julien Tap – Environmental Microbiology

Review: The intestinal microbiome and health – Susan Tuddenham – Current Opinion in Infectious Diseases

Review: Trimethylamine N-Oxide From Gut Microbiota in Chronic Kidney Disease Patients: Focus on Diet – Cristiane Moraes – Journal of Renal Nutrition

Review: Gut permeability, its interaction with gut microflora and effects on metabolic health are mediated by the lymphatics system, liver and bile acid – Cuong D Tran – Future Medicine

Microbiome models

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock – Xue Liang – PNAS

Viability of gut microbes as a complementary earthworm biomarker of metal exposure – Shin Woong Kim – Ecological Indicators

Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles – Troy D. Hubbard – Scientific Reports

Which games are growing bacterial populations playing? – Xiang-Yi Li – Interface

Animal microbiome

Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin – Caroline Denesvre – Virus Genes

Variations in microbiota of culex (melanoconion) ocossa and culex (culex) declarator across periurban and rural environments – M Nelson Starkey – Honors Thesis – Andrews University

Plasmids from the gut microbiome of cabbage root fly larvae encode SaxA that catalyzes the conversion of the plant toxin 2-phenylethyl isothiocyanate – Cornelia U. Welte – Environmental Microbiology

Plant, root, and soil microbiome

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
Shengjing Shi – mBio

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities – Michael S. Strickland – Frontiers in Microbiology

Changes in soil microbial community functionality and structure in a metal-polluted site: The effect of digestate and fly ash applications – M. Garcia-Sánchez – Journal of Environmental Management

Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species – Hieu X. Cao – Frontiers in Microbiology

Microbial composition alters the response of litter decomposition to environmental change – Kristin L. Matulich – Ecology

Plant community richness and microbial interactions structure bacterial communities in soil – Daniel C. Schlatter – Ecology

Plant diversity effects on soil microbial functions and enzymes are stronger than warming in a grassland experiment – Katja Steinauer – Ecology

Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging – Chris Greening – PNAS

Review: Current overview on the study of bacteria in the rhizosphere by modern molecular techniques: a mini‒review – L. Lagos – Journal of soil science and plant nutrition

Review: Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering – Liliana Quiza – Frontiers in Plant Science

Water microbiome

The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems – Clara Ruiz-González – Global Ecology and Biogeography

Dissimilatory Arsenate Reduction and In Situ Microbial Activities and Diversity in Arsenic-rich Groundwater of Chianan Plain, Southwestern Taiwan – Suvendu Das – Microbial Ecology

Freshwater ice as habitat: Partitioning of phytoplankton- and bacteria between ice and water in central European reservoirs – R.M.L. McKay – Environmental Microbiology Reports

Urban microbial ecology of a freshwater estuary of Lake Michigan – Jenny C. Fisher – Elementa

Review: Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways – Thomas A. Bobik – Molecular Microbiology

Metagenomics and bioinformatics

SuRankCo: supervised ranking of contigs in de novo assemblies – Mathias Kuhring – BMC Bioinformatics

More microbe research

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri – Thomas R Conno – eLIFE

The Cipher Code of Simple Sequence Repeats in “Vampire Pathogens” – Geng Zou – Scientific Reports

Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis – Tanmoy Roychowdhury – Scientific Reports

Protein synthesis by ribosomes with tethered subunits – Cédric Orelle – Nature

Long-term social dynamics drive loss of function in pathogenic bacteria – Sandra Breum Andersen – PNAS

New approaches to understanding the immune response to vaccination and infection –
David Furman – Vaccine

Microbes in the news

Would You Wear a Face Mask Made From Bacteria? – Jenna Rosenstein – Allure

Times-Picayune asks – Did a moldy building kill 4 New Orleans Professors – Jonathan Eisen – MicroBEnet

How the bugs in your gut keep you healthy – Keri Wiginton – Chicago Tribune

Scientists successfully breed symbiotic bacteria in mosquitoes to control dengue fever – ZeeNews India

Weight-Loss Surgery Changes Gut Bacteria – Rachael Rettner – Live Science

Volcanic bacteria take minimalist approach to survival – Otago University

Science, publishing, and career

Achieving Speaker Gender Equity at the American Society for Microbiology General Meeting – Arturo Casadevall – mBio

Bik’s Picks

This one was striking: Lightning strike as a possible cause of mortality of Australian sea lions, Neophoca cinerea – Peter D. Shaughnessy – Marine Mammal Science

Chilly at Work? Office Formula Was Devised for Men – Pam Belluck – New York Times
Belongs to: Energy consumption in buildings and female thermal demand – Boris Kingma & Wouter van Marken Lichtenbelt – Nature Climate Change

This Map Shows How New Yorkers View The Rest Of The United States. Finally, proof! – Carly Ledbetter – Huffington Post

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July 8, 2015

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Just a short post today. PLOS ONE has a paper about burn victims and gut microbiome, in which both humans as well as mice were studied, but I really disliked the mouse experiments, where mice were deliberately burned (by shaving them and dipping them in near-boiling water). As a scientist, I realize that animal experiments can be useful, but I very much dislike animal studies that involve deliberate burns, enormous tumors, and parabiosis. I hope that these types of experiments can soon be replaced by more animal-friendly versions.

In other news: a bacterium on satellite survived entry into the Earth’s atmosphere. How cool is that?

Human respiratory microbiome

Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients – Wouter A A de Steenhuijsen Piters – The ISME Journal

Human/animal model gut microbiome

I really dislike the mouse part of this paper: Burn Injury Alters the Intestinal Microbiome and Increases Gut Permeability and Bacterial Translocation – Zachary M. Earley – PLOS ONE

Animal microbiome

Diet shapes the gut microbiome of pigs during nursing and weaning – Steven A. Frese – Microbiome

Plant, root, and soil microbiome

Editorial: Symbiosis: Receptive to infection – Sharon R. Long – Nature

Receptor-mediated exopolysaccharide perception controls bacterial infection – Y. Kawaharada – Nature

Water microbiome

Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water – Mikkel Bentzon-Tilia – mBio

More microbiology

Eye-like ocelloids are built from different endosymbiotically acquired components –
Gregory S. Gavelis – Nature

Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth’s Atmosphere on FOTON-M4 Satellite Landing Module – Alexander Slobodkin – PLOS ONE

Microbes in the news

Justin and Erica Sonnenburg: The Gut Connection – The Insight

Together bacteria invade antibiotic landscapes – Phys.org

Now You Can Buy Shampoo and Cleanser That Promote the Growth of “Good” Bacteria – L.V. Anderson – Slate

Just How Gross Is It to Leave Your Toothbrush In The Bathroom? – Lindsay Colameo – Allure

Science, publishing, and career

Postdocs will be getting a raise – Justin Kiggins – The Spectroscope
and
Will Obama’s revamp of the overtime rules mean postdocs are paid more? – Drugmonkey

Bik’s Picks

Shark selfies: Shark Files: Baited Cameras to Count World Sharks – Lori Cuthbert – Discovery

Scientists Discover a ‘Complex Cocktail of Many Chemicals’ in Snail Venom That Could Treat Cancer, Pain and Addiction – Liz Klimas – The Blaze

These Plastic Chemicals May Be Just As Dangerous As What They Replace – Justin Worland – Time

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June 30, 2015

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Metabolomics and gut colonization of gnotobiotic mice, metabolomics of mice treated with antibiotics, inter-individual and temporal variation in human oral microbiotas, and several papers on microbes in agricultural-use soil.

Events

Free Cell Press webinar on Microbiome, Antibiotics and Human Disease: July 28th – Cell Press

Microbiome of pregnancy and birth

Book chapter: The Effect of Diet and Probiotics on the Human Gut Microbiome – Lorenzo Morelli – Metabolic Syndrome and Complications of Pregnancy

Human oral microbiome

Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals – Yukuto Sato – PLOS ONE

Oral microflora of supragingival and subgingival biofilms in Algerian healthy adults – Sara Ziouani – African Journal of Microbiology Research

Human respiratory microbiome

Airway bacteria and respiratory symptoms are common in ambulatory HIV-positive UK adults – Camus Nimmo – European Respiratory Journal

Oral application of lactic acid bacteria following treatment with antibiotics inhibits allergic airway inflammation – Qiuxiang Zhang – Journal of Applied Microbiology

Human vaginal microbiome

Soluble Immune Mediators and Vaginal Bacteria Impact Innate Genital Mucosal Antimicrobial Activity in Young Women – Rebecca Pellett Madan – American Journal of Reproductive Immunology

Human gut microbiome

Fetal programming of overweight through the microbiome: boys are disproportionately affected – A. L. Kozyrskyj – Journal of Developmental Origins of Health and Disease

Impact of fluoroquinolones on human microbiota. Focus on the emergence of antibiotic resistance – Victoire de Lastours – Future Microbiology

Animal models

Metabolome progression during early gut microbial colonization of gnotobiotic mice – Angela Marcobal – Scientific Reports

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment – Yael R. Nobel – Nature Communications

Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice – Joshua S. Son – PLOS ONE

Animal microbiome

Review: The use of probiotics in aquaculture – Ngo Van Hai – Journal of Applied Microbiology

Thesis: Roles of the symbiotic microbial communities associated with sponge hosts in the nitrogen and phosphorus cycles – Russell T Hill – University of Maryland

Master Thesis: Arsenic Exposure Alters the Microbiome of Larval Zebrafish: A Metagenomic Analysis – Dylan A. Dahan – Bard Digital Commons

Discovery of a novel circular DNA virus in the Forbes sea star, Asterias forbesi – Elizabeth Fahsbender – Archives of Virology

Sexual transmission of beneficial microbes – Chad C. Smith – Trends in Ecology & Evolution

Plant, root, and soil microbiome

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards – Ingrid H. Franke-Whittle – Plant and Soil

Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers – Viia Kõiv – Scientific Reports

Maternal effects on tree phenotypes: considering the microbiome – Maria Vivas – Trends in Plant Science

Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature – Rafael Bargiela – Scientific Reports

Soil Microbial Communities are Shaped by Plant-Driven Changes in Resource Availability During Secondary Succession – Lauren C. Cline – Ecology

Warmer temperature accelerates methane emissions from the Zoige wetland on the Tibetan Plateau without changing methanogenic community composition – Mengmeng Cui – Scientific Reports

Water microbiome

Constitutive presence of antibiotic resistance genes within the bacterial community of a large subalpine lake – Andrea Di Cesare – Molecular Ecology

Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater – Alexander L. Greninger – Genome Announcements

Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea – Sung-Suk Suh – PLOS ONE

Built environment / water treatment microbiology

Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system – Qi Hu – Research in Microbiology

Impact of disinfection on drinking water biofilm bacterial community – Zilong Mi – Journal of Environmental Sciences

Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy – H. Hu – The Journal of Hospital Infection

A review of melanized (black) fungal contamination in pharmaceutical products – incidence, drug recall and control measures – Rajendran Vijayakumar – Journal of Applied Microbiology

Bioinformatics and metagenomics

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS – Bruno Fosso – BMC Bioinformatics

Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial) – Adina Howe – Frontiers in Microbiology

Metabolomics

Human Urinary Composition Controls Antibacterial Activity of Siderocalin – Robin R. Shields-Cutler – The Journal of Biological Chemistry

Human Urine Decreases Function and Expression of Type 1 Pili in Uropathogenic Escherichia coli – Sarah E. Greene – mBio

New techniques

To Celebrate Marriage Equality, Illumina to Release “BiSeq” Genome Sequencer – The Allium

More microbiology

More than the sum of its parts – Julia Fahrenkamp-Uppenbrink – Science

Ecological communities by design – James K. Fredrickson – Science

The bacterial pangenome as a new tool for analyzing pathogenic bacteria – Laetitia Rouli – New Microbes and New Infections

Microbes in the news

Antibiotics and the Gut Microbiome: Antibiotics given to infant mice may have long-term effects on the animals’ metabolism and gut microbiota – Anna Azvolinsky – The Scientist

Study: Breast milk helps babies develop immunity-boosting gut bacteria – Deena Shanker – Quartz

Your Diet May Be Causing Your Urinary Tract Infections – Mandy Oaklander – Time

uBiome and OpenBiome Partner for Microbiome Study in FMT Patients – Study will provide new insights on mechanics of fecal microbiota transplantation in C. difficile patients – uBiome

Passive Aggressive: Drosophila microbiota influence behavior – Julie Wolf – mBioSphere

Soil water, microbes influence carbon in world’s coldest desert, study finds – Phys.org

Invisible You: Art and Microbiology at the Eden Project – Microbe Post

Science, publishing, and career

The Myth of the Academic Lottery – Kelly J. Baker – Chronicle Vitae

Bik’s Picks

I saw this last night and it was so pretty: Venus and Jupiter to Put on ‘Best Backyard Sky Show of 2015’ – Alyssa Newcomb – ABC News

Say hello to the centipede from hell – Rachel Feltman – Washington Post

California governor signs strict law requiring vaccinations for most kids – Liz Szabo – USA Today

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June 11, 2015

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Exciting edition today, with microbiomes from scorpions, kombucha, Korean infants, and a Yosemite lake.

Pregnancy and birth

Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing – Sang A Lee – Nutrition Research and Practice

Human skin microbiome

Review: Effects of Fermented Dairy Products on Skin: A Systematic Review – Alexandra R. Vaughn – The Journal of Alternative and Complementary Medicine

Human gut microbiome

The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome – Zev H. Davidovics – Journal of Parental & Enteral Nutrition

Review: Association of the Intestinal Microbiota and Obesity – Andrea A. López-Cepero, Cristina Palacios – Puerto Rico Health Sciences Journal

Microbiome models

Alteration of the rat cecal microbiome during colonization with the helminth Hymenolepis diminuta – Erin A McKenney – Gut Microbes

Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus –
Kristian Daly – Environmental Microbiology

Ecobiotherapy Rich in Firmicutes Decreases Susceptibility to Colitis in a Humanized Gnotobiotic Mouse Model – Jane M. Natividad – Inflammatory Bowel Diseases

Animal microbiome

Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota –
Luis M. Bolaños – Environmental Microbiology

Water microbiome

Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea – Bo Yang – Antonie van Leeuwenhoek

Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA – Curtis J. Hayden – Environmental Microbiology

Food microbiology

Metabarcoding of the kombucha microbial community grown in different microenvironments – Oleg N Reva – AMB Express

More microbiology

I thought this was a very attractive paper: Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes – Sebastian Kolinko – Environmental Microbiology

Review: Small but Mighty: Cell Size and Bacteria – Petra Anne Levin and Esther R. Angert – Cold Spring Harbor Perspectives in Biology

Preview: Bacteria Moving into Focus of Human Cancer – Francesco Boccellato, Thomas F. Meyer – Cell Host & Microbe

Microbes in the news

Microbe-mediated adaptation to a novel diet: Symbiotic bacteria enabled bugs to feed on plant seeds and promoted species diversity – Max Planck Institute for Chemical Ecology

Bespoke diets based on gut microbes could help beat disease and obesity – Ian Sample – The Guardian

Engineers create origami paper-based bacteria-powered battery – Nanowerk

Journal club: Response to May 29, 2015 Journal Club: “Modulation of Post-Antibiotic Bacterial Community Reassembly and Host Response by Candida Albicans” – Human Microbiome Journal Club

Alberta researchers hot on the trail of deadly bacteria: detection time of E. coli in meat cut in half – Alexis Kienlen – Alberta Farmer

Sauerkraut Could Be The Secret To Curing Social Anxiety – Carolyn Gregoire – Huffington Post

Microbiomes might differ between mice: Reproducibility: Use mouse biobanks or lose them – Kent Lloyd – Nature

ESCMID introduces two new study groups to create networks for forensic and veterinary microbiology – News Medical

Science, publishing, and career

Nobel Laureate Resigns Post After Comments on Female Scientists – Dan Bilefsky – New York Times

Funny article, in response to Tim Hunt’s comments: Female scientists post ‘distractingly sexy’ photos – BBC News

African academics challenge homophobic laws – Scientific report demolishes assertions used to back criminalization of homosexuality – Linda Nordling – Nature

Workforce: The joys of research in retirement – Klaus Wittmaack – Nature

Bik’s Picks

Population genomics of Bronze Age Eurasia: low-coverage genomes from 101 ancient humans from across Eurasia – Morten E. Allentoft – Nature

#CureBatten: Celebrities rally for sisters battling rare brain disease – Chris Serico – Today

Three cheers for Samantha Cristoforetti, smasher of space records – Rachel Feltman – Washington Post

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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 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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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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May 23, 2015

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Human vaginal microbiome

Vaginal Biofilm: Much Ado About Nothing, or a New Therapeutic Challenge? – Jack D. Sobel – Clinical Infectious Diseases

Human respiratory microbiome

Correlation between Either Cupriavidus or Porphyromonas and Primary Pulmonary Tuberculosis Found by Analysing the Microbiota in Patients’ Bronchoalveolar Lavage Fluid – Yuhua Zhou – PLOS ONE

Human gut microbiome

Temporal and technical variability of human gut metagenomes – Anita Y Voigt – Genome Biology

Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men – Ilias Lagkouvardos – Molecular Nutrition & Food Research

Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation – Kaija-Leena Kolho – American Journal of Gastroenterology

The impact of ciprofloxacin and clindamycin administration on Gram-negative bacteria isolated from healthy volunteers and characterizing the resistance genes they harbour – Roderick M. Card – Antimicrobial Agents and Chemotherapy

Review: The Role of the Microbiome in Mental Health: A Psychoneuroimmunologic Perspective – Kelly Brogan – Alternative and Complementary Therapies

Review: Dysbiosis and Immune Dysregulation in Outer Space – Jorge L. Cervantes – International Reviews of Immunology

Models of microbiome research

Effects of two whole-grain barley varieties on caecal SCFA, gut microbiota and plasma inflammatory markers in rats consuming low- and high-fat diets – Yadong Zhong – British Journal of Nutrition

Animal microbiome

Dogs: Characterization of Microbial Dysbiosis and Metabolomic Changes in Dogs with Acute Diarrhea – BC Guard – PLOS ONE

Coral: Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses – David M Baker – ISME Journal

Plant and soil microbiome

Quantitative assessment of the differential impacts of arbuscular and ectomycorrhiza on soil carbon cycling – Nadejda A. Soudzilovskaia – New Phytologist

Soil pH and biome are both key determinants of soil archaeal community structure –
Binu M. Tripathi – Soil Biology and Biochemistry

Solarization makes a great impact on the abundance and composition of microbial communities in soil – Kazunori Yokoe – Soil Science and Plant Nutrition

The relationship between successional vascular plant assemblages and associated microbial communities on coal mine spoil heaps – G. Woźniak – Community Ecology

Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover – Yuting Liang – ISME Journal

Differential acquisition of amino acid and peptide enantiomers within microbial community groups and its implications for carbon and nitrogen cycling in soil – R.C.I. Broughton – Soil Biology and Biochemistry

Molecular mechanisms underlying the close association between soil Burkholderia and fungi – Nejc Stopnisek – ISME Journal

Water microbiome

Editorial: Computational eco‐systems biology in Tara Oceans: translating data into knowledge – Shinichi Sunagawa – Molecular Systems Biology

Editorial: The making of Tara Oceans: funding blue skies research for our Blue Planet – Eric Karsenti – Molecular Systems Biology

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes – Jacob A Cram – ISME Journal

Air microbiome

Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest – A. M. Womack – Biogeosciences Discuss

Bioreactor microbiology

Palygorskite changes heavy metal bioavailability and microbial functional diversity in sewage sludge composting – Siying Liu – Environmental Technology

Evaluation of System Performance and Microbial Communities of a Bioaugmented Anaerobic Membrane Bioreactor Treating Pharmaceutical Wastewater – Kok Kwang Ng – Water Research

Bioinformatics and Metagenomics

Read Mapping on de Bruijn graph – Antoine Limasset and Pierre Peterlongo – arXiv

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation – Roie Levy – BMC Bioinformatics

Consortium of the ‘bichlorophyllous’ cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome based description – Natalia Velichko – Environmental Microbiology Reports

A new approach for detecting fungal and oomycete plant pathogens in next generation sequencing metagenome data utilising electronic probes – Andres Espindola – International Journal of Data Mining and Bioinformatics

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity – Yan He – Microbiome

Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries – Kathy N Lam – Microbiome

Metabolomics

Using community metabolomics as a new approach to discriminate marine microbial particulate organic matter in the western English Channel – Carole A. Llewellyn – Progress in Oceanography

Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat – Xueju Lin – ISME Journal

Phages, viruses, CRISPRs

Computational Detection of CRISPR/crRNA Targets – Ambarish Biswas – CRISPR Methods in Molecular Biology

Creation and Analysis of a Virome: Using CRISPR Spacers – Michelle Davison – CRISPR Methods in Molecular Biology

More microbes

Not open access, alas. van Leeuwenhoek microscopes—where are they now? – Lesley A. Robertson – FEMS Microbiology Letters

Microbes in the news

Headline from 2030: Is your space commute making you sick? Microbiomes undergo weird changes in space – Alexandra Ossola – Popular Science

Leaf bacteria fertilize trees, researchers claim – Elizabeth Pennisi – Science

The bugs within us – Hordes of bacteria live inside animals, affecting their health, food choices and mating – Roberta Kwok – Student Science

Report from the 1st Annual Translational Microbiome Conference: Moving from lab to clinic: Microbiome on the move – Taconic Insights

Recent Built Environment Microbiology papers – Elisabeth Bik – MicroBE.net

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May 22, 2015

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Several special issues this week: Science features results from the Tara ocean plankton biodiversity expedition, Microbes and Infection has a special on the oral microbiome, and Frontiers bundled several papers under the not-so-pretty name The Human Gutome.

General microbiome

The Microbiome and Autoimmune Disease: Report from a Noel R. Rose Colloquium – Jobert G. Barin – Clinical Immunology

New developments providing mechanistic insight into the impact of the microbiota on allergic disease – Kathy D. McCoy – Clinical Immunology

Review: Self or non-self? The multifaceted role of the microbiota in immune-mediated diseases – Martin A. Kriegel – Clinical Immunology

Human oral microbiome

Special issue of Microbes and Infection (7 papers but most have already been posted in this blog). Editorial with links to 7 papers: A New Frontier: Oral Microbes without Borders – Özlem Yilmaz
Extracellular DNA in oral microbial biofilms – Nicholas S. Jakubovics

Not microbiome but cool: The Diet of Three Medieval Individuals from Caravate (Varese, Italy). Combined Results of ICP-MS Analysis of Trace Elements and Phytolith Analysis Conducted on Their Dental Calculus – A. M. B. Lazzati – International Journal of Osteoarchaeology

Human gut microbiome

Frontiers Research Topic (papers have been posted previously in this blog): The Human Gutome: Nutrigenomics of Host-Microbiome Interactions

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Model: Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico – Almut Heinken – Applied and Environmental Microbiology

Review: Intestinal microbiota and allergic diseases: A systematic review – L.C.F.L. Melli – Allergologia et Immunopathologia

Human urogenital microbiome

Editorial: Cervicovaginal Microbiota: Simple Is Better – Smita Gopinath – Immunity

Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract – Melis N. Anahtar – Immunity

The New World of the Urinary Microbiome in Women – Linda Brubaker, Alan J Wolfe – American Journal of Obstetrics and Gynecology

Plant and soil microbiome

Root-associated bacterial endophytes from Ralstonia solanacearum resistant and susceptible tomato cultivars and their pathogen antagonistic effects – Reshmi Upreti and Pious Thomas – Frontiers in Microbiology

Distinct Circular Single-Stranded DNA Viruses Exist in Different Soil Types – Brian Reavy – Applied and Environmental Microbiology

Water microbiome

Special Science issue: Tara Oceans studies plankton at Planetary Scale – P. Bork- Science

pH levels drive bacterial community structure in sediments of the Qiantang River as determined by 454 pyrosequencing – Shuai Liu – Frontiers in Microbiology

Distribution and diversity of fungi in freshwater sediments on a river catchment scale – Jie Liu – Frontiers in Microbiology

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction
Ping Zhang – Applied and Environmental Microbiology

Extremophile microbiome

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms – Young-Mo Kim – Frontiers in Microbiology

Abundance and Distribution of Dimethylsulfoniopropionate Degradation Genes and the Corresponding Bacterial Community Structure at Dimethyl Sulfide Hot Spots in the Tropical and Subtropical Pacific Ocean – Yingshun Cui – Applied and Environmental Microbiology

Built environment microbiome

Feasibility study involving the search for natural strains of microorganisms capable of degrading graffiti from heritage materials – Patricia Sanmartín – International Biodeterioration & Biodegradation

Bioreactor microbiology

Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water – M. Shahinoor Islam – Applied and Environmental Microbiology

Metagenomics

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes – Stefanía Magnúsdóttir – Frontiers in Genetics

Metabolomics

Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters – Tina Netzker – Frontiers in Microbiology

Species interactions differ in their genetic robustness – Lon M. Chubiz – Frontiers in Microbiology

Functional foods

Probiotics for Weight Loss: A Systematic Review and Meta-Analysis – Sunmin Parka, Ji-Hyun Baeb – Nutrition Research

Viruses and phages

Badger, mongoose, otter: Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses – Nádia Conceição-Neto – Virology Journal

Review: The Virome in Host Health and Disease – Ken Cadwell – Immunity

More microbiology

Editorial: recent discoveries in evolutionary and genomic microbiology – Anton G. Kutikhin and Arseniy E. Yuzhalin – Frontiers in Microbiology

Financial evaluations of antibiotic stewardship programs—a systematic review – Jan-Willem H. Dik – Frontiers in Microbiology

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach – Román Zapién-Campos – Frontiers in Microbiology

Microbes in the news

What’s Next for the Microbiome? – Jo Handelsman and Elizabeth R. Stulberg – Whitehouse.gov
The White House wants input on the future of microbiome research (by June 15) – Jonathan Eisen – Microbe.net

Ocean’s microbiome has incredible diversity – and human likeness – Colin Barras – New Scientist
Three-year ocean voyage discovered thousands of new, unfamiliar viruses: A study of plankton reveals just how little we know about the ocean – Arielle Duhaime-Ross – The Verge
Scientists Map 5,000 New Ocean Viruses – Carl Zimmer – Quanta Magazine

Help fund koala microbiome study – Andy Fell – Egghead Research at UC Davis

Nurturing a baby’s microbiome, before and after birth – Kate Gammo – Populair Science

Meet the caesarean mums who are ‘seeding their baby’s microbiome’ – Best Daily

Long-gone bacteria blows the whistle on gold deposits – Geology Page

Microbes and money

Why bacteria is becoming big business – Stephen Valdivia – Fortune
Danone’s big bet on tiny bacteria – Erica Fry – Fortune

uBiome Partners with PicnicHealth: Participants diagnosed with Inflammatory Bowel Disease (IBD) will receive a complementary PicnicHealth account as well as a complementary uBiome research kit. – PR Rocket

Science, publishing, and career

(Satire) The Allium Top Tips For Scientists and Engineers – The Allium
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