It’s been a long day, but here is a Storify on the SF Microbiome Meetup at IndieBio, a biotech startup accelerator in San Francisco. Thanks, George Roche, Stephen Martis, and host Jun Axup for organizing! We had a bigger audience than we anticipated, but we could not say no to anyone who showed up.
My apologies for some typos…. I am better at Twitter when I got a bigger keyboard!
Storify on the SF Microbiome Meetup at IndieBio
Cover photo by Alexander Probst, @AlexJProbst
Colon cancer tumor location and Fusobacterium nucleatum abundance, eczema in infants, fungi in Crohn’s disease, pH 4 in Yellowstone.
Pregnancy and early life
Altered Gut Microbiota Composition Associated with Eczema in Infants – Huajun Zheng – PLOS ONE
Predominant Lactobacillus species types of vaginal microbiota in pregnant Korean women: quantification of the five Lactobacillus species and two anaerobes – Jeong Hyun Kim – The Journal of Maternal-Fetal & Neonatal Medicine
Human respiratory microbiome
The endotracheal tube microbiome associated with Pseudomonas aeruginosa or Staphylococcus epidermidis – An Hotterbeekx – Scientific Reports
Human gut microbiome
Fungal Microbiota Profile in Newly-diagnosed Treatment-naïve Children with Crohn disease – Mohammad El Mouzan – Journal of Crohn’s and Colitis
Analysis of the Duodenal Microbiome in Autistic Individuals: Association with Carbohydrate Digestion – Kushak, Rafail I. – Journal of Pediatric Gastroenterology and Nutrition
Fusobacterium nucleatum in Colorectal Carcinoma Tissue According to Tumor Location – Kosuke Mima – Clinical and Translational Gastroenterology
Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkinsonism & Related Disorders
Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota – Francesco Miragoli – FEMS Microbiology Ecology
Title is confusing; “No change in mucosal gut Mycobiome” would have been more clear. No Change in the Mucosal Gut Microbiome is Associated With Celiac Disease-Specific Microbiome Alteration in Adult Patients – Valeria D’Argenio – American Journal of Gastroenterology
Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter
Review: Role of vitamin D on gut microbiota in cystic fibrosis – Mansi Kanhere – The Journal of Steroid Biochemistry and Molecular Biology
Review: Nutrition and the Gut Microbiome in the Elderly – Nuria Salazar – Gut Microbes
Addendum: Support for the Microgenderome Invites Enquiry into Sex Differences – Amy Wallis – Gut Microbes
Animal models
Genomic Variants Associated with Resistance to High Fat Diet Induced Obesity in a Primate Model – R. Alan Harris – Scientific Reports
Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria – Dorothy A Kieffer – Journal of Nutrition
Animal microbiome
Identifying bacterial predictors of honey bee health – Giles E. Budge – Journal of Invertebrate Pathology
Plant, root, and soil microbiome
Over-winter dynamics of soil bacterial denitrifiers and nitrite ammonifiers influenced by crop residues with different carbon to nitrogen ratios – Enrico Tatti – Applied Soil Ecology
Bacterial and fungal community structure and diversity in a mining region under long-term metal exposure revealed by metagenomics sequencing – Ramya Narendrula-Kotha – Ecological Genetics and Genomics
Conversion of grassland to arable decreases microbial diversity and alters community composition – Katherine E. French – Applied Soil Ecology
Water and extremophile microbiome
Differences in Bacterial Diversity and Communities Between Glacial Snow and Glacial Soil on the Chongce Ice Cap, West Kunlun Mountains – Guang Li Yan – Scientific Reports
Microbial community analysis of pH 4 thermal springs in Yellowstone National Park – Xiaoben Jiang – Extremophiles
Food microbiology
Microbiota of high-pressure-processed Serrano ham investigated by culture-dependent and culture-independent methods – N. Martínez-Onandia – International Journal of Food Microbiology
Applicability of commercial phage-based products against Listeria monocytogenes for improvement of food safety in Spanish dry-cured ham and food contact surfaces – Diana Gutiérrez – Food Control
Pollution and waste microbiology
Limited Bacterial Diversity within a Treatment Plant Receiving Antibiotic-Containing Waste from Bulk Drug Production – Nachiket P. Marathe – PLOS ONE
Microbes in the news
Costa Rican ants might have the secret to better antibiotics – L. Arias – TicoTimes
Waterfowl Worry: Recurring disease kills loons, other birds – Washington Times
STEM Gets Marvelous for a Local Student – how the microbes on the scalp could impact the hair growth – NCTV17.com
Best-selling cleanser recalled over dangerous levels of bacteria. Liz Earle’s ‘Cleanse & Polish Hot Cloth Cleanser’ found to contain potentially dangerous bacteria – Ben Kentish – Interdependent
Microbes and the market
APC Microbiome Institute: Alimentary discoveries produce a gut reaction among investors – Companies aim to exploit one of the 21st century’s big advances – Financial Times
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!
Elisabeth Bik, previously Stanford University, now working at uBiome.
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
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
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
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
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
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
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
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
Microbiome Digest - Bik's Picks 