Author Archives: eliesbik

My new contact information

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Stanford University unexpectedly shut down my email account a couple of days ago. Of course I knew that was going to happen eventually when you leave work. But I had assumed that I would get a couple of months continued email access, like all my other coworkers got who left the university. I had checked with several others, but they all got 6 or 12 months extension without any problems.

Alas, I am not getting the same privileges, and so I have no way to contact collaborators, access and finish due peer reviews, or continue to mentor that high school student. I am trying to change all the many accounts that I have, but there are probably many that I cannot remember right now.

So here is my gmail address, in case you want to reach out to me. I deeply apologize to whatever journal is still waiting for my peer review!

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Elisabeth Bik, previously Stanford University, now working at uBiome.

November 5, 2016

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Several microbiome-related papers in Cell this week, Candida in kids’ saliva, two middle ear microbiome papers, yeasts in vineyards, and a database of viruses.

General microbiome

Cell has a microbiome special this week:

Review: The Central Nervous System and the Gut Microbiome – Gil Sharon
Colonic Crypt Protects Stem Cells from Microbiota-Derived Metabolites – Gerard E. Kaiko
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity – Melanie Schirmer
Host and Environmental Factors Influencing Individual Human Cytokine Responses – Rob ter Horst
A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans – Yang Li

How multi-partner endosymbioses function – Angela E. Douglas – Nature Reviews Microbiology

Human oral microbiome

Prevalence of Candida albicans and carriage of Candida non-albicans in the saliva of preschool children, according to their caries status – Carla Paola Lozano Moraga – Acta Odontologica Scandinavica

Nutritional Correlates of Human Oral Microbiome – Ikuko Kato – Journal of the American College of Nutrition

Human respiratory microbiome

Respiratory Syncytial Virus Bronchiolitis: Enter the Microbiome – James E. Gern – American Journal of Respiratory and Critical Care Medicine

Human skin and ear microbiome

Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene – Regie Lyn P. Santos-Cortez – Infectious Diseases of Poverty

Identification of the Bacterial Reservoirs for the Middle Ear Using Phylogenic Analysis – Chun Ling Chan – JAMA Otolaryngol Head Neck Surg.

Human gut microbiome

Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status – Monica Di Paola – Frontiers in Microbiology

Phylogenetic profile of gut microbiota in healthy adults after moderate intake of red wine – Elvira Barroso – Molecular Nutrition & Food Research

Review: Targeting gut microbiota: a potential promising therapy for diabetic kidney disease – Zhonge Chen – Am J Transl Res

Microbes in human blood

The plasma virome of febrile adult Kenyans shows frequent parvovirus B19 infections and a novel arbovirus (Kadipiro virus) – Carolyne Ngoi – Journal of General Virology

Animal experiments

Responses of earthworms and microbial communities in their guts to Triclosan – Lili Ma – Chemosphere

Animal microbiome

Gradual Changes of Gut Microbiota in Weaned Miniature Piglets – Jun Hu – Frontiers in Microbiology

Mussels: Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis – Ruby Ponnudurai – the ISME Journal

Sponges: Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment – Ana Rita Moura Polónia – Journal of Sea Research

The Origin of Mucosal Immunity: Lessons from the Holobiont Hydra – Katja Schröder – mBio

Plant, root, and soil microbiome

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature – Marc D. Auffret – PLOS ONE

Review: Yeasts found in vineyards and wineries – Cristian Varela – Yeast

Water microbiome

Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River – Jayaraman Suriya – Applied Microbiology and Biotechnology

Book chapter: Anaerobic Microbial Communities and Processes Involved in the Methane Cycle in Freshwater Lakes-a Focus on Lake Pavin – Anne-Catherine Lehours – Lake Pavin

Book chapter: Study of Prokaryotes and Viruses in Aquatic Ecosystems by Metagenetic and Metagenomic Approaches – Gisèle Bronner – Lake Pavin

Review: Quorum Sensing in Marine Microbial Environments – Laura R. Hmelo – Annual Review of Marine Science

Review: SAR11 Bacteria: The Most Abundant Plankton in the Oceans – Stephen J. Giovannoni – Annual Review of Marine Science

Phages and viruses

Pharmacometabolomics Informs Viromics toward Precision Medicine – Angeliki Balasopoulou – Frontiers in Pharmacology

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses – David Paez-Espino – Nucleic Acids Research

Metagenomics and bioinformatics

Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Metabarcoding Sequence Data – Rodney T. Richardson – Molecular Ecology Resources

Metabolomics

Experimental Evolution of Metabolic Dependency in Bacteria – Glen D’Souza – PLOS Genetics

Microbes in the news

Well-Fed Microbiome Cookbook Update – Kristina Campbell – The Intestinal Gardener

Researcher studying squid-human bacteria connection – Southern Illinois University

Discovery of new bacteria complicates problem with salmon poisoning in dogs – Phys.org

VIDEO: Gut microbiome key influencer of weight, metabolic syndrome – Healio

18min podcast: Harvesting the Aquatic Microbiome for New Drugs – The BioReport

Microbes and the market

Go with the gut – at uBiome Inc., science meets business opportunity – The Globe and Mail

Listen To Your Gut – JentleBiz

The health test that could transform your wellbeing – for just £279 – The Telegraph

November 4, 2016

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A very short Digest today, since Stanford unexpectedly closed my email account, so I cannot access most eTOCs. I had requested a couple of months extension, but it did not happen 😦   Here is what I found for you today:

Plant, root, and soil microbiome

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’ – Tess E. Brewer – Nature Microbiology

Mycorrhizal compatibility and symbiotic seed germination of orchids from the Coastal Range and Andes in south central Chile – Hector Herrera – Mycorrhiza

Microbes in the news

One of our reporters tried to do CRISPR. He failed miserably – Jon Cohen – Science

Polysorbate as possible E. coli food poisoning fix – Barfblog

Food Additive Could Treat E. Coli Food Poisoning – ValueWalk

A penguin in the Bombay Zoo that recently died: Dory’s death: one more test confirms bacterial infection – Tanvi Deshpande
Finding Dory’s killer? Authorities in no rush – Rupsa Chakraborty – Midday

Microbes on the market

OptiBiotix Health Plc Presentation of data at European Microbiome Summit – Directors Talk Interviews

Enterome Appoints Christophe Bonny as Chief Scientific Officer – PR Newswire

#BacteriaHysteria

The dirt on phones: See what you’re holding in your hands – WIBW

 

 

November 3, 2016

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Prevotella and Bacteroides associations with diet, parasite-microbiota interactions in wild animals, Staphylococcus/fungus interactions in cheese rind.

General microbiome

The Underestimation of Global Microbial Diversity– Jay T. Lennon -mBio

Next-Generation High-Throughput Functional Annotation of Microbial GenomesNext-Generation High-Throughput Functional Annotation of Microbial Genomes – Ralph S. Baric – mBIo

Human vaginal microbiome

The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next? – Anita Mitra – Microbiome

Human gut microbiome

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns – Francesca De Filippis – Microbiome

(PubMed link) Early Changes in Microbial Community Structure Are Associated with Sustained Remission After Nutritional Treatment of Pediatric Crohn’s Disease – Dunn KA – Inflammatory Bowel Diseases

(PubMed link) Review: The role of the gut microbiota in food allergy – Rachid R – Curr Opin Pediatr

Review: Intestinal Microbiome Changes and Stem Cell Transplantation: Lessons Learned – Ying Taur – Virulence

Human urinary tract microbiome

Review: Urinary Tract Infection: Pathogenesis and Outlook – Lisa K. McLellan – Trends in Molecular Medicine

Animal microbiome

Parasite-microbiota interactions potentially affect intestinal communities in wild mammals – Tuomas Aivelo – bioRxiv

Plant, root, and soil microbiome

Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator – J. L. Wood – Scientific Reports

Food microbiology

Cheese: Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species – Erik K. Kastman – mBio

Press: Fungi boost bacterium. A study of 25 cheeses finds that a slow-growing bacterium can outcompete its relatives with the help of fungi – Nature

Storage techniques

Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies – Erikka Loftfield – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Why Gut Bacteria Are Having a Moment. Jessica Richman, CEO of uBiome at Fortune’s Brainstorm Health summit- Beth Kowitt – Fortune

The Life, the Sea and the Space Viking, Searching for Extremophiles – Seti

Are You Ready to Swallow a Pill Full of Poop? OpenBiome believes in the power of pure, barely processed poop – Katie M. Palmer – Wired

Gut microbiome profiles predict response to low FODMAP diet in IBS – Healio

Study links intestinal microbial population to production of inflammatory proteins – Economic TImes

Guts of Fecal Transplant Patients Resemble their Donors’ – HCP Live – Refers to this paper: http://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-016-0698-z

Microbiome Skincare: Is Bacteria the Key to Perfect Skin? A primer on the science that could fix our skin woes once and for all – Wing Sze Tang – Flare

November 2, 2016

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Microbiome and precision medicine, bacterial responses to the Deepwater Horizon oil spill, bacterial dynamics in a water distribution system, and uBiome launches a clinical gut test.

General microbiome

Introducing the Microbiome into Precision Medicine – Thomas M. Kuntz – Trends in Pharmacological Sciences

Press: Making the microbiome part of precision medicine – EurekAlert

Probiotics / Skin microbiome

Bacterial Etiology and Risk Factors Associated with Cellulitis and Purulent Skin Abscesses in Military Trainees – Ryan C. Johnson – PLOS ONE

Local Application of Probiotic Bacteria Prophylaxes against Sepsis and Death Resulting from Burn Wound Infection – Anne Argenta – PLOS ONE

Animal microbiome

Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Fever – Soo Jin Jeon – PLOS ONE

Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation – Henk J. van Lingen – PLOS ONE

Water microbiome

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill – Kim M Handley – bioRxiv

Built environment microbiome

Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System – E. I. Prest – PLOS ONE

Bioinformatics and metagenomics

Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification – Florian P Breitwieser – bioRxiv

Microbes in the news

‘Living buildings’ could use bacteria for heat, electricity and repairs – Helen Massy-Beresford – Horizon Magazine

Bacteria can’t get a grip on self-healing, slippery surface
Inspired by nature, a high-tech, low-adhesive coating for medical devices could help prevent infection – EurekAlert

Biocement from genetically modified bacteria could react to changes in environment – Brian Wang – Next Big Future

Purple bacteria shine path to super-efficient light harvesting – University of Queensland

Microbes on the marketplace

uBiome Announces World’s First Sequencing-Based Clinical Microbiome Test – PR Web
uBiome launches gut microbiome sequencing test, reels in Series B – FierceBiotech

The ultimate guide to DIY DNA testing kits – April Long – Elle

Microbiome Study Suggests an Opportunity to Reduce Healthcare Facility Costs by 30%. Poor Indoor Air Quality and Healthcare Associated Infections (HAIs) as Key Burdens – Digital Journal

 

November 1, 2016

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Ribosomal gene sequencing as a clinical diagnostic tool, probiotic microcins in the inflamed gut, toxic sugar metabolism by a bee symbiont, bacteria as indicators of soil condition, viruses of the human body.

General microbiome

Omics Approaches To Probe Microbiota and Drug Metabolism Interactions – Robert G. Nichols – Chemical Research in Toxicology

Review: Microbial interactions: ecology in a molecular perspective – Raíssa Mesquita Braga – Brazilian Journal of Microbiology

Human skin microbiome

Understanding the role of Propionibacterium acnes in acne vulgaris: the critical importance of skin sampling methodologies – Hélène Omer – Clinics in Dermatology

Human respiratory microbiome

Editorial: Macrolides, inflammation and the lung microbiome: untangling the web of causality – Robert P Dickson – Thorax

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Review: Emerging pathogenic links between microbiota and the gut–lung axis
– Kurtis F. Budden – Nature Reviews Microbiology

Human gut microbiome

16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions – Daniel E Almonacid – bioRxiv

Detecting beer intake by unique metabolite patterns – Gözde Gürdeniz – Journal of Proteome Research

Metabolite and Microbiome Interplay in Cancer Immunotherapy – Caroline H. Johnson – Cancer Research

The infant gut microbiome correlates significantly with rotavirus vaccine response in rural Ghana – Vanessa C. Harris – Journal of Infectious Diseases
Could the gut microbiome be key to understanding and improving rotavirus vaccine performance in high disease burden settings? – Journal of Infectious Diseases

Fecal metabolomics in pediatric spondyloarthritis implicate decreased metabolic diversity and altered tryptophan metabolism as pathogenic factors – M L Stoll – Genes and Immunity

Can the composition of the intestinal microbiota predict the development of urinary tract infections? – Casper DJ den Heijer – Future Microbiology

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Review: Good Bugs, Bad Bugs in the Gut: The Role of Microbiota Dysbiosis in Chronic Gastrointestinal Consequences of Infection – Andre G Buret – American Journal of Gastroenterology

Review: Soy and Gut Microbiota: Interaction and Implication for Human Health – H Huang – J Agric Food Chem

Review: The gut microbiome and hypertension – M Pevsner-Fisher

Probiotics

Microcins mediate competition among Enterobacteriaceae in the inflamed gut – Martina Sassone-Corsi – Nature

Press: How good gut bacteria wrest control from the bad – Cosmos Magazine

Novel encapsulation improves recovery of probiotic strains in fecal samples of human volunteers – Volker Mai – Applied Microbiology and Biotechnology

Psychobiotics and the Manipulation of Bacteria–Gut–Brain Signals – Amar Sarkar – Trends in Neurosciences

Press: Psychobiotics: What Do We Know and Where Do We Go? – Laurie Anne Walden – Contagion Live

Review: Eosinophils, probiotics, and the microbiome – Helene F. Rosenberg – Journal of Leukocyte Biology

Animal experiments

Sex differences in colonization of gut microbiota from a man with short-term vegetarian and inulin-supplemented diet in germ-free mice – Jing-jing Wang – Scientific Reports

Functional Characterization of Inflammatory Bowel Disease–Associated Gut Dysbiosis in Gnotobiotic Mice – Hiroko Nagao-Kitamoto – CMGH Cellular and Molecular Gastroenterology and Hepatology

Obese Mice Fed a Diet Supplemented with Enzyme-Treated Wheat Bran Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition

Animal microbiome

Metabolism of Toxic Sugars by Strains of the Bee Gut Symbiont Gilliamella apicola – Hao Zheng – mBio

Microenvironmental heterogeneity of gut compartments drives bacterial community structure in wood- and humus-feeding higher termites – Aram Mikaelyan – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacteria as emerging indicators of soil condition – Syrie M. Hermans – Applied and Environmental Microbiology

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode – M. Imran Hamid – FEMS Microbiology Ecology

Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens – Longfei Jiang – Scientific Reports

Endophytic Bacillus cereus effectively controls Meloidogyne incognita on tomato plants through rapid rhizosphere occupation and repellent action – Haijing Hu – Plant Disease

Drivers of yeast community composition in the litter and soil of a temperate forest –
Tereza Mašínová – FEMS Microbiology Ecology

Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat – Michele Perazzolli – BMC Genomics

The root growth of wheat plants, the water conservation and fertility status of sandy soils influenced by plant growth promoting rhizobacteria – Naeem Khan – Symbiosis

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices – Jae-Hyung Ahn – Journal of Microbiology

Partitioning the effect of composition and diversity of tree communities on leaf litter decomposition and soil respiration – Mark Davidson Jewell – Oikos

Effects of Land use on the Structural Diversity of Soil Bacterial Communities in South Eastern Iran – Ghobad Jalali – Biosciences Biotechnology Research

Successive soybean-monoculture cropping assembles rhizosphere microbial communities for the soil suppression of soybean cyst nematode – M. Imran Hamid – FEMS Microbiology Ecology

Antarctic strict anaerobic microbiota from Deschampsia antarctica vascular plants rhizosphere reveals high ecology and biotechnology relevance – Rafael José Marques Peixoto – Extremophiles

The influence of the host plant is the major ecological determinant of soil presence of the nitrogen-fixing root nodule symbiont, Cluster II Frankia – Kai Battenberg – Applied and Environmental Microbiology

Review: Fungal endophytes and their interactions with plants in phytoremediation: A review – Zujun Deng – Chemosphere

Water and extremophile microbiome

Optical properties of dissolved organic matter relate to different depth-specific patterns of archaeal and bacterial community structure in the north Atlantic ocean – Elisa Guerrero-Feijóo

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products – Miguel David Marfil-Santana – Journal of Microbiology

Food microbiology

Different flour microbial communities drive to sourdoughs characterized by diverse bacterial strains and free amino acid profiles – Giuseppe Celano – Frontiers in Microbiology

Built environment microbiome

Drinking water: One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria – Antonia Bruno – Microbiology Open

Weathering of a Roman Mosaic—A Biological and Quantitative Study on In Vitro Colonization of Calcareous Tesserae by Phototrophic Microorganisms – Addolorata Marasco – PLOS ONE

Bioinformatics and metagenomics

Phylogenetic Dirichlet-multinomial model for microbiome data – Yunfan Tang – arXiv

More microbiology

Bacterial evolution: Genomics of metabolic trade-offs – Martin F. Polz – Nature Microbiology

What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015 – Erik Munson – Journal of Clinical Microbiology

Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences – Huimin Zhang – Molecular Biotechnology

Review: A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets – Rico Lucas – FEMS Microbiology Ecology

Microbes in the news

Viruses of the Human Body. Some of our resident viruses may be beneficial – Eric Delwart – The Scientist

Naval Special Warfare Trainees Face Tiny Enemy: Bacteria – Sara G. Miller – Live Science

Could a disrupted sleep also disturb your gut? – Fiona Pepper for The Health Report

Researchers think they’ve finally figured out why bacteria only causes acne in some people. And how to stop it. – Fiona MacDonald – Science Alert

Microbes and the market

uBiome CEO Jessica Richman Joins Sean Parker, Maria Shriver, Arianna Huffington and Others, Speaking at Fortune Brainstorm HEALTH

Science, publishing, and career

2016 Life Sciences Salary Survey. Most researchers feel stimulated by their work but are dissatisfied with their compensation, according to this year’s results – Karen Zusi – The Scientist

October 31, 2016

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Happy Halloween! Today is the first day at my new employer uBiome. But the blog continues. Today’s blog features the gut microbiome of Type 2 Diabetes patients and the transportome of mycorrhiza.

Human skin microbiome

Inhibition of HDAC8 and HDAC9 by microbial short-chain fatty acids breaks immune tolerance of the epidermis to TLR ligands – James A. Sanford – Science Immunology

Press: Acne Gives Up Secret That Points to New Treatments – Amy Norton – WebMD

Human gut microbiome

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients – Lianshuo Li – Genomics, Proteomics & Bioinformatics

Animal microbiome

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome – Lizi Bensoussan – Environmental Microbiology

Plant, root, and soil microbiome

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza – Kevin Garcia – Trends in Plant Science

Microbes in the news

Bacteria, other contaminants make costume contact lenses risky – NBC

Nurses’ Scrubs Carry Bad Bacteria. Healthcare workers, patients, and environment form ‘transmission triangle’ – Liz Highleyman – MedPage Today

A Word from Dr. Pfenninger: The weird disease of tetanus – John L. Pfenninger – Midland Daily News

Doctors transfer the power of gut bacteria – Emery Cowan – AZ Daily Sun

October 29, 2016

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Laryngeal microbiome, nitrogen fixation by bivalve symbionts, subalpine snow in California, sequence data compression tools. Flying back to Cali today, blogging from Phoenix.

Human respiratory microbiome

The human laryngeal microbiome: effects of cigarette smoke and reflux – Marie E. Jetté – Scientific Reports

Animal microbiome

This is pretty cool: Nitrogen fixation in a chemoautotrophic lucinid symbiosis – Sten König – Nature Microbiology

Fecal Bacterial Composition of Sichuan Snub-Nosed Monkeys (Rhinopithecus roxellana) – Chen Su – International Journal of Primatology

Lesion recovery and the bacterial microbiome in two Caribbean gorgonian corals – Kartick P. Shirur – Marine Biology

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth-Promoting Rhizobacteria (PGPR) from the Rhizosphere of Sugarcane in Saline and Non-Saline Soil – Elham Lamizadeh – International Journal of Current Microbiology and Applied Science

Different responses of rhizosphere and non-rhizosphere soil microbial communities to consecutive Piper nigrum L. monoculture – Zhigang Li – Scientific Reports

Note: 16S rRNA amplicon study, not metagenomics. Proceed with caution. Looking for Rhizobacterial Ecological Indicators in Agricultural Soils Using 16S rRNA metagenomic Amplicon Data – José R. Valverde – PLOS ONE

Comparison of Microbial Community Composition and Diversity in Native Coastal Wetlands and Wetlands that Have Undergone Long-Term Agricultural Reclamation – Shiqi Xu – Wetlands

Review: Biology and evolution of arbuscular mycorrhizal symbiosis in the light of genomics – Laurent Kamel – New Phytologist

Review: Plant microbiomes and sustainable agriculture – Philip Hunter – EMBO press

Water and extremophile microbiome

Microbial community structure of subalpine snow in the Sierra Nevada, California – Chelsea J. Carey – Arctic, Antarctic, and Alpine Research

Unique community structure of viruses in a glacier soil of the Tianshan Mountains, China – Li-Li Han – Journal of Soils and Sediments

Composition and distribution of microbial communities in natural river wetlands and corresponding constructed wetlands – Qingqing Ca – Ecological Engineering

The culturable mycobiota of a Mediterranean marine site after an oil spill: Isolation, identification and potential application in bioremediation – Elena Bovio – Science of the Total Environment

Metagenomics and bioinformatics

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes – Daniel R. Mende – Nucleic Acids Research

Comparison of high-throughput sequencing data compression tools – Ibrahim Numanagić – Nature Methods

Phages and ecology

Ecological conditions determine extinction risk in co-evolving bacteria-phagepopulations – Rosanna C. T. Wright – BMC Evolutionary Biology

Microbes in the news

‘Rare’ and ‘unusual’ bacteria discovered on Muni by SFSU researchers – Alyssa Pereira – SF Gate

How lack of oxygen makes bacteria cause acne and how to stop it – Andy Coghlan – New Scientist

Necrotizing Fasciitis: A Profound Mystery In Medical Microbiology – Alex Berezow – American Council on Science and Health

Doctors warn of bacteria in salt water after Jacksonville officer almost dies – Letisha Bereola – Action News Jax

Healdsburg company makes ‘food’ for the gut’s bacteria – Press Democrat

October 28, 2016

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Still in Albuquerque at UNM where I gave a talk today hosted by Joe Alcock. Another great example of how Twitter (at least some parts of it!) can bring scientists together.

Two studies published in Nature Genetics this month coupling variations in the human gut microbiome with genetic variations in the human genome. Also: predicting facial skin microbiome and how does Wolbachia do it?

Human skin microbiome

Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome – Souvik Mukherjee – Scientific Reports

Human gut microbiome

Editorial: The gut microbiome—an emerging complex trait – Andrew K Benson – Nature Genetics
Association of host genome with intestinal microbial composition in a large healthy cohort – Williams Turpin – Nature Genetics
The effect of host genetics on the gut microbiome – Marc Jan Bonder – Nature Genetics

Can the composition of the intestinal microbiota predict the development of urinary tract infections? – Casper DJ den Heijer – Future Microbiology

Review: Personalized microbiome-based approaches to metabolic syndrome management and prevention – H Shapiro – J Diabetes (NCBI link)

Animal microbiome

Microbiota associated with Bactrocera carambolae and B. dorsalis (Insecta: Tephritidae) revealed by next-generation sequencing of 16S rRNA gene – Hoi-Sen Yong – Meta Gene

The microbiome of neotropical ticks parasitizing on passerine migratory birds – Khemraj Budachetri – Ticks and Tick-borne Diseases

Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification – Guowei Zhou – Scientific Reports

Commentary: Open questions: how does Wolbachia do what it does? – Francis M. Jiggins – BMC Biology

Plant, root, and soil microbiome

Inducing the rhizosphere microbiome by biofertilizer application to suppress banana Fusarium wilt disease – Lin Fu – Soil Biology and Biochemistry

A new primer set for DNA metabarcoding of soil Metazoa – E. Capra – European Journal of Soil Biology

Functional foods

The effect of bacteriophages on the acidification of a vegetable juice medium by microencapsulated Lactobacillus plantarum – Claude P. Champagne – Food Microbiology

More microbiology

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae – M. Tofazzal Islam – BMC Biology

Microbes in the news

Gaining new insights into the health promoting properties of kefir – Waterford Today

Antibiotics Linked to Sepsis Risk. Disturbing healthy bacteria during hospital admission associated with later sepsis – Michael Smith – MedPage Today

 

October 27, 2016

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Kavli Foundation grants, mycobiome of root canal infections, post-stroke infections,  Thai vegetarians, antibiotic treatment of gorillas, licorice plants under salt stress, and bacterial camouflage on Crustaceans. Greetings from New Mexico!

Jobs and grants

Open Positions at NC State University: Microbiomes and Complex Microbial Communities

Uniting Diverse Sciences to Tackle the Microbiome – Kavli Foundation

Human oral microbiome

The mycobiome of root canal infections is correlated to the bacteriome – Ilona F. Persoon – Clinical Oral Investigations

Near-sterile human body sites

Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method – the observation of DNAemia – T. Gosiewski – European Journal of Clinical Microbiology & Infectious Diseases

Human respiratory microbiome

Translocation and dissemination of commensal bacteria in post-stroke infection – Dragana Stanley – Nature Medicine

Bacteria in the respiratory tract—how to treat? Or do not treat? – Cristina Prat – International Journal of Infectious Diseases

Human gut microbiome

Human Microbiome Fusobacterium Nucleatum in Esophageal Cancer Tissue Is Associated with Prognosis – Kensuke Yamamura – Clinical Cancer Research

Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk – Supatjaree Ruengsomwong – Journal of Microbiology and Biotechnology

Effect of Bifidobacterium breve on the Intestinal Microbiota of Coeliac Children on a Gluten Free Diet: A Pilot Study – Andrea Quagliariello – Nutrients

Review: Rethinking Diet to Aid Human–Microbe Symbiosis – Muriel Derrien – Trends in Microbiology

Review: Feeding the Microbiota-Gut-Brain Axis: Diet, Microbiome and Neuropsychiatry – Kiran V. Sandhu – Translational Research

Review: Microbiota dysbiosis: a new piece in the understanding of carcinogenesis puzzle – Valeria García-Castillo – Journal of Medical Microbiology

Review: The evolving role of the microbiome in liver failure and liver transplantation – Kymberly D. Watt – Liver Transplantation

Animal models

Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla) – Klára Vlčková – Microbial Ecology

Commensal Microbe-specific Activation of B2 Cell Subsets Contributes to Atherosclerosis Development Independently of Lipid Metabolism – Lin Chen – EBioMedicine

Commentary: Intestinal Microbiome and Atherosclerosis – J. David Spence – EBioMedicine

A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model – Susanne C. Diesner – Clinical Immunology

Kinetic changes of intestinal microbiota in the course of intestinal sensitization – Liang Xiao – Oncotarget

Animal microbiome

Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts – Gwynneth F. Matcher – Microbiology Open

Plant, root, and soil microbiome

Divergent responses of β-diversity among organism groups to a strong environmental gradient – Micael Jonsson – Ecosphere

Phylogenetic congruence between subtropical trees and their associated fungi – Xubing Liu – Ecology and Evolution

Microbial cooperation in the rhizosphere improves liquorice growth under salt stress – Dilfuza Egamberdieva – Bioengineered

Extremophile microbiome

Extremophiles: Life at the deep end – Sonja-Verena Albers – Nature

Built environment microbiome

Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital – Applied Microbiology and Biotechnology

Bioreactor microbiology

In vitro study of soil arsenic release by human gut microbiota and its intestinal absorption by Caco-2 cells – Naiyi Yin – Chemosphere

Probiotics

Probiotic With or Without Fiber Controls Body Fat Mass, Associated With Serum Zonulin, in Overweight and Obese Adults—Randomized Controlled Trial  – Lotta K. Stenman – EBioMedicine

More microbes

Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods – Laura E. Bagge – Current Biology

Press: Crustaceans in the ocean’s ‘twilight zone’ wear CAMOUFLAGE: Bacteria coating helps creatures avoid a predator’s gaze – Sarah Griffiths – Daily Mail

Microbes in the news

Videos from Microbiomes of the Built Environment NAS meeting posted – Jonathan Eisen – MicroBEnet

Iron-Loving Bacteria a Model For Mars Life – Elizabeth Howel –  Space.com

Dogs go on poop patrol to sniff out fecal bacteria. Rescue dogs trained to detect human fecal matter – Barbara Besteni – Local 10

Bacteria Sent In Space Could Be Potentially Infectious, Harmful – Elaine Hannah – Science World Report

Florida’s orange groves are being wiped out by tree-killing bacteria – CBS News

Rio fights Zika with biggest release yet of bacteria-infected mosquitoes. Wolbachia-infected mosquitoes will be widely deployed in two South American cities to combat viral infections – Ewen Callaway – Nature

Cranberries crush bacteria’s communication networks – Lisa-Ann Lee – New Atlas

Neonatal vaccination of mice with bacteria prevents cockroach-induced asthma as adults – News Medical

Bacteria and bugs in guts and gallbladders – Claire O’Connell – The Irish Times