Category Archives: Human gut

June 2, 2015

Posted on by

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

[hr]

Another June 1, 2015

Posted on by

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

[hr]

June 1, 2015

Posted on by

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.

[hr]

May 29, 2015

Posted on by

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

[hr]

May 28, 2015

Posted on by

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

[hr]

May 23, 2015

Posted on by

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

[hr]

May 21, 2015

Posted on by

Nature has a special this week about bees, and how to cure appendicitis without surgery.

Human gut microbiome

Survival of Lactobacillus casei strain Shirota in the intestines of healthy Chinese adults – Ran Wang – Microbiology and Immunology

Animal microbiome

Special in Nature: Bees – Michelle Grayson – Nature

Microbiome: The puzzle in a bee’s gut – Alla Katsnelson – Nature

Plant and soil microbes

Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media – N. Eevers – Microbial Biotechnology

Metagenomic Next-Generation Sequencing of Viruses Infecting Grapevines – Johan T. Burger – Plant Pathology

Metagenomics Approaches Based on Virion-Associated Nucleic Acids (VANA): An Innovative Tool for Assessing Without A Priori Viral Diversity of Plants – Denis Filloux – Plant Pathology

Taxonomic diversity of bacterial populations inhabiting gametophytes of Sphagnum mosses from different geographic regions of Russia – A.V. Shcherbakov – Agronomy Research

Biotic interactions mediate soil microbial feedbacks to climate change – Thomas W. Crowther – PNAS

Extremophile microbiology

Halophiles – Shiladitya DasSarma – eLS

Other microbiology papers

157 fungal genomes: Fungal Traits That Drive Ecosystem Dynamics on Land – Kathleen K. Treseder – Microbiology and Molecular Biology Reviews

Spread of tetracycline resistance genes at a conventional dairy farm – Martina Kyselkova – Frontiers in Microbiology

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria – Ido Yosef – PNAS

Microbiology: Taking the bad with the good – Carl T. Bergstrom & Benjamin Kerr – Nature

Counteraction of antibiotic production and degradation stabilizes microbial communities – Eric D. Kelsic – Nature

Microbes in the news

From Germ Theory to the Microbiome: Why Microbes Still Rule Our Lives – Alanna Collen – Huffington Post

The diet of worms: Soil dwellers emerge as climate change heroes in study – Renee Lewis – Al Jazeera

Richman of uBiome: Scientists can accelerate FMT research – Gut Microbiota For Health

Antibiotics resurface as alternative to removing appendix – Gina Colata – New York Times

Video: School Microbiome Art Project: Students quickly draw and discuss some of their thoughts about the microbial world we live in – Kat Gilbert – YouTube

How a Tiny Bacterium Called Wolbachia Could Defeat Dengue – Scott O’Neill – Scientific American

Science, publishing, and career

No more hidden solutions in bioinformatics: Precision medicine cannot advance without full disclosure of how commercial genome sequencing and interpretation software works – Mauno Vihinen – Nature

Publish or perish: Universities should release reports to show what they are doing to tackle misconduct — and funders should help them to do so effectively – Nature

UK universities slow to publish reports of misconduct investigations: Few institutions have followed research integrity guidelines to the letter – Elizabeth Gibney – Nature
[hr]

May 20, 2015

Posted on by

Human wound microbiome

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds – Mary Cloud B. Ammons – PLOS ONE

Human gut microbiome

Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects – Mark Pimentel – PLOS ONE

Editorial: Microbiota key to diet-associated risk of colon cancer – Nature Reviews Microbiology

Microbiome models

Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes – Sophie Candon – PLOS ONE

Changes in Gut Microbiota in Rats Fed a High Fat Diet Correlate with Obesity-Associated Metabolic Parameters – Virginie Lecomte – PLOS ONE

Gut Microbiota Dynamics during Dietary Shift in Eastern African Cichlid Fishes – Laura Baldo – PLOS ONE

Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant – Dongming Liu – Microbial Biotechnology

Animal microbiome

The Fecal Microbiome in Cats with Diarrhea – Jan S. Suchodolski – PLOS ONE

Plant and soil microbiome

Effect of crop management and sample year on abundance of soil bacterial communities in organic and conventional cropping systems – C.H. Orr – Journal of Applied Microbiology

Water microbiome

Characterization of the relative importance of human- and infrastructure-associated bacteria in grey water: a case study – S.P. Keely – Journal of Applied Microbiology

Techniques

PCR-Based Multiple Species Cell Counting for In Vitro Mixed Culture – Ruijie Huang – PLOS ONE

Bioinformatics

FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data – Takeru Uchiyama – PLOS ONE

Microbes in the news

Manipulating the Microbiome Produces Hope, but Uneven Results – Monica J. Smith – Gastroenterology & Endoscopy News

In America, is our food, in fact, too clean? – Kate Murphy – Herald Tribune

Study reveals intestinal bacteria succession during recovery from cholera in Bangladesh – Eureka Alert

Targeting Antibiotic-Resistant Bacteria with CRISPR and Phages – Anna Azvolinsky – The Scientist

Marine Bacteria Can Control Chemistry of Sea Spray Ejected into Atmosphere – SciNews

[hr]

May 19, 2015

Posted on by

Two papers today on the microbiome of the Giant Panda – it’s not good at digesting bamboo!

Microbiome of pregnancy and birth

Bacterial community structure associated with elective cesarean section versus vaginal delivery in Chinese newborns – Liu D, et al. – J Pediatr Gastroenterol Nutr

The microbiota at multiple body sites during pregnancy in a rural Tanzanian population and the effects of Moringa supplemented probiotic yogurt – Jordan E. Bisanz – Applied and Environmental Microbiology

Review: Gut microbiome and immunity: possible role in sudden infant death syndrome (SIDS) – Paul N. Goldwater – Frontiers in Immunology

Human oral microbiome

Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics
Bo-Young Hong – PLOS ONE

Review: The human saliva proteome: overview and emerging methods for characterization
Timothy J. Griffin – SPIE Proceedings

Human gut microbiome

Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD – C. Casén – Alimentary Pharmacology and Therapeutics

Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women : a randomized, double-blind placebo controlled study – Mi-young Song – Nutrition Research

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans – Lawrence A. David – mBio

Food Fight: Our gut microbes are no fans of junk food – Laura Beil – Science News

Human vaginal microbiome

Review: Antimicrobial and immune modulatory effects of lactic acid and short chain fatty acids produced by vaginal microbiota associated with eubiosis and bacterial vaginosis – Muriel Aldunate – Frontiers in Physiology

Microbiome models

Composition and function of the undernourished neonatal mouse intestinal microbiome – Geoffrey A. Preidis – The Journal of Nutritional Biochemistry

Maternal microbiota regulate glucocorticoids levels and placental development in mice – Maha Al-Asmakh – Endocrine Abstracts

Different Dynamic Patterns of β-Lactams, Quinolones, Glycopeptides and Macrolides on Mouse Gut Microbial Diversity – Jia Yin – PLOS ONE

Relationships Between Diet-Related Changes in the Gut Microbiome and Cognitive Flexibility – K.R. Magnusson – Neuroscience

Physiological variability in volatile organic compounds (VOCs) in exhaled breath and released from faeces due to nutrition- and somatic growth in a standardized caprine animal model – Sina Fischer – Journal of Breath Research

Animal microbiome

The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations – Zhengsheng Xue – mBio

The evolution of the gut microbiota in the giant and the red pandas – Ying Li – Scientific Reports

Patterns of Gut Bacterial Colonization in Three Primate Species – Erin A. McKenney – PLOS ONE

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis
Whitney M. Holden – Biological Conservation

Plant and Soil microbiome

Bacterial and Fungal Communities in a Degraded Ombrotrophic Peatland Undergoing Natural and Managed Re-Vegetation – David R. Elliott – PLOS ONE

Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2 and soil temperature in a rice paddy – Gaidi Ren – Plant and Soil

Patterns in Species Persistence and Biomass Production in Soil Microcosms Recovering from a Disturbance Reject a Neutral Hypothesis for Bacterial Community Assembly
Fen-Guo Zhang – PLOS ONE

Time-dependent effect of graphene on the structure, abundance and function of the soil bacterial community – Wenjie Ren – Journal of Hazardous Materials

Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions – Shaomei He – mBio

Nano titania aided clustering and adhesion of beneficial bacteria to plant roots to enhance crop growth and stress management – G. M. Palmqvist – Scientific Reports

Review: Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions – J. M. Barea – Journal of soil science and plant nutrition

Water microbiome

The influence of land-use, nutrients, and geography on microbial communities and fecal indicator abundance at Lake Michigan beaches – Danielle D. Cloutier – Applied and Environmental Microbiology

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison – Catherine M. Febria – Frontiers in Microbiology

Built environment microbiome

Distribution and population structure characteristics of microorganisms in urban sewage system – Yanchen Liu – Applied Microbiology and Biotechnology

Extremophile microbiome

Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China – Ping Li – PLOS ONE

Microbial diversity in engineered haloalkaline environments shaped by shared geochemical drivers observed in natural analogues – Talitha C. Santini – Applied and Environmental Microbiology

Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan – O. V. Kutovaya – Eurasian Soil Science

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Food microbiology

An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea – Ming Zhao – Scientific Reports

Review: Foodomics in microbiological investigations – Yong-Jiang Xu – Current Opinion in Food Science

Metagenomics and Bioinformatics

Review: Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies – Anastasis Oulas – Bioinformatics and Biology Insights

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods – Jullien M. Flynn – Ecology and Evolution

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? – Emily A. Brown – Ecology and Evolution

Sharing is caring – Claudio Nunes-Alves – Nature Reviews Microbiology

Microbes in the news

Kitty Kickstarter: See the Microbes That Live in Your Cat – Becky Oskin – Live Science

Eden unveils The Human Microbiome this week – West Briton

Bodyguards for precious seeds—without chemical mace – Phys.org

Panda poop reveals they’re bad at digesting bamboo – Laura Geggel – CBS News

Giant Panda Microbiome Ill-Suited for Bamboo Diet, Study Finds – Genome Web

[hr]

May 16, 2015

Posted on by

Posting might be irregular in the coming days because of international travel, but I will try to keep you all updated as best as I can.

Human oral microbiome

Increased infection with key periodontal pathogens during gestational diabetes mellitus – Himabindu Gogeneni – Journal of Clinical Periodontology

Human respiratory microbiome

Airway microbiota and acute respiratory infection in children – Kohei Hasegawa – Expert Review of Clinical Immunology

Human gut microbiome

Microbiota—implications for immunity and transplantation – Jonathan S. Bromberg – Nature Reviews Nephrology

Poster: Association of classical microbiology and 16S rDNA metagenetic Aanalysis to evaluate the presence of Clostridium difficile ina a belgian nursing home (sic) – Rodriguez Diaz, Cristina – 5th International Human Microbiome Congres

Review: Probiotics, antibiotics and the immune responses to vaccines – Ira Praharaj – Philosophical Transactions B

Microbiome models

Exposure to soil, house dust, and decaying plants increases gut microbial diversity and decreases serum IgE levels in BALB/c mice – Dongrui Zhou – Environmental Microbiology

Water microbiome

Metagenomics reveals the high PAH-degradation potential of abundant uncultured bacteria from chronically-polluted subantarctic and temperate coastal marine environments – Claudia L. Loviso – Journal of Applied Microbiology

Plant root and soil microbiome

Early rhizosphere microbiome composition is related to the growth and Zn uptake of willows introduced to a former landfill – Terrence H. Bell – Environmental Microbiology

Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa – S. Geisen – Molecular Ecology

Soil microbial communities vary as much over time as with chronic warming and nitrogen additions – Alexandra R. Contosta – Soil Biology and Biochemistry

Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia oxidizing bacteria – María C. Zabaloy – Pest Management Science

Changes in soil aggregation and microbial community structure control carbon sequestration after afforestation of semiarid shrublands – N. Garcia-Francoa – Soil Biology and Biochemistry

Air microbiome

Challenges and Opportunities of Airborne Metagenomics – Hayedeh Behzad – Genome Biology and Evolution

Food microbiology

Bacteriophages isolated from chicken meat and the horizontal transfer of antimicrobial resistance genes– Amira Shousha – Applied and Environmental Microbiology

Techniques

A simple method of normalization of DNA extraction for improving the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR – M. Li – Letters in Applied Microbiology

Microbes in the news

The kittybiome Project – background and some plans – Jonathan Eisen – MicroBEnet

Science, publishing, and career

Why Medicine is Plagued with Fake Research – Chloe Della Costa – Business Cheat Sheet

Physics Paper on the Higgs Boson Has Record 5,154 Authors – Softpedia (link to actual pdf)

Bik’s Picks

Giant Squid Lore and Legends Date Back Centuries – Benjamin Radford – Discovery

Cocaine Use Could be Determined by a Fingerprint, New Study – Silvia Fernandez – Pierce Pioneer

New map shows most distinct causes of death by state – Marilyn Malara – UPI

[hr]