Aug 08, 2018

Good morning! Today’s Microbiome Digest highlights are the modeling of the gut microbiome, trotter horse urine metabolome, selection of appropriate metagenome taxonomic classifiers and news about the improvement of gut health. Enjoy reading.

General microbiome

Mini-Review: Conducting metagenomic studies in microbiology and clinical research – Tiphaine C. Martin – Applied Microbiology and Biotechnology

Human gut microbiome

Challenges in modeling the human gut microbiome – Parizad Babaei – Nature Biotechnology

Review: Rebuilding the Gut Microbiota Ecosystem – Antonella Gagliardi – International Journal of Environmental Research and Public Health

Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model – NooraOttman – Journal of Allergy and Clinical Immunology

Animal experiments

Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility – Kristopher D. Parker – Frontiers in Microbiology

Animal microbiome

Characterization of trotter horses urine metabolome by means of proton nuclear magnetic resonance spectroscopy – Chenglin Zhu – Metabolomics

Water and extremophile microbiome

Metagenomic analysis of geothermal water reservoir sites exploring carbohydrate-related thermozymes – GirijaKaushal – International Journal of Biological Macromolecules

Bioinformatics

Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research – Irina M. Velsko – mSystems

Microbes in the news

New Emerging Research Suggests Montmorency Tart Cherries May Help Enhance Gut Health

Cherries improve gut health

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July 02, 2018

Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

 Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology

Bioinformatics

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology

Techniques

Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system

 

Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine

June 22, 2018

Have a happy weekend! Today in Microbiome Digest: reviews on microbiome immunity and type 1 diabetes,  metatranscriptome analysis of vaginal microbiome, Differences in gut microbiota associated with age, sex, and stool consistency, microbes in the news, and more…

Events and jobs

Scientist – Genomics and Microbiome – Madison, WI

Bioinformatics Scientific Programmer – Quadram Institute Bioscience

General microbiome

Review: Communication Between the Microbiota and Mammalian Immunity – Kyla S. Ost – Annual Review of Microbiology

Host genotype-specific microbiota do not influence the susceptibility of Dmagna to a bacterial pathogen – Marilou P. Sison-Mangus – Scientific Reports

Pregnancy and early life

Book chapter: Implantation Failure 1: Intrauterine Circumstances and Embryo–Endometrium Synchrony at Implantation – Keiji Kuroda – Treatment Strategy for Unexplained Infertility and Recurrent Miscarriage

Special Issue: Microbiome in normal and pathological pregnancies: A literature overview – Carla R. Taddei – American Journal of Reproductive Immunology

Multi-site human microbiome

Bacterial invasion of dentinal tubules from the external root surface with and without an intact cemental layer- a confocal laser scanning microscopic study – Jovita D’souza – Advances in Tissue Engineering and Regenerative Medicine

Human respiratory microbiome

Review: Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria – Jiang S – Journal of Dental Research

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study –  Abigail L. Coughtrie – Journal of Medical Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

Human vaginal microbiome

Review: Pharmacology of Antiretrovirals in the Female Genital Track for HIV Prevention – Melanie R. Nicol – The Journal of Clinical Pharmacology

Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis – Zhi-Luo Deng – mSphere 

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes/Metabolism Research and Reviews

A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile – Thanissery R – Frontiers in Microbiology

Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects – Tomohisa Takagi – Journal of Gastroenterology

Dietary Supplementation with a Magnesium-Rich Marine Mineral Blend Enhances the Diversity of Gastrointestinal Microbiota – Erin K. Crowley – Marine Drugs

The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks – Microbiome

Review: Potential Role of the Gut Microbiome in ALS: A Systematic Review – Michelle L. Wright – Biological Research for Nursing

Animal experiments

Lack of liver steatosis in germ-free mice following hypercaloric diets – Stephan C. Bischoff – European Journal of Nutrition

 Plant, root, and soil microbiome

Exploring Elicitors of the Beneficial Rhizobacterium Bacillus amyloliquefaciens SQR9 to Induce Plant Systemic Resistance and Their Interactions With Plant Signaling Pathways – Gengwei Wu – Molecular Plant-Microbe Interactions

Correlation and Distribution of Xenobiotics Genes and Metabolic Activities with Level of Total Petroleum Hydrocarbon in Soil, Sediment and Estuary Water in the Niger Delta Region of Nigeria U. O. Edet – Asian Journal of Biotechnology and Genetic Engineering

Review: Status and future of disease protection and grape berry quality alteration by microorganisms in viticulture – Misa Otoguro – Letters in Applied Microbiology

Editorial: The contribution of plant microbiota to economy growth – Angela Sessitsch – Microbial Biotechnology

Water and extremophile microbiome

Mini-Review: Future direction in marine bacterial agarases for industrial applications -Saeid Tamadoni Jahromi – Applied Microbiology and Biotechnology

Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands) – M. Papale – Extremophiles

Taxonomy, phylogeny and ecology of cultivable fungi present in seawater gradients across the Northern Antarctica Peninsula – Vívian N. Gonçalves – Extremophiles 

A strong link between marine microbial community composition and function challenges the idea of functional redundancy – Pierre E. Galand – The ISME Journal

Probiotics / prebiotics

Gut Microbiota, Probiotics, and Sport: From Clinical Evidence to Agonistic Performance – Marco Pane – Journal of Clinical Gastroenterology

 Microbes in the news

‘Green’-feed: Industrial microbes could feed cattle, pigs, chicken

SMU researchers hope microbes will lead them to strike oil offshore

Scientists Reveal How Gut Microbes ‘Recover’ After Antibiotic Treatment

Celebrate your gut microbiota on the first World Microbiome day!

 Microbes on the market (news about biotech companies)

Human Microbiome Market – Global Industry Analysis, Size, Share, Growth, Trends, and Forecast 2018 – 2026

MaaT Pharma and Lutech Sign Licensing Agreement on Microbiome Therapy for Graft-vs-Host Disease

 

Ashok’s non-microbiology picks

The Rheumatoid Arthritis-Associated Citrullinome – Ronak Tilvawala – Cell Chemical Biology

Inflammation-Induced, STING-Dependent Autophagy Restricts Zika Virus Infection in the Drosophila Brain – Yuan Liu – Cell Host & Microbe

Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells – Patrick Fernandes Rodrigues – Nature Immunology

A synaptic threshold mechanism for computing escape decisions – Dominic A. Evans – Nature