Category Archives: General Microbiome

June 8, 2015

Posted on by

General microbiome

Minireview: The brain’s Geppetto—microbes as puppeteers of neural function and behaviour? – Roman M. Stilling – Journal of NeuroVirology

Thesis: Novel computational approaches to investigate microbial diversity – Qingpeng Zhang – Michigan State University

Microbiome of pregnancy and birth

Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Antenatal Microbiome: Potential Contributor to Fetal Programming and Establishment of the Microbiome in Offspring – Michelle L. Wright, Angela R. Starkweather – Nursing Research

Review: Should Abnormal Vaginal Flora in 2 nd Trimester of Pregnancy be Treated to Prevent Preterm Labor – Gunjan Kumari, Anjali Tempe – Journal of Medical Sciences

Human oral microbiome

The oral mucosal and salivary microbial community of Behcet’s syndrome and recurrent aphthous stomatitis – Noha Seoudi – Journal of Oral Microbiology

Human gut microbiome

Review: Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota – Elin Org – Atherosclerosis

Review: The Effects of Diet and the Microbiome on Reproduction and Longevity: A Comparative Review Across 5 Continents – Stephanie N. Chilton – Nutrition and Food Sciences

Animal models of microbiome research

Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome – Dapeng Jin – Clinical Therapeutics

Animal microbiome

Acromyrmex leaf-cutting ants have simple gut microbiota with nitrogen-fixing potential – Panagiotis Sapountzis – Applied and Environmental Microbiology

Anemone: Response of bacterial colonization in Nematostella vectensis to development, environment and biogeography – Benedikt Mortzfeld – Environmental Microbiology

Plant root and soil microbiome

Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress – Juan Ling – Ecotoxicology

Analyses of microbial biomass and community diversity in kiwifruit orchard soils of different planting ages – Qingxia Fu – Acta Ecologica Sinica

The effects of the presence of Bt-transgenic oilseed rape in wild mustard populations on the rhizosphere nematode and microbial communities – Yongbo Liu – Science of The Total Environment

Long-term conservation tillage influences the soil microbial community and its contribution to soil CO2 emissions in a Mollisol in Northeast China – Shuxia Jia – Journal of Soils and Sediments

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity – Weimin Sun – Journal of Microbiology

Differential degradation of polycyclic aromatic hydrocarbon mixtures by indigenous microbial assemblages in soil – Przemyslaw Sawulski – Letters in Applied Microbiology

A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil – Mariana Silvia Cretoiu – Applied Microbiology and Biotechnology

Book chapter: Irrigation with Treated Wastewater: Potential Impacts on Microbial Function and Diversity in Agricultural Soils – Ana Rita Lopes – The Handbook of Environmental Chemistry 2015

Water microbiome

Response of bacteria and meiofauna to iron oxide colloids in sediments of freshwater microcosms – Sebastian Höss – Environmental Toxicology and Chemistry

Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site – Federico Baltar – FEMS Microbiology Ecology

Book Chapter: Marine Litter as Habitat and Dispersal Vector – Tim Kiessling – Marine Anthropogenic Litter

Thesis: Metagenomic profiling of microbial metal interaction in Red Sea deep-anoxic brine pools – Hanna, Mina Magdy Abdelsayed – American University in Cairo

Built environment microbiome

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam – Katja Sonja Nitzsche – Chemosphere

The role of bacterial communities and carbon dioxide on the corrosion of steel – K.M. Usher – Corrosion Science

Extremophile microbiome

Review: Metagenomics of extreme environments – DA Cowan – Current Opinion in Microbiology

Food microbiology

Review: The impact of climate change on existing and emerging microbial threats across the food chain: An island of Ireland perspective – Linda D. Stewart – Trends in Food Science & Technology

Review: Microbial decontamination of food by electron beam irradiation – Hsiang-Mei Lung – Trends in Food Science & Technology

Bioreactor microbiome

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

Bioinformatics and metagenomics

CCLasso: Correlation Inference for Compositional Data through Lasso – Huaying Fang – Bioinformatics

GAML: genome assembly by maximum likelihood: combination of diverse sequencing datasets into a single assembly – Vladimír Boža – Algorithms for Molecular Biology

Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data – Sophie J Weiss – PeerJ

Review: Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms – Qingfa Wu – Annual Reviews Phytopathology

Metabolomics

Mapping microbial response metabolomes for induced natural product discovery – Dagmara K. Derewacz – ACS Chemical Biology
http://pubs.acs.org/doi/abs/10.1021/acschembio.5b00001

Techniques

Analysis of microsamples of human faeces: a non-invasive approach to study the bioavailability of fat-soluble bioactive compounds – E. Hernandez-Alvarez – European Journal of Nutrition

Microbes in the news

Say hello to your little friends: Making sense of gut bacteria – Wency Leung – Globe and Mail

Surfers help science in fight against antibiotic resistant bacteria with their poop – Luigi Lugmayer – i4u

Effects of zinc oxide on intestinal microbiota – All About Feed

Video: Waxworm Bacteria Could Recycle Plastic Trash – NBC News

Is That Water Hot Enough to Kill Germs? – C. Claiborne Ray – New York Times

Gut bacteria play a vital role to your health – Sharon Ní Chonchuir – Irish Examiner

New microscope technique could speed identification of deadly bacteria – EurekAlert

Science, publishing, and career

Better advice for ‘Bothered’ – Science Careers Staff – Science Magazine

Retractions and High Profile Journals – Peter Edmonds

Bik’s Picks

Black Hole Hunters – Dennis Overbye – New York Times

Everything You Need to Know About Bill Nye’s Crazy Experimental Spaceship – Jack Linshi – Time

Under the Sea: Google Views for World Oceans Day – Patrick J. Kiger – Discovery

[hr]

Evaluation of MicrobiomeDigest – feedback welcome

Posted on by

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

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

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

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

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

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

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

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

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

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

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

[hr]

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]

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 22, 2015

Posted on by

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
[hr]

May 14, 2015

Posted on by

General microbiome

Yesterday’s Cell Host & Microbe issue contains a special on “The Host-Microbiota Balance”. Lots of great papers and editorials here! Several papers are listed below in their respective categories, or I already included them in previous posts.

Microbiota and Host Nutrition across Plant and Animal Kingdoms – Stéphane Hacquard – Cell Host & Microbe

Microbiota and Autoimmunity: Exploring New Avenues – Leonid A. Yurkovetskiy – Cell Host & Microbe

Pregnancy and birth

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life – Fredrik Bäckhed – Cell Host & Microbe – with editorial: Birth of the Infant Gut Microbiome: Moms Deliver Twice! – Steven A. Frese, David A. Mills – Cell Host & Microbe

Restricted access: Bacterial communities in neonatal feces are similar to mothers’ placentae – Xu-Dong Dong – Canadian Journal of Infectious Diseases & Medical Microbiology

Review: Antibiotics, Pediatric Dysbiosis, and Disease – Pajau Vangay – Cell Host & Microbe

Human oral microbiome

Pseudomonas aeruginosa and Periodontal Pathogens in the Oral Cavity and Lungs of Cystic Fibrosis Patients: a Case-Control Study – Rocio Rivas Caldas – Journal of Clinical Microbiology

Human gut microbiome

Review: An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases – Marta Wlodarska – Cell Host & Microbe

Review: Control of Brain Development, Function, and Behavior by the Microbiome – Timothy R. Sampson, Sarkis K. Mazmanian – Cell Host & Microbe

Review: Microbiota in Allergy and Asthma and the Emerging Relationship with the Gut Microbiome – Kei E. Fujimura – Cell Host & Microbe

Editorial: Prevention: Tending the gut. Drugs, lifestyle changes and other measures might lower the risk of colorectal cancer — but the evidence is a long time coming. – Lauren Gravitz – Nature

Editorial: Microbiome: Microbial mystery. Gut bacteria have an important but elusive role in the formation of colorectal cancer. – Sarah DeWeerdt – Nature

Animal models

Editorial: Message in a Biota: Gut Microbes Signal to the Circadian Clock – Emily V. Marcinkevicius, Mimi M. Shirasu-Hiza – Cell Host & Microbe

Animal microbiome

Coprophilic dipteran community associated with horse dung in Malaysia – C.C. Heo – Halteres

Water microbiome

Bacteria in the injection water differently impacts the bacterial communities of production wells in high-temperature petroleum reservoirs – Hongyan Ren – Frontiers in Microbiology

Assessment of nitrogen and sulphur cycle bacteria and shrimp production in ponds treated with biological products – Thangapalam Jawahar Abraham – Journal of Coastal Life Medicine

 

More microbiology

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons – Kelly M. Wetmore – mBio

Microbes in the news

Maturation of the Infant Microbiome – Kerry Grens – The Scientist
Infant antibiotic use linked to adult diseases – Science Daily

Bacteria on shoes could help forensic teams catch suspects – Stefano Vanin – The Conversation
Forensic scientists could use bacteria to catch criminals – Brooks Hays – UPI

The microbiome and the midnight snack: How gut microbes influence the body’s clock – Matt Wood – ScienceLife

Bacteria the Newest Tool in Detecting Environmental Damage – University of Tennessee

Bacteria May Be Remaking Drugs in Sewage: Microbes that clean our water may also be piecing some pharmaceuticals back together – Brian Bienkowski – Scientific American

If Microbes Could Tweet… Small Things Considered – Daniel P. Haeusser

Microbiology: Fungus against the wall. Paul O’Maille – Nature

Science, publishing, and career

“It’s invigorating to be around that student energy the first time they learn about science,” Adjunct teaching: For love of the lecture – Kendall Powell – Nature

This scientific paper has 2,863 authors. How? – Danielle Wiener-Bronner – Fusion

Bik’s Picks

MIT And UC Berkeley Duking It Out Over CRISPR – Cas 9 – Clayton Browne – Value Walk

Survey: Almost half of all bee hives in the U.S. died in the past year – Mashable

Scientists have discovered the first fully warm-blooded fish – Chelsea Harvey – Washington Post
[hr]

May 11, 2015

Posted on by

General microbiome / Microbial ecology

Microbiomes raise privacy concerns: DNA from microbes living on the human body can be used to identify individuals – Ewen Callaway – Nature

Identifying personal microbiomes using metagenomic codes – Eric A. Franzosa – PNAS USA

Unraveling interactions in microbial communities – from co-cultures to microbiomes – Justin Tan – Journal of 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

Human oral microbiome

Hospitalisation impacts on oral hygiene: an audit of oral hygiene in a metropolitan health service – Rachael Danckert – Scandinavian Journal of Caring Sciences

DGGE: Dynamic Shifts in the Oral Microbiome during Radiotherapy – Tine De Ryck – Clinical Research in Infectious Diseases

Effects of Source- versus Household Contamination of Tubewell Water on Child Diarrhea in Rural Bangladesh: A Randomized Controlled Trial – Ayse Ercumen – PLOS ONE

Human vaginal microbiome

Review: Biofilms: An Underappreciated Mechanism of Treatment Failure and Recurrence in Vaginal Infections – Christina A. Muzny – Clinical Infectious Diseases

Human gut microbiome

Editorial: The Gut Microbiota Strikes Again – Debra D. Poutsiaka – Clinical Infectious Diseases
Belongs to:
Acute Gastrointestinal Graft-vs-Host Disease Is Associated With Increased Enteric Bacterial Bloodstream Infection Density in Pediatric Allogeneic Hematopoietic Cell Transplant Recipients – Anya Levinson – Clinical Infectious Diseases

Review: Exploring the role of environmental enteropathy in malnutrition, infant development and oral vaccine response – Allissia A. Gilmartin , William A. Petri – Philosophical Transactions B

Review: Role of the gastrointestinal ecosystem in the development of type 1 diabetes – Joseph G Daft – Pediatric Diabetes

Plant and soil microbiome

Ectomycorrhizal fungal communities coinvading with Pinaceae host plants in Argentina: Gringos bajo el bosque – Jeremy Hayward – New Phytologist

Atmospheric N Deposition Alters Connectance, but not Functional Potential Among Saprotrophic Bacterial Communities – Zachary B. Freedman – Molecular Ecology

Rhizospheric changes of fungal and bacterial communities in relation to soil health of multi-generation apple orchards – F. Caputo – Biological Control

Permafrost microbial community traits and functional diversity indicate low activity at in situ thaw temperatures – Jessica G. Ernakovich – Soil Biology and Biochemistry

Switchgrass Biochar Effects on Plant Biomass and Microbial Dynamics in Two Soils from Different Regions – Charlene N. Kelly – Pedosphere

Water microbiome

Melting glacier impacts community structure of Bacteria, Archaea and Fungi in a Chilean Patagonia fjord – Marcelo H. Gutiérrez – Environmental Microbiology

Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure – Christopher Staley – Journal of Microbiological Methods

Thesis: Bacterial Community Structure and Petroleum Hydrocarbon Degradation in the Baltic Sea – Anna Reunamo – University of Turku

Phages and viruses

Editorial: A CRISPR sense of self – Naomi Attar – Nature Reviews Microbiology

Bioinformatics and metagenomes

Nucleotide 9-mers Characterize the Type II Diabetic Gut Metagenome – Balazs Szalkai – ArXiv

CS-SCORE: Rapid identification and removal of human genome contaminants from metagenomic datasets – Mohammed Monzoorul Haque – Genomics

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters – Tilmann Weber – Nucleic Acids Research

Review: Alignment of Next-Generation Sequencing Reads – Knut Reinert – Annual Review of Genomics and Human Genetics

Metabolic dependencies drive species co-occurrence in diverse microbial communities – Aleksej Zelezniak – PNAS USA

Functional Foods

Probiotics can improve the clinical outcomes of hepatic encephalopathy: An update meta-analysis – Li-Na Zhao – Clinics and Research in Hepatology and Gastroenterology

Microbes in the news

How Germs Might Shape the Future of Architecture – Vicky Gan – City Lab

FDA digging into hand cleaners in hospitals – Jonathan Eisen – MicroBEnet

Essay: The Fight Against the Fight Against the Fight Against Bacteria – Daniel Yin – University of Oxford

Freshman Biology, Creativity, and Extra Credit… – Mark O. Martin – MicrobesRule

You Asked: Should I Use Antibacterial Soap? – Markham Heid – Time
About Tim Spector book “The Diet Myth”: Fast food kills gut bacteria that can keep you slim, study finds – Daniel Costa-Roberts

About the Sonnenburgs’ book “The Good Gut”: To be healthy, take care of your microbiome – Kate Allen – The Start

Should you put yogurt on your face? The benefits of probiotics go beyond improved digestion – Victoria Dawson Hoff – Elle Beauty

My Archaea, My Brother – Genome Web

“This Idle No More movement is like bacteria, it has grown a life of its own all across this nation,” – RCMP apologizes for Idle No More ‘bacteria’ comparison – APTN

Calls for global database on bacteria contained in food – Channel News Asia

Antibiotic-Resistant Typhoid Spreading Abroad – Dennis Thompson – WebMD

“You may not want to eat lunch with Misty Bever”: Intestinal fortitude: There’s an illness lurking that causes chronic, debilitating pain. The cure, however, comes from deep within.– Dan England – The Tribune

Bik’s Picks

Mars sunsets are beautiful — and blue, NASA photo shows – Matthew T. Hall – UT San Diego

What do these new alien photos reveal about Roswell UFO crash – Sam Catherman – State Column

Google says its self-driving cars have had 11 crashes – Chris Woodyard – USA Today

[hr]

May 5, 2015

Posted on by

General human microbiome

Review: The Human Microbiota: The Rise of an “Empire” – Gidon Berger – Rambam Maimonides Medical Journal

Human gut microbiome

Human colon-derived soluble factors modulate gut microbiota composition – Arancha Hevia – Frontiers in Oncology

Dysbiosis of Intestinal Microbiota Associated With Inflammation Involved in the Progression of Acute Pancreatitis – Tan, Chaochao – Pancreas

Review: Does the Gut Microbiota Contribute to Obesity? Going beyond the Gut Feeling – Marisol Aguirre and Koen Venema – Microorganisms

Review: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – The Gastrointestinal Microbiome – NIH

Human respiratory microbiome

Prevalence of oropharyngeal antibiotic-resistant flora among residents of aged care facilities: a pilot study – Christopher D. Etherton-Beer – Respirology

Animal models of microbiomes

Modulatory effects of a cranberry extract co-supplementation with Bacillus subtilis CU1 probiotic on phenolic compounds bioavailability and gut microbiota composition in high-fat diet-fed mice – Stéphanie Dudonné – PharmaNutrition

Animal microbiome

Characterization of the cellulolytic bacteria communities along the gastrointestinal tract of Chinese Mongolian sheep by using PCR-DGGE and real-time PCR analysis – Yan Zeng – World Journal of Microbiology and Biotechnology

Soil microbiome

Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands – Chelsea J. Carey – Frontiers in Microbiology

Water microbiome

A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling – Linda E. Graham – Journal of Phycology

Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre – Emily A. Walsh – Aquatic Microbial Ecology

Extremophiles

The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert – S. Gombeer – Geobiology

Microbial diversity and metabolic networks in acid mine drainage habitats – Celia Mendez-Garcia – Frontiers in Microbiology

Metabolomics

Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps – Cody R. Goodwin – Chemistry & Biology

Techniques

Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data – Jake Jervis-Bardy – Microbiome

More microbes

Antibacterial activity of silver-killed bacteria: the “zombies” effect – Racheli Ben-Knaz Wakshlak

Review: The dormant blood microbiome in chronic, inflammatory diseases – Marnie Potgieter – FEMS Microbiology Reviews

Microbes and art

Faecal transplants and bio-art – Eden Project’s latest exhibition Invisible You explores the science of microbes – Nicola Davis – The Guardian

Microbiology printable labels or buffet cards blue and black – LoveBacteriaArt – Etsy

Microbes in the news

1h Video: Seth Bordenstein: The microbiome and Darwin’s Mystery of Mysteries – University of Michigan Early Career Scientists Symposium

Cervicovaginal microbiome holds promise in preventing preterm birth – interview with Dr. Michal Elovitz at the annual meeting of the American Congress of Obstetricians and Gynecologists – Mary Ellen Schneider #ACOG15

Episode 6 of The Microbiome Podcast: The microbiome, autism, and serotonin production with Dr. Elaine Hsiao – MicrobiomeInstitute

Some beards as dirty as toilets: Microbiologist tests beards for germs – Royale Da – KOAT

(See more beard microbiome articles from these past days in The Beard Microbiome)

“You’re covered in poo bacteria.” No, your beard isn’t full of poop (probably) – Rachel Feltman – The Washington Post

HuMiX – Emulating human microbiome on a chip – Bactavatchalou Sivakumar

Nanoparticles in consumer products can significantly alter normal gut microbiome – Phys.org

Never a dull day for microbiologist – Kathryn Bernard up for Women of Distinction prize – Winnipeg Free Press

Agricultural microbiology draws Chinese researchers to Argentina – Xinhua – Want China Times

Expert’s Corner: Physician-scientist on why he recommends probiotics – University of Massachusetts

Gut Wars: One Man’s Adventure With Antibiotics and Ulcerative Colitis – Alexandra Carmichael – uBiome blog

Show Me Your Moves: Updated classics and new techniques help microbiologists get up close and quantitative – Marissa Fessenden – The Scientist

‘Zombie’ Bacteria May Help Heal Wounds – Discovery

Ocean currents disturb methane-eating bacteria – Phys.org

Bacteria could prove key in the fight against cholesterol – Paul Healy – Independent

Free book (for a limited time): The Squid, the Vibrio & the Moon – Small Friends Books

Science, publishing, and career

DNA editing takes a serious step forward — for better or worse – Eryn Brown – LA Times

Bik’s Picks

Llamas as Lab Rats: From diagnostics to vaccines, llama antibodies point to new directions in HIV research – Jenny Rood – The Scientist

Big whales have stretchy nerves to help them gulp – Jonathan Webb – BBC

Is sleepwalking genetic? Study suggests it runs in the family – ZME Science

[hr]