November 16, 2017

Today we have a very nice serving to digest, with some impactful gut microbiome studies for human health/therapeutics, a whitepaper on the challenges of clinical microbiome research.  We also have clusters of related studies on the environment, drinking water, and antibiotic resistance.  There are even a few studies on the microbiota found in caves!  Give these all a read, there is a lot of amazing research today.  Don’t forget to have yourself a few extra side servings of my own non-microbial picks, in honor of the upcoming Thanksgiving US holiday.

Human oral microbiome

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

Human respiratory microbiome

The microbiota protects against respiratory infection via GM-CSF signaling – Rebecca L. Brown – Nature

Human gut microbiome

Microbiota: A high-pressure situation for bacteria – David A. Relman – Nature

Quantitative microbiome profiling links gut community variation to microbial load – Doris Vandeputte – Nature

Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature

A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li – PLOS ONE

Plant, root, and soil microbiome

[Doctoral Thesis] Plant biomass-degrading microbial consortia: Ecology, lignocellulolytic machinery and biotechnological potential – Jiménez Avella – University of Groningen

Direct evidence for the enhanced acquisition of phosphorus in the rhizosphere of aquatic plants: A case study on Vallisneria natans – Xigang Xing – Science of the Total Environment

Effect of Phosphate Solubilization Microorganisms and Plant Growth Promoting Rhizobacteria on Yield and Yield Components of Corn – Amin Fathi – Scientia Agriculturae

Water and extremophile microbiome

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients – Alyse K. Hawley – Nature

Comparison of bacterial and archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary) – Dóra Anda – Journal of Cave and Karst Studies

Comparisons of Soil Properties, Enzyme Activities and Microbial Communities in Heavy Metal Contaminated Bulk and Rhizosphere Soils of Robinia pseudoacacia L. in the Northern Foot of Qinling Mountain – Yurong Yang – Forests

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data – Stéphane Pfendler – Science of the Total Environment

Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system – Lingwei Meng – Journal of Environmental Sciences

Field assessment of bacterial communities and total trihalomethanes: Implications for drinking water networks – Carolina Montoya-Pachongo – Science of the Total Environment

Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water – Hao-Chang Su –  Science of the Total Environment

Bioinformatics

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene – Yifei Zhang – PLOS ONE

Microbes in the news

Probiotics: Health boost or waste of cash?

Microbes on the market

* uBiome Launches HPV, STD, Vaginal Microbiome Test for Self-Collected Samples – genomeweb

* [Whitepaper] The Microbiome in Clinical Trials: Opportunities and Challenges – Brian Murphy – MedPace

Bacteria Hysteria

Fort Mitchell woman attacked by flesh-eating bacteria back home after 45 days in hospital

Fecal Bacteria Discovered In Public Well Serving Seymour, Oxford

Ed’s non-microbiology picks

Epistemic rationality: Skepticism toward unfounded beliefs requires sufficient cognitive ability and motivation to be rational – Tomas Ståhl – Personality and Individual Differences

Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing – Hao Yin – Nature

Increased food production and reduced water use through optimized crop distribution – Kyle Frankel Davis – Nature Geoscience

* Fructan, Rather Than Gluten, Induces Symptoms in Patients With Self-reported Non-celiac Gluten Sensitivity – Gry I. Skodje – Gastroenterology

* Does Money Matter in the Long Run? Effects of School Spending on Educational Attainment – Joshua Hyman – American Economy Journal: Economic Policy

* Hippocampal GABA enables inhibitory control over unwanted thoughts – Taylor W. Schmitz – Nature

Daytime variation of perioperative myocardial injury in cardiac surgery and its prevention by Rev-Erbα antagonism: a single-centre propensity-matched cohort study and a randomised study – David Montaigne – The Lancet Cardiac Surgery

The reminiscence bump: why America’s greatest year was probably when you were young

Study: Americans are retiring later, dying sooner and sicker in-between

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October 26, 2017

In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

September 27, 2017

Human oral microbiome

Complex Intratissue Microbiota Forms Biofilms in Periodontal Lesions – Baek K – Journal of Dental Research

Human vaginal microbiome

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case–control study – Robin van Houdt – Sexually Transmitted Infections

Human gut microbiome

[Review] Modulation of Type 1 Diabetes Risk by the Intestinal Microbiome – Knip M – Current Diabetes Reports

[Review] The Relationship Between the Human Genome and Microbiome Comes into View – Julia K. Goodrich – Annual Review of Genetics

Animal microbiome

[pre-print] The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C. Medd – bioRxiv

Characterisation of North American Brucella isolates from marine mammals – Adrian M. Whatmore – PLOS ONE

Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach – Ann Arfken – PLOS ONE

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology – Sarah E. Macdonald – PLOS ONE

Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps – Gianluigi Mauriello – PLOS ONE

Plant, root, and soil microbiome

Multiscale Investigation on Biofilm Distribution and its Impact on Macroscopic Biogeochemical Reaction Rates – Zhifeng Yan – Water Resources Research

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia – Tarek A. A. Moussa – PLOS ONE

Bacterial and diazotrophic diversities of endophytes in Dendrobium catenatum determined through barcoded pyrosequencing – Ou Li – PLOS ONE

A secreted antibacterial neuropeptide shapes the microbiome of Hydra – René Augustin – Nature Communications

Probiotics / prebiotics

Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: A non-randomised paired-design clinical trial of efficacy – Minseok Seo – PLOS ONE

Bioinformatics

Predicting metabolic adaptation from networks of mutational paths – Christos Josephides & Peter S. Swain – Nature Communications

Microbes in the news 

Florida Seawater Bacteria Death Toll Rises – Patch

Researchers Find New Microbial Communities in Human Body

Microbes on the market

Paris-based Eligo Bioscience secures $20 million to bring Precision Medicine to the Microbiome – EU-Startups

Science, publishing, and career

New open-access journal Metabarcoding & Metagenomics joins the lines of publisher Pensoft – EurekAlert!

Ed’s non-microbiology picks

Infants make more attempts to achieve a goal when they see adults persist – Julia A. Leonard – Science

University of Tokyo pair invent loop-based quantum computing technique

Cancer immunotherapy with recombinant poliovirus induces IFN-dominant activation of dendritic cells and tumor antigen–specific CTLs – Michael C. Brown – Science Translational Medicine

Stereodivergent synthesis with a programmable molecular machine – Salma Kassem, – Nature

Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques – Ling Xu – Science

August 29, 2017

A short list to digest today toward the end of the month.

Multi-site human microbiome

Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low Microbial Content Samples – Clarke EL – American Journal of Respiratory and Critical Care Medicine

Human oral microbiome

Smoking May Lead to Marginal Bone Loss around Non-submerged Implant during Bone Healing by Altering Salivary Microbiome: A Prospective Study – Xiaobo Duan – Journal of Periodontology

Human skin microbiome

The mammalian skin microbiome – Ross, Ashley Anne – UWSpace

Human vaginal microbiome

Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity – Abdelmaksoud AA – PLoS One

The cervico-vaginale microbiota in chlamydia trachomtais notified women: a case–control study at the sexually transmitted infection outpatient clinic in Amsterdam – Charlotte van der Veer – Virus Evolution

Human gut microbiome

Targeting the gut microbiota by dietary nutrients: a new avenue for human health – Li D – Critical Reviews in Food Science and Nutrition

Animal experiments

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome – Lamoureux EV – mSystems

Plant, root, and soil microbiome

The Effects of Low Concentrations of Silver Nanoparticles on Wheat Growth, Seed Quality, and Soil Microbial Communities – Guangfu Liu – Water, Air, & Soil Pollution

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Microbiome Dynamics in a Shrimp Grow-out Pond with Possible Outbreak of Acute Hepatopancreatic Necrosis Disease – Wei-Yu Chen – Nature Scientific Reports 7

Microbes in the news

Science Is Showing How Gut Bacteria Affect The Brain, But Don’t Bother Taking Probiotics Yet – David DiSalvo – Forbes

Over 80% of airborne bacteria identical in Seoul, Beijing: report – Kim Da-sol – The Korea Herald

Ed’s non-microbiology picks 

Spontaneous fine-tuning to environment in many-species chemical reaction networks – Jordan M. Horowitz – PNAS

Bee-derived antibacterial peptide, defensin-1, promotes wound re-epithelialisation in vitro and in vivo – Marcela Bucekova – Nature Scientific Reports 7

Family Planning Funding Cuts and Teen Childbearing – Analisa Packham – Miami University

July 19, 2017

Today’s digest is a long one! There is high diversity of studies, with a high abundance of gut microbiome studies, a few publications on fecal transplant, and some very interesting early life/pregnancy/mother-infant science.  A normal serving of animal studies, of course a nice colony of environmental microbial studies, and a study reporting the presence of bacteria in Alzheimer’s post-mortem brains.

Events and jobs

Postdoctoral research fellow in translational microbiome research – Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet

General microbiome

Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

[Review]  The human microbiome – Hubert E. Blum – Advances in Medical Sciences

Microbiome and Metabolome Data Integration Provides Insight Into Health and Disease – Michael Shaffer – Translational Research

Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge – Neelam Devpura – International Biodeterioration & Biodegradation

Impact of the Microbiota on Bacterial Infections during Cancer Treatment – Jessica Galloway-Peña – Trends in Microbiology

Pregnancy and early life

** The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut – Elana Biagi – Frontiers in Microbiology | Evolutionary and Genomic Microbiology

* What’s Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings – Lorena Ruiz – Frontiers in Immunology | Nutritional Immunology

Microbiome Associated with Severe Caries in Canadian First Nations Children – M. Agnello – Journal of Dental Research

* Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes – Ronan M. Doyle – PLoS One

Human oral microbiome

Characterization of Oral Microbiota in Removable Dental Prosthesis Users: Influence of Arterial Hypertension – Leila Maria Marchi-Alves – BioMed Research International

Human vaginal microbiome

The association between ethnicity and vaginal microbiota composition in Amsterdam, the Netherlands – Hanneke Borgdorff – PLoS One

Human nearly-sterile sites

** 16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain – David C. Emery – Frontiers in Aging Neuroscience

Human gut microbiome

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia – Sayaka Fujio-Vejar – Frontiers in Microbiology | Microbial Symbioses

*[Review] Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients – Hoda M. Eid – Frontiers in Pharmacology | Ethnopharmacology

MOLECULAR CHARACTERIZATION OF FECAL MICROBIOTA OF HEALTHY CHINESE TOBACCO SMOKER SUBJECTS IN SHAANXI PROVINCE, XI’AN CHINA – Ishaq HM – Journal of Ayub Medical College

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Psychosomatic Medicine

The Impact of Gut Microbiota on Gender-Specific Differences in Immunity – Floris Fransen – Frontiers in Immunology | Nutritional Immunology

Involvement of gut microbiota in the association between gastrointestinal motility and 5‑HT expression/M2 macrophage abundance in the gastrointestinal tract – Mo Yang – Molecular Medicine Reports

Correspondence: Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial – Benjamin H Mullish – Hepatology

Going to the Bank: Fecal Microbiota Transplantation in Pediatrics – Elaine Barfield – Clinical Pediatrics

INTERRELATIONSHIPS BETWEEN GUT MICROBIOTA AND HOST: Paradigms, Role in Neurodegenerative Diseases and Future Prospects – Villarraso JC – CNS & Neurological Disorders Drug Targets

Faecal microbiota transplant: a novel biological approach to extensively drug-resistant organism-related non-relapse mortality – Innes AJ – Bone Marrow Transplantation

* Gut microbiota is critical for the induction of chemotherapy-induced pain – Shiqian Shen – Nature Neuroscience

Relationships between Gastrointestinal Microbiota and Blood Group Antigens – Anuhya Gampa – Physiological Genomics

[Masters Thesis] Evaluating the Effectiveness of Select Bacteria Against Clostridium difficile – Choquette, Kelsey Rose – Iowa State University, ProQuest Dissertations Publishing

* Potential and active functions in the gut microbiota of a healthy human cohort – Alessandro Tanca – Microbiome

[Letter to Editor] The necessity of gut microbiome characterization in diseases prevention and therapy – Sama Rezasoltani – Gastroenterology and Hepatology from Bed to Bench

[Review Article] The Intricate Interaction between Enteric Microbiota and Brain: Principles and Clinical Implications – Giovanni Gherardi – Journal of Digestive Diseases and Hepatology

Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults – K Lippert – Beneficial Microbes

Animal experiments

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K – The American Journal of Pathology

Grape pomace improves performance, antioxidant status, fecal microbiota and meat quality of piglets – I. Kafantaris – Animal

Animal microbiome

Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans – Lobos O – Italian Journal of Food Safety

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations – Xiaoping He – Microbial Ecology

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change – Cheng-Yu Chen – PLoS One

Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny – François-Étienne Sylvain – Scientific Reports

Microbiome overview in swine lungs – Franciele Maboni Siqueira – PLoS One

Plant, root, and soil microbiome

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops – Zhaojin Chen – Ecotoxicology and Environmental Safety

Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology – Davide Francioli – Microbial Ecology

Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers – Alastair W. Tait – Frontiers in Microbiology | Extreme Microbiology

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil – Mengting M. Yuan – Global Change Biology

[PrePrint] Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome 

Performance and bacterial community structure of a 10-years old constructed mangrove wetland – Tingting Tian – Marine Pollution Bulletin

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields – Hai-liang Wang – PLoS One

Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania – Cecilia M. Chiriac – Microbiology of Aquatic Systems

Built environment

Pilot study to determine if microbial contamination levels in hospital washrooms are associated with hand drying method – Mark H. Wilcox – Journal of Hospital Infection

Probiotics / prebiotics

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – BBA

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic – Rebeca Martin – Frontiers in Microbiology | Food Microbiology

Bioinformatics

* Abundance estimation and differential testing on strain level in metagenomics data – Martina Fischer – Bioinformatics

Techniques

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures – Lucía Vázquez – Frontiers in Microbiology | Food Microbiology

Next-generation Sequencing of the DNA Virome from Fecal Samples – Monaco CL – Bio-protocol

Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery – Yutong Shi – Environmental Microbiology

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly – K. S. Zadesenets – Russian Journal of Genetics

Microbes on the market

Microbiome Sequencing Services Market: trends, analysis, Overview, forecast up to 2021

Ed’s non-microbiology picks

Heavy metal accumulation by Saccharomyces cerevisiae cells armed with metal binding hexapeptides targeted to the inner face of the plasma membrane – Lavinia Liliana Ruta –Applied Microbiology and Biotechnology

Fracking can contaminate rivers and lakes with radioactive material, study finds

Subacute normobaric oxygen and hyperbaric oxygen therapy in drowning, reversal of brain volume loss: a case report – Paul G Harch – Medical Gas Research

No Effect of Commercial Cognitive Training on Neural Activity During Decision-Making – Joseph W. Kable – Journal of Neuroscience

Health Insurance Expansion and Incidence of Out‐of‐Hospital Cardiac Arrest: A Pilot Study in a US Metropolitan Community – Eric C. Stecker – Journal of the American Heart Association

June 15, 2017

Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

Microbiome at BioData World West 2017

Last month, from April 26th to April 27th, I attended the BioData World West conference representing GENEWIZ, where I am a Bioinformatics Analyst (developer) working primarily on metagenomics.  The focus of the conference were three major areas: Genomics & Health, Precision Medicine, and Artificial Intelligence.  The conference, in San Francisco, hosted a variety of forward thinking and interdisciplinary organizations ranging from the top academic institutions to big industry players from abroad (Google, Merck, Illumina, etc.) to start ups in AI/tech/biotech/pharma.  The talks and conversations I had there were exciting and educational and the networking opportunities were amazing – I believe a number of collaborations were born there.   You can see details about the conference through this link: BioData World West 2017

My highlighted talks were by Atul Butte (UCSF), Jeff Dean (Google), Ronald Pryzgodski (MVP), Steve Miller (USCF, developed SURPI), Ali Torkamani (Scripps), and Sylvain Costes (NASA).  However, every talk was fascinating in its own way and I’d highly recommend this conference to anyone in this space – I could write 10 posts about what I learned but I’ll focus on the microbiome below.  It seemed everyone loved to talk and learn from each other about microbiome-related science, even the people focused mainly on AI.

In regard to the microbiome, many if not most talks incorporated, mentioned, or focused on the importance of this area of research.  Here are some of my high level notes related to the microbiome:

  • Phenotyping is a big area that we need to develop and are establishing right now.  The microbiome is an aspect of our phenotype and should be considered a distinct biomarker.
  • Mobile / site of study lab and metagenomic techniques are important to develop
  • We need to work together to share our genomic data, including metagenomic data
  • AI can be used to find new information where we never thought to look – this, in my opinion, will have implications in studying the massive network of interactions between microbes but also in discovery of new microbes among other things
  • Steve Miller’s (SURPI) talk was fascinating.  Without going into too many details he is moving forward clinically with using metagenomics for pathogen detection and diagnoses – something I believe will be the future of infectious disease diagnostics (or at least could be used to establish accurate SNP-based panels).  I’d highly recommend following his publications and well as Dr. Chiu.  I believe exciting things are coming from his lab in the next year or so http://profiles.ucsf.edu/steve.miller
  • Cannabis microbiome studies are paramount because microbes are the only risk for cannabis – and pesticides typically cannot be used in production

I hope this post was interesting – the conference surely was – I can’t wait to see the advances we’ve made presented there next year!

Edward Messick