Category Archives: Events and jobs

December 18, 2016

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Virome of the human respiratory tract, vendor effects on mouse gut, soils under beech and spruce, variations in Scottish soils, portable pathogen detection.

Events

Poster submission started: 3rd Annual Translational Microbiome Conference – April 11-13, 2017, Boston, USA

Pregnancy and early life

Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi – Lorenzo Drago – The ISME Journal

Review: Pathogenesis of NEC: Impact of an altered intestinal microbiome – Josef Neu – Seminars in Perinatology

Human oral microbiome

Changes in the oral ecosystem induced by the use of 8% arginine toothpaste – British Dental Journal

Human respiratory microbiome

* Review: The Virome of the Human Respiratory Tract – Kristine M. Wylie – Clinics in Chest Medicine

Human vaginal microbiome

Comparison of Culture-dependent and Culture-Independent Molecular Methods for Characterisation of Vaginal Microflora – Shirali Pandya – Journal of Medical Microbiology

Human gut microbiome

Distinct microbiome-neuroimmune signatures correlate with functional abdominal pain in children with autism spectrum disorder – Ruth Ann Luna – CMGH Cellular and Molecular Gastroenterology and Hepatology

Alterations of the gut microbiome in Chinese patients with systemic lupus erythematosus
Zhixing He – Gut Pathogens

Altered Gut Microbiota in Patients With Chronic Pancreatitis is Associated With Gut Barrier Dysfunction and Metabolic Abnormalities – Rupjyoti Talukdar

Dietary Changes Impact the Gut Microbe Composition in Overweight and Obese Men with Prostate Cancer Undergoing Radical Prostatectomy – Andrew D. Frugé – Journal of the Academy of Nutrition and Dietetics

The human intestinal microbiota of constipated-predominant irritable bowel syndrome patients exhibits anti-inflammatory properties – Alain P. Gobert – Scientific Reports

The Interactions Between Gut Microbiota and Lynch Syndrome – Xiao-juan Lu – Clinical Gastroenterology and Hepatology

Review: Enterosalivary nitrate metabolism and the microbiome: intersection of microbial metabolism, nitric oxide and diet in cardiac and pulmonary vascular health – Carl D Koch – Free Radical Biology and Medicine

Review: Community metabolic modeling approaches to understanding the gut microbiome: bridging biochemistry and ecology – Helena Mendes-Soares – Free Radical Biology and Medicine

Review: Microbiota Small RNAs in Inflammatory Bowel Disease – Anca T. Filip – Journal of Gastrointestinal and Liver Diseases

Review: Intestinal Microbiome, Akkermansia muciniphila, and Medicinal Nutrition Therapy – Jeffrey Bland – integrative Medicine

Review: Using the Human Gastrointestinal Microbiome to Personalize Nutrition Advice: Are Registered Dietitian Nutritionists Ready for the Opportunities and Challenges? – Ruth Harvie – Journal of the Academy of Nutrition and Dietetics

Review: Bacterial Biofilms in Colorectal Cancer Initiation and Progression – Shan Li – Trends in Molecular Medicine

Animal experiments

* Vendor Effects on Murine Gut Microbiota Influence Experimental Abdominal Sepsis – Tobias Hilbert – Journal of Surgical Research

The critical role of microbiota within cecal crypts on the regenerative capacity of the intestinal epithelium following surgical stress – Alexander Zaborin – American Journal of Physiology Gastrointestinal and Liver Physiology

Source of supplemental dietary copper, zinc, and manganese affects fecal microbial relative abundance in lactating dairy cows – M.J. Faulkner – Journal of Dairy Science

Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics – Natália C. Gaeta – Journal of Dairy Science

Animal microbiology

Riptortus pedestris and Burkholderia symbiont: an ideal model system for insect–microbe symbiotic associations – Kazutaka Takeshita – Research in Microbiology

Bird: Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota – Lindsay K Newbold – The ISME Journal

Plant, root, and soil microbiome

* Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce – Heiko Nacke – Frontiers in Microbiology

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia – Bruno L. Mello – Scientific Reports

The biogeography of soil archaeal communities on the eastern Tibetan Plateau – Yu Shi – Scientific Reports

Depth-resolved microbial community analyses in two contrasting soil cores contaminated by antimony and arsenic – Enzong Xiao – Environmental Pollution

Comprehensive Virus Detection Using Next Generation Sequencing in Grapevine Vascular Tissues of Plants Obtained from the Wine Regions of Bohemia and Moravia (Czech Republic) – Aleš Eichmeier – PLOS ONE

* Scottish soil: It is elemental: Soil nutrient stoichiometry drives bacterial diversity – Manuel Delgado-Baquerizo – Environmental Microbiology

Microbial soil community analyses for forensic science: Application to a blind test – Sandrine Demanèche – Forensic Science International

Review: Mycorrhiza: The Oldest Association Between Plant and Fungi – Jagnaseni Barman – Resonance

Book Chapter: Bioprospecting Soil Metagenomes for Antibiotics – Chiara Borsetto – Bioprospecting

Water and extremophile microbiome

The Distribution Pattern of Sediment Archaea Community of the Poyang Lake, the Largest Freshwater Lake in China – Yantian Ma – Archaea

Characterization of the first cultured representative of a Bacteroidetes clade specialized on the scavenging of cyanobacteria – Wajdi Ben Hania – Environmental Microbiology

Book chapter: Bioprospecting Archaea: Focus on Extreme Halophiles – André Antunes – Bioprospecting

Food microbiology

Analysis of the bacterial biodiversity of peaches under refrigerated storage after treatment by high hydrostatic pressure – Maria José Grande Burgos – Food and Bioproducts Processing

Bioreactor, biotechnology, and pollution microbiology

Correlating methane production to microbiota in anaerobic digesters fed synthetic wastewater – K. Venkiteshwaran – Water Research

Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes – Georgina Robinson – Scientific Reports

Trace Elements Induce Predominance among Methanogenic Activity in Anaerobic Digestion – Babett Wintsche – Frontiers in Microbiology

Bioinformatics and metagenomics

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes – Mohammadkarim Saeedghalati – arXiv

A simple statistical test of taxonomic or functional homogeneity using replicated microbiome sequencing samples – Daniel H. Huson – Journal of Biotechnology

Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota – Sébastien Raguideau – PLOS Computational Biology

Now published: IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – Genome Biology

Metabolomics

Evaluating metabolic response to light exposure in Lactobacillus species via targeted metabolic profiling – Mengyang Xu – Journal of Microbiological Methods

Review: Phytanic acid consumption and human health, risks, benefits and future trends: A review – P. Roca-Saavedra – Food Chemistry

Viruses and phages

Perspective: Viruses and the origin of microbiome selection and immunity – Steven D Quistad – The ISME Journal

Techniques

* Detection of ESKAPE bacterial pathogens at the point-of-care using isothermal DNA-based assays in a portable, de-gas microfluidic diagnostic assay platform
Lars D. Renner – Applied and Environmental Microbiology

Press: Portable detection system can rapidly identify virulent, multi-drug resistant pathogens in remote areas – News-Medical

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing – Dieter M. Tourlousse – Nucleic Acids Research

Microbes in the news

Gardening Etcetera: Life down under in northern Arizona – Cindy Murray – AZ Daily Sun

CSI: Chem trail: a new way for investigators to narrow down suspect pools using chemical traces found on cellphones – Kelly Kasulis – Boston Globe

China expresses alarm as chilli ‘conspiracy’ heats up Indonesians – South China Morning Post

Adapting and adopting microbiome data into clinical practice – Silvio Pitlik & Omry Koren- BioMed Central

Bacteria that boost insulin-producing cells could yield new diabetes approaches – Arlene Weintraub – Fierce Biotech

Microbes in the market

Research focused on the human microbiome market worth 658 million USD by 2023 – Whatech

AOBiome Launches Phase 2 Clinical Trial Using Novel Bacterial Platform for Treatment of Hypertension – PR Newswire

Live Stock Coverage: What’s Ahead for Seres Therapeutics Inc After Today’s Huge Increase? – Linda Rogers- Frisco Fastball

 

December 15, 2016

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Preannouncement of the second SF Bay Area Microbiome Meetup in January, enteric dysfunction in Malawian children, gastric microbiota in twins, Antarctic fish, soil of a medieval foundry.

Events

Preannouncement: 2nd SF Bay Area Microbiome Meetup – January 31, 2017 – Illumina, San Francisco – SF Biome

3rd Translational Microbiome Conference – April 11-13, 2017, Boston

Human gut microbiome

Environmental Enteric Dysfunction and the Fecal Microbiota in Malawian Children – M. Isabel Ordiz – Am J Trop Med Hyg

Characterization of Gastric Microbiota in Twins – Quanjiang Dong – Current Microbiology

Faecal Carriage of Gram-Negative Multidrug-Resistant Bacteria among Patients Hospitalized in Two Centres in Ulaanbaatar, Mongolia – Bayaraa Baljin – PLOS ONE

Lifestyle and geographic insights into the distinct gut microbiota in elderly women from two different geographic locations – Ji-Hee Shin – Journal of Physiological Anthropology

Ability of Lactobacillus kefiri LKF01 (DSM32079) to colonize the intestinal environment and modify the gut microbiota composition of healthy individuals – Marco Toscano – Digestive and Liver Disease

Review: The intestinal microbiota in allogeneic hematopoietic cell transplant and graft-versus-host disease – Anna Staffas – Blood

Review: A story of metformin-butyrate synergism to control various pathological conditions as a consequence of gut microbiome modification: Genesis of a wonder drug? –
Kunal Maniar – Pharmacological Research

Animal models

Selective photoantisepsis – David M. Harris – Lasers in Surgery and Medicine

Press: Laser Treatments Shown Effective in Killing Bacteria That Cause Dental Disease – Photonics

Induction of FXR signaling in germ-free mice colonized with a human microbiota – Annika Wahlström – Journal of Lipid Research

Modulation of urinary siderophores by the diet, gut microbiota and inflammation in mice –
Xia Xiao – Journal of Nutritional Biochemistry

Value added by Spirulina platensis in two different diets on growth performance, gut microbiota, and meat quality of Japanese quails – Mohamed S. Yusuf – Veterinary World

Triatomine bugs, their microbiota and Trypanosoma cruzi: asymmetric responses of bacteria to an infected blood meal – Sebastián Díaz – Parasites & Vectors

Dietary Keratan Sulfate from Shark Cartilage Modulates Gut Microbiota and Increases the Abundance of Lactobacillus spp. – Qingsen Shang – Marine Drugs

New insights into the role of the porcine intestinal yeast, Kazachstania slooffiae, in intestinal environment of weaned piglets – Vladimir Urubschurov – FEMS Microbiology Ecology

Animal microbiome

The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis – Wei Song – BioMed Research International

Plant, root, and soil microbiome

It is elemental: Soil nutrient stoichiometry drives bacterial diversity – Manuel Delgado-Baquerizo – Environmental Microbiology

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression – Jie Hu – mBio

Composition of endophytic fungal community associated with leaves of maize cultivated in south Brazilian field – Vivian J. Szilagyi-Zecchin – Acta Microbiologica et Immunologica Hungarica

Vegetation type and layer depth influence nitrite-dependent methane-oxidizing bacteria in constructed wetland – Mengxi Yang – Archives of Micobiology

Water and extremophile microbiome

Nitrate addition has minimal short-term impacts on Greenland ice sheet supraglacial prokaryotes – Karen A. Cameron – Environmental Microbiology Reports

Insights into bacterioplankton community structure from Sundarbans mangrove ecoregion using Sanger and Illumina MiSeq sequencing approaches: A comparative analysis – Anwesha Ghosh – Genomics Data

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics – Luciana Principal Antunes – Scientific Reports

Pollution microbiology

Atmospheric Deposition-Carried Zn and Cd from a Zinc Smelter and Their Effects on Soil Microflora as Revealed by 16S rDNA – Feng Shen – Scientific Reports

Paleomicrobiology to investigate copper resistance in bacteria: Isolation and description of Cupriavidus necator B9 in the soil of a medieval foundry – David C. Gillan – Environmental Microbiology

More microbiology

Stochastic Model for Direction Changes of Swimming Bacteria – Guido Fier – bioRxiv

Microbes in the news

Pitt study links cystic fibrosis lung inflammation to opportunistic bacteria – Lydia Nuzum – BizJournals

December 12, 2016

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Review on human milk microbiome, oral microbiome changes in seasonal athletes, gut microbiome and bipolar disorder.

Jobs

Assistant Professor In Quantitative Ecology or Evolution of Microbes – UCLA – MicroBEnet

Pregnancy and early life

Effect of probiotics in prevention of atopic dermatitis is dependent on the intrinsic microbiota at early infancy – Ekaterina Avershina – Journal of Allergy and Clinical Immunology

* Review: Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk – Michelle K McGuire – Current Opinion in Biotechnology

Human respiratory microbiome

Review: Viral–bacterial co-infections in the respiratory tract – Lauren O Bakaletz – Current Opinion in Microbiology

Human oral microbiome

* I was wondering if testing same group of athletes participating in 2 different sports could not be confounded with seasonal effects of maybe different study loads during the different year. But no access to the paper, so can not see details. Elevated salivary IgA, decreased anxiety, and an altered oral microbiota are associated with active participation on an undergraduate athletic team – Ashley L. Lamb – Physiology & Behavior

Human gut microbiome

* The gut microbiome composition associates with bipolar disorder and illness severity – Simon J. Evans – Journal of Psychiatric Research

Letter of the Editor: A Microbiome Assessment of Medical Marijuana – George Thompson III – Clinical Microbiology and Infection

Review: Archaea: essential inhabitants of the human digestive microbiota – Vanessa Demonfort Nkamga – Human Microbiome Journal

Animal experiments

Application of a dynamic gastrointestinal in vitro model combined with a rat model to predict the digestive fate of barley dietary fibre and evaluate potential impact on hindgut fermentation – Cristina Teixeira – Bioactive Carbohydrates and Dietary Fibre

Animal microbiome

Characterization and identification of microbial communities in bovine necrotic vulvovaginitis – N.Y. Shpigel – The Veterinary Journal

Crab: Gut Microbiota and Metabolic Phenotype of Portunus Trituberculatus – Ting-Lan Zeng – Chinese Journal of Analytical Chemistry

Plant, root, and soil microbiome

Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata – Suvendu Das – Journal of Hazardous Materials

Food microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Impact of NaCl reduction on lactic acid bacteria during fermentation of Nocellara del Belice table olives – Paola Zinno – Food Microbiology

Bioinformatics and metagenomics

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics – Karel Sedlar – Computational and Structural Biotechnology Journal

Microbes in the news

Predatory bacteria used to release bioplastics – Tim Sandle – Digital Journal

The Secret Soviet Virus That Helps Kill Bacteria. Antibiotic resistance is threatening to render antibiotics useless, but scientists may have found their answer in bacteria-eating viruses. – Trace Dominguez – Seeker

Bacteria found in close to two-thirds of NZ supermarket chicken – TV New Zealand

Science, publishing, and career

This would not be my headline choice: Trump says ‘nobody really knows’ if climate change is real – Juliet Eilperin – Washington Post

December 2, 2016

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Role of microbiome in an animal model of Parkinson’s disease, benchmarking reveals false discoveries in microbiome studies, the microbes of Patagonia, and the new uBiome blog.

The  uBiome blog

* Handshakes: Sharing the Love, Sharing the Microbes – Julie Taylor – uBiome

Jobs

Assistant Professor in Microbial Systems Biology at U. Tennessee, Knoxville – MicroBE.net

Human vaginal microbiome

Informativeness of NGS Analysis for Vaginal Fluid Identification – Saverio Giampaoli – Journal of Forensic Sciences

Animal models

* Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease – Timothy R. Sampson – Cell

News: Axial Biotherapeutics Announces the Groundbreaking Discovery of a Biological Link Between the Gut Microbiome and Parkinson’s Disease Published in Cell – Businesswire
Gut check: Newest microbiome startup concentrates on autism, Parkinson’s disease – John Carroll – Endpoints News

Multiple paternity in a wild population of Armadillidium vulgare: influence of infection with Wolbachia? – V. Valette – Journal of Evolutionary Biology

Plant, root, and soil microbiome

Field-grown transgenic switchgrass (Panicum virgatum L.) with altered lignin does not affect soil chemistry, microbiology, and carbon storage potential – Jennifer M. DeBruyn – GCB Bioenergy

Vertical zonation of soil fungal community structure in a Korean pine forest on Changbai Mountain, China – World Journal of Microbiology and Biotechnology

* Book: Biology and Biotechnology of Patagonian Microorganisms – Editors: Nelda Lila Olivera, Diego Libkind, Edgardo Donati – Springer

Bioinformatics

* Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies – Jonathan Thorsen – Microbiome

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography – Silvia Argimón – Microbial Genomics

More microbiology

Quest for Ancestors of Eukaryal Cells Based on Phylogenetic Analyses of Aminoacyl-tRNA Synthetases – Ryutaro Furukawa – Journal of Molecular Evolution

The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite – Tatiana Yurchenko – Open Biology

High levels of antibiotic tolerance and persistence are induced by the commercial anti-microbial triclosan – Corey S Westfall – bioRxiv

Microbes in the news

A citizen science project studying the microorganisms fauna found at the tip of our tongue – Euroscientist

Knowledge of skin microbiome provides insights into dermatological conditions – Skin microbes perform harmful and beneficial functions – Louise Gagnon – Dermatology Times

Digital Microbes Could Give More Insight into Gut Health – Nutrition Horizon

Healthy Gut, Healthy Brain? Microbes and Brain Health Under the Microscope During Mind, Mood & Microbes Conference – PR Newswire

Doctors warn about lung illness attributed to bacteria in showers and hot baths – Catherine Bosley – Cleveland19

Microbes on the market

Microbiome CNS upstart launches with $19.15M Series A – Ben Adams – Fierce Biotech

Boston startup hopes to use bacteria to treat autism – Robert Weisman

Upcoming North American Microbiome Congress in San Diego

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A while ago I wrote about the (North American) Microbiome Congress, to be held in San Diego in January 2017, because of the lack of women among the speakers. Jonathan Eisen also wrote a post about that.

I was pleasantly surprised to see that the conference organizer, Kisaco Research, has taken our criticism to heart, and has worked hard to improve the diversity of the invited speakers. They now have a great line-up with Jessica Metcalf, Emma Taylor, David Pride, Julia Oh, Sarkis Mazmanian, Embriette Hyde, Susan Holmes, Rob Knight, Jeff Leach, George Weinstock, Curtis Huttenhower, and Catherine Lozupone.

They also feature the following statement on the conference’s website:

“The process of choosing a speaker faculty has many complicated variables, but it is clear that our choices should have been more diverse. I sincerely apologize to those who are offended by the decisions we have made. We recognize that it is our responsibility to help ensure that the speaker faculty reflect the diversity and culture of the field and science as a whole. In this instance we failed to live up to our own standards of sensitivity and diversity, for which we sincerely apologize. Kisaco Research is deeply committed to producing events that represent the diversity of the scientific fields we work with. We are embarrassed that this has been previously overlooked and are currently working to make this, and all other programmes, ones that the leading scientists are proud to be a part of.

Stephanie Jaczniakowska-McGirr
Conference Director
Kisaco Research
sjm@kisacoresearch.com”

Kudos to Kisaco Research for listening, apologizing, and taking action. That takes courage and I so, so, appreciate this.

Their new line-up looks like a wonderful set of speakers, and you might want to give this conference a second look. The North American Microbiome Congress from January 24-25 in San Diego.

Full disclosure: Kisaco Research has invited me to come to the congress, which I accepted. I might see you there!

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November 14, 2016

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Infant gut microbiota, oral microbiota of farmworkers with pesticide exposure, critically ill patients, probiotics and Alzheimer’s, Sutterella is a commensal.

Events

Cheese Cultures & Microbiology Class, December 2, 2016, Petaluma – California Artisan Cheese Guild – Eventbrite

Pregnancy and early life

A comparison of intestinal microbiota in a population of low-risk infants exposed and not exposed to intrapartum antibiotics: The Baby & Microbiota of the Intestine cohort study protocol – Julia Simioni – BMC Pediatrics

Establishment and development of the intestinal microbiota of preterm infants in a Lebanese tertiary hospital – Tarek Itania – Anaerobe

Human oral microbiome

Human Oral Buccal Microbiomes Are Associated with Farmworker Status And Azinphos-methyl Agricultural Pesticide Exposure – Ian B. Stanaway – Applied and Environmental Microbiology

News: Study finds link between pesticide exposure and microbiome changes – Brooks Hays – UPI
Pesticide exposures can cause changes in oral microbiome – ASM

Molecular detection of bacteria associated to caries activity in dentinal lesions – Beatriz Gonçalves Neves – Clinical Oral Investigations

Review: Microbial Profiles and Detection Techniques in Peri-Implant Diseases: a Systematic Review – Miguel Padial-Molina – J Oral Maxillofac Res

Human skin microbiome

A Precision Microbiome Approach Using Sucrose for Selective Augmentation of Staphylococcus epidermidis Fermentation against Propionibacterium acnes – Yanhan Wang – Int J Mol Sci

A novel enzyme with antioxidant capacity produced by the ubiquitous skin colonizer Propionibacterium acnes – Maria Allhorn – Scientific Reports

Skin bacteria could protect against disease – Science Daily

Human vaginal microbiome

Escherichia coli and Enterococcus faecalis are able to incorporate and enhance a pre-formed Gardnerella vaginalis biofilm – Joana Castro – Pathogens and Disease

Human gut microbiome

Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study – Jacqueline M. Lankelma – Intensive Care Medicine

Mucosal Prevalence and Interactions with the Epithelium Indicate Commensalism of Sutterella spp. – Kaisa Hiippala – Frontiers in Microbiology

Review: Impact of Microbes on the Pathogenesis of Primary Biliary Cirrhosis (PBC) and Primary Sclerosing Cholangitis (PSC) – Jochen Mattner – Int J Mol Sci

Animal microbiome

Review: Microbiota-host interplay at the gut epithelial level, health and nutrition – Jean-Paul Lallès – Journal of Animal Science and Biotechnology

Plant, root, and soil microbiome

Root bacterial endophytes alter plant phenotype, but not physiology – Jeremiah A. Henning – Peer J

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria – Pious Thomas – Microbial Ecology

Water microbiome

Unraveling the microbial community of a cold groundwater catchment system – Burga Braun – Water Research

Built environment microbiome

Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations – Min Gao – Environmental Pollution

Metabolomics

Review: Emerging roles of xenobiotic detoxification enzymes in metabolic diseases – Michael C. Petriello – Reviews on Environmental Health

Probiotics

Effect of probiotic supplementation on cognitive function and metabolic status in Alzheimer’s disease: a randomized, double-blind, and controlled trial – Elmira Akbari -Frontiers in Aging Neuroscience

News: Probiotics improve cognition in Alzheimer’s patients – Medical Xpress

More microbiology

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence – Yok Hian Chionh – Nature Communications

Cracking the code for dormant bacteria. Newly discovered genetic code controls bacterial survival during infections – Anne Trafton – MIT News Office

Microbes in the news

Monitoring in Real Time the Formation and Removal of Biofilms From Clinically Relevant Pathogens – PR Web

From the American College of Rheumatology Annual Scientific Meeting: Gut bacteria may be a trigger for antiphospholipid syndrome – EurekAlert

Three University of Maryland students are sending bacteria samples into space – Rachel Kuipers – the Diamondback

University of Texas at Dallas named “Milestones in Microbiology” – Joanna Urban – ASM

Bethany professor Matthew Swearingen receives research grant – Weirton Daily Times

Scientists try bacteria to halt invasive cheatgrass overwhelming the West – Keith Ridler – LA Times

November 11, 2016

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The human microbiome before birth, the HIV lung microbiome, leprosy in squirrels, and ticklish rats. That latter story has nothing to do with microbiology, but we can all use some uplifting stories.

Events

Advancing Microbiome Research Symposium: Microbiome & Disease – November 17, 2016 – Chicago, IL, USA

HIV Microbiome Workshop 2016 – November 17-18, 2016 – Bethesda, MD, USA.

2nd Annual European Microbiome Congress – November 30-Dec 1, 2016 – London, UK

Microbiome Drug Development Summit Europe – Jan 24-26 January 2017. Paris, France

North American Microbiome Congress / Human Microbiome Conference January 24-25 2017, San Diego, CA

Pregnancy and early life

The Human Microbiome before Birth – Martin J. Blaser and Maria G. Dominguez-Bello

Human respiratory microbiome

The bronchial epithelial cell bacterial microbiome and host response – Marc A. Sze – BMC Pulmonary Medicine

Biofilms in ventilator-associated pneumonia – Laia Fernández-Barat – Future Microbiology

Human gut microbiome

An evaluation of the therapeutic potential of fecal microbiota transplantation to treat infectious and metabolic diseases – Albert K Groen – EMBO Molecular Medicine

Association of colorectal carcinogenesis pathway with life style and intestinal microbiome based on the genome and epigenome abnormalities – Nihon Shokakibyo Gakkai Zasshi

Perspective: The Liver at the Nexus of Host-Microbial Interactions – Andrew J. MacPharson – Cell Host & Microbe

Animal experiments

Expression of recombinant human lysozyme in transgenic chicken promotes the growth of Bifidobacterium in the intestine and improves postnatal growth of chicken – Hai Wang – AMB Express

Chronic Early-life Stress in Rat Pups Alters Basal Corticosterone, Intestinal Permeability, and Fecal Microbiota at Weaning: Influence of Sex – Nabila Moussaoui – J Neurogastroenterol Motil.

Animal microbiome (and infection)

Red squirrels in the British Isles are infected with leprosy bacilli – Charlotte Avanzi – Science
Red squirrels in the British Isles are infected with leprosy bacteria – Phys.org
Leprosy Surprise: Medieval Scourge Is Lurking In British Squirrels – Michaeleen Doucleff – NPR

Bacterial Associations Across House Fly Life History: Evidence for Transstadial Carriage From Managed Manure – Klara Zurek – Journal of Insect Science

Built environment microbiology

Review: Constructed Wetlands Revisited: Microbial Diversity in the -omics Era. – Olga Sánchez – Microbial Ecology

Metagenomics and bioinformatics

Commentary: Insights into microbial ecosystems using a new computational approach – Thuy Do – Oral Diseases

Microbes in the news

Are we ready for consumer microbiome testing? – Juliet Preston – MedCityNews

Raining Cats and Dogs… and Bacteria? – Julie Taylor – uBiome

Scientists Try Bacteria to Halt Invading Cheatgrass in West – Keith Ridler – ABC News / Associated Press

Targeting pathogenic bacteria – using phage-derived proteins, proteins developed from the bacteria-invading viruses, for detection of pathogenic bacteria – Science Daily

Your flu risk may be linked to the year you were born – Jacqueline Howard – CNN

How ‘Psychobiotics’ Use Gut Bacteria To Treat Mental Illness. Targeting the gut could create a new class of psychiatric treatments – Carolyn Gregoire – The Huffington Post

Animal Science Professor Identifies Gut Microbiota Signatures of Healthy Aging – ScienceBlog

Quest to map Africa’s soil microbiome begins. Sub-Saharan project could one day help ecosystems to resist climate change and improve agriculture – Sarah Wild – Nature

Microbiome, Hidden Chemical Secrets, Being Accessed At Scripps Pier In San Diego – PR Newswrire

New Method Allows Scientists to Detect the Presence in Ham of the Parasite that Causes Toxoplasmosis – SciCasts

Bik’s non-microbiology Picks

Why are we ticklish? Scientists who tickled rats offer an intriguing answer – Karen Kaplan – LA Times
Neural correlates of ticklishness in the rat somatosensory cortex – S. Ishiyama – Science

November 8, 2016

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I’m sick at home but my inbox is exploding with new papers, so I scraped myself together for a new Microbiome Digest.

Precision medicine and the microbiome, salivary microbiome of Tsimane mothers and infants, food emulsifiers promote colon cancer in mice, microplastics in urban rivers, and a hypothetical silver Nobel prize for Jeffrey Gordon.

Events

SF Bay Area Microbiome meetup – a new LinkedIn group for people in the San Francisco area interested in all things microbiome!

Society of Nutrition Education and Behavior (SNEB) Webinar – Probiotics: Understanding The Microbiome And The Role Of Probiotics In Long Term Health – Wednesday, December 7 at 12:00 p.m. EST

This one is about me: Stanford Microbiome Pioneer Elisabeth Bik Becomes New Science Editor at uBiome – uBiome

General microbiome

Introducing the Microbiome into Precision Medicine – Thomas M. Kuntz, Jack A. Gilbert – Trends in Pharmacological Sciences

Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche – Sarah M. Kopac – Frontiers in Microbiology

Opinion: Do antibodies select a healthy microbiota? – Jason L. Kubinak & June L. Round – Nature Reviews Immunology

Editorial: Complexity at the sub-genus level – Andrea Du Toit – Nature Reviews Microbiology

Human oral microbiome

Salivary microbiomes of indigenous Tsimane mothers and infants are distinct despite frequent premastication – Cliff S. Han – PeerJ

A Pilot Study to Evaluate the Oral Microbiome and Dental Health in Primary Open-Angle Glaucoma – Polla, Daniel – Journal of Glaucoma

Sputum microbiology predicts health status in COPD – DCW Braeken – International Journal of Chronic Obstructive Pulmonary Disease

Human respiratory microbiome

Assessing the Airway Microbiota in Cystic Fibrosis – Jordana E. Hoppe – Clinical Microbiology Newsletter

Review: The microbiome-metabolome crosstalk in the pathogenesis of respiratory fungal diseases – Samuel M. Gonçalves – Virulence

Human vaginal microbiome

Effects of pelvic organ prolapse ring pessary therapy on intravaginal microbial flora – Kazuaki Yoshimura – International Urogynecology Journal

Review: Why do lactobacilli dominate the human vaginal microbiota? – SS Witkin – BJOG

Human gastric microbiome

Characterization of the Gastric Microbiota in a Pediatric Population According to Helicobacter pylori Status – Llorca, Laura – The Pediatric Infectious Disease Journal

Human gut microbiome

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome – Hailiang Xie – Cell Systems

Culture of previously uncultured members of the human gut microbiota by culturomics – Jean-Christophe Lagier – Nature Microbiology

Impact of Cystic Fibrosis Disease on Archaea and Bacteria Composition of Gut Microbiota – Francesco Miragoli – FEMS Microbiology Ecology

Animal models

Systems-level metabolism of the altered Schaedler flora, a complete gut microbiota
– Matthew B Biggs – The ISME Journal

Gut microbiota induce IGF-1 and promote bone formation and growth – Jing Yan – PNAS

Dietary emulsifier-induced low-grade inflammation promotes colon carcinogenesis – Emilie Viennois – Cancer Research

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth – Upsornsawan Itthitaetrakool – PLOS ONE

Sex-specific modulation of the gut microbiome and behavior in Siberian hamsters – Kristyn E. Sylvia – Brain, Behavior, and Immunity

Animal microbiome

Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates – Julie C. McInnes – Methods in Ecology and Evolution

High-throughput sequencing highlights the significant influence of seasonal housing and teat preparation on the raw milk microbiota – Conor J Doyle – Applied and Environmental Microbiology

Metagenomic analysis reveals the influences of milk containing antibiotics on the rumen microbes of calves – Wei Li – Archives of Microbiology

Repeated sampling of white syndrome-affected corals reveals distinct microbiome at disease lesion fronts – F. Joseph Pollock – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest – Cheng Gao – New Phytologist

AMF, phylogeny, and succession: specificity of response to mycorrhizal fungi increases for late-successional plants – Liz Koziol – Ecosphere

Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils – William A. Argiroff – Microbial Ecology

Effect of disturbance by oil pollution on the diversity and activity of bacterial communities in biological soil crusts from the Sultanate of Oman – Raeid M.M. Abed – Applied Soil Ecology

Book chapter: Root-Microbe Interactions in Response to Soil Conditions – Anil Somenahally – Global Soil Security

Water and extremophile microbiome

Microplastic in surface waters of urban rivers: concentration, sources, and associated bacterial assemblages – Amanda R. McCormick – Ecosphere

Evidence for microbial mediation of subseafloor nitrogen redox processes at Loihi Seamount, Hawaii – Jason B. Sylvan – Geochimica et Cosmochimica Acta

Bacterial metacommunity organization in a highly-connected aquatic system – Silke Langenheder – FEMS Microbial Ecology

Microbial communities and their predicted metabolic characteristics in deep fracture groundwaters of the crystalline bedrock at Olkiluoto, Finland – Malin Bomberg – Biogeosciences

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia
– Shipeng Lu – Environmental Microbiology Reports

Review: Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook – Kela P. Weber – Water

Bioinformatics and metagenomics

Alternative for PiCRUST: Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes – Shoko Iwai – PLOS ONE

Measurement of bacterial replication rates in microbial communities – Christopher T Brown – Nature Biotechnology

Microbes in the news

If there was a Nobel silver medal, I’d award it to Jeffrey Gordon and our gut microbes – Tim Spector – The Conversation

The Microbiome Hits #1 for 2017: Cleveland Clinic’s announcement of the Top 10 Medical Innovations came at the conclusion of the 2016 Medical Innovation Summit.

Gut Instincts: The Link Between Diet, the Gut Microbiota and the Brain – Kiana West – Imperial College London

Q&A with Stanford statistics Professor Susan Holmes: Statistics in the era of big data – Stanford News

Conference report: Gut microbes linked to immunotherapy response in melanoma patients – EurekAlert

Gut bacteria ‘may help drugs fight cancer’ – James Gallagher – BBC

Assistant professor Joanna Slusky recognized for work with antibiotic-resistant bacteria – The University Daily Kansan

Three Soundcloud episodes by the Yale Journal of Biology and Medicine on the microbiome, to accompany their September issue:

  1. Microbiome: Episode I: history of the field, current techniques used in microbiome research, and how the microbiome influences our health
  2. Microbiome: Episode IIMicrobiome: Episode II: Dr. Martin Kriegel discusses articles published in our issue, – Yale Journal of Biology and Medicine
  3. Microbiome: Episode III: Dr. Camille Konopnicki, talks about current on going research on the microbiome here at Yale and how microbiome research is evolving and changing.

Companies Bet on Designer Bacteria as New Way to Treat Disease – MIT Technology Review

About Bethany Rader: Researcher studying squid-human bacteria connection – Tim Crosby – The Southern Illinoisan

Horrible title, but nice student work: Students create Frankenstein’s monster of bacteria to detect toxic chemicals – New Atlas

 

Storify San Francisco Microbiome Meetup #SFBiome

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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

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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