Category Archives: Events and jobs

March 2, 2018

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Events and jobs

Enter our ‘scientist at work’ photo contest – Nature

General microbiome

Review: To respond or not to respond — a personal perspective of intestinal tolerance – AM Mowat – Nature Reviews

“Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system – AE Naas – BMC Microbiome

Human vaginal microbiome

Fractional CO2 laser for genitourinary syndrome of menopause in breast cancer survivors: clinical, immunological, and microbiological aspects – A Becorpi – Lasers in Medical Science

Human gut microbiome

Environment dominates over host genetics in shaping human gut microbiota – D Rothschild – Nature

The gut microbiota and immune checkpoint inhibitors – A Humphries – Human Vaccines and Immunotherapeutics

Probiotic supplementation increases obesity with no detectable effects on liver fat or gut microbiota in obese Hispanic adolescents: a 16-week, randomized, placebo-controlled trial. – RB Jones – Pediatric Obesity

Adaptation of adherent-invasive E. coli to gut environment: Impact on flagellum expression and bacterial colonization ability. – G Sevrin – Gut Microbes

Editorial: Gut microbiomes and their metabolites shape human and animal health – W Park –  Journal of Microbiology

Review: Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease – T Eom – Journal of Microbiology

Review: Targeting friend and foe: Emerging therapeutics in the age of gut microbiome and disease – JA Cho – Journal of Microbiology

Review: Mind-altering with the gut: Modulation of the gut-brain axis with probiotics – N Kim – Journal of Microbiology

Gut microbial composition in patients with psoriasis – FM Codoñer – Scientific Reports

Clostridium scindens is present in the gut microbiota during Clostridium difficile infection. A metagenomic and culturomic analysis. – S Amrane – Journal of Clinical Microbiology

Letter to Editor: Microbiome and Esophageal Adenocarcinoma—Letter – NO Kaakoush – Cancer Research

Animal experiments 

Altered gut microbiome promotes proteinuria in mice induced by Adriamycin – Q Jiang – AMB Express

Functional Anthocyanin-Rich Sausages Diminish Colorectal Cancer in an Animal Model and Reduce Pro-Inflammatory Bacteria in the Intestinal Microbiota. – G Fernández – Genes (Basel)

Animal microbiome 

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen – RD Stewart – Nature Communications

The Ruminococci: key symbionts of the gut ecosystem – AJL Reau – Journal of Microbiology

Plant, root, and soil microbiome

Concepts & Synthesis: Toward more robust plant-soil feedback research – MJ Rinella – Ecology

Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. – FP Cid – Extremophiles

Competition–colonization tradeoffs structure fungal diversity – GR Smith – The ISME Journal

Water microbiome and extremophile 

Environmental factors driving fungal distribution in freshwater lake sediments across the Headwater Region of the Yellow River, China – J Tian – Scientific Reports

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river. – A Isabwe – The Science of the Total Environment

Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation – R Omrani – Biodegradation

Built environment 

‘Cyclical Bias’ in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation – A Rodriguez-Palacios – Scientific Reports

Phages and viruses

Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics – JA Grasis – Viral Metagenomics

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere – J Abrahão – Nature Communications

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages – L Cheng – BMC Microbiology

Techniques

Highly sensitive detection and quantification of the secreted bacterial benevolence factor RoxP using a capacitive biosensor: A possible early detection system for oxidative skin diseases. – G Ertürk – PLoS One

Review: Emerging Technologies for Molecular Diagnosis of Sepsis – M Sinha – Clinical Microbiology Reviews

Microbes in the news

Biofilm Replaces Plastic Packaging in this Dutch Supermarket Aisle – Futurism

For the Microbiome, the Nature vs. Nurture Debate Comes into Focus – GEN

With $36M series B, Finch goes full speed ahead in microbiome therapy – Fierce Biotech

Genetics or lifestyle: What is it that shapes our microbiome? – Science Daily

More than soap scum: Learning about biofilms – Silive

7 Startups Treating Disease Using the Microbiome – Nanalyze

ATM keypads, restaurant menus full of bacteria – News3Channel

Non-microbiology picks

Intellectual Synthesis in Mentorship Determines Success in Academic Careers – JF Lienard – bioRxiv

 

February 22, 2018

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Events and jobs

Microbiology Adjunct Instructor – Diablo Valley College

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Pregnancy and early life

Review: Maternal Microbiota, Prepregnancy Weight, and Mode of Delivery
Intergenerational Transmission of Risk for Childhood Overweight and Obesity – Giulia Paolella – JAMA Pediatrics

 

Human ear, nose and throat microbiome

*A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera – Rachael Lappan – BMC Microbiology

The Tracheal Microbiota in Patients with a Tracheostomy Before, During, and After an Acute Respiratory Infection – Pérez-Losada, Marcos – The Pediatric Infectious Disease Journal

Human oral microbiome

Shift of microbial composition of peri-implantitis-associated oral biofilm as revealed by 16S rRNA gene cloning – Ali Al-Ahmad – Journal of Medical Microbiology

Human vaginal microbiome

Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida – Gilbert Gerard Ghislain Donders – Journal of Medical Microbiology

Human gut microbiome

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn’s disease of the terminal ileum – Rodrick J. Chiodini – Journal of Medical Microbiology

Gut microbiota trajectory in early life may predict development of celiac disease – Marta Olivares – BMC Microbiome

A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis – Atsushi Hirano – Journal of Gastroenterology and Hepatology

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease – Nicholas A Kennedy – Inflammatory Bowel Diseases

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Animal experiments

Regulation of vitamin D metabolism following disruption of the microbiota using broad spectrum antibiotics – Stephanie A. Bora – The Journal of Nutritional Biochemistry

Soluble dietary fiber improves energy homeostasis in obese mice by remodeling the gut microbiota – Haiyuan Wang – Biochemical and Biophysical Research Communications

Lactobacillus and Bifidobacterium Ameliorate Memory and Learning Deficits and oxidative stress in Aβ (1-42) Injected Rats – Somayeh Athari Nik Azm – Applied Physiology, Nutrition, and Metabolism

*Chronic helminth infection perturbs the gut-brain axis, promotes neuropathology and alters behaviour – Paul R Giacomin – The Journal of Infectious Diseases

*Endometriosis induces gut microbiota alterations in mice – Ming Yuan – Human Reproduction

*Strain differences in the susceptibility to the gut–brain axis and neurobehavioural alterations induced by maternal immune activation in mice – Morais, Livia H – Behavioural Pharmacology

Specific synbiotics in early life protect against diet-induced obesity in adult mice
Mona Mischke – Diabetes, Obesity, and Metabolism

Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse – Barbora Kuntová – Frontiers in Genetics

Lactobacillus accelerates ISCs regeneration to protect the integrity of intestinal mucosa through activation of STAT3 signaling pathway induced by LPLs secretion of IL-22 – Qihang Hou – Cell Death and Differentiation

Animal microbiome

Review: Gut barrier function: Effects of (antibiotic) growth promoters on key barrier components and associations with growth performance – Leon J Broom – Poultry Science

Fecal microbiota transplantation in puppies with canine parvovirus infection – Giorgio Q. Pereira – Journal of Veterinary Internal Medicine

Water and extremophile microbiome

Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae – Pamela Alvarado – Antonie van Leeuwenhoek

 

Resistome

The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany – Robert Häsler – BMC Microbiome

Transferable vancomycin resistance in clade B commensal-type Enterococcus faecium – François Lebreton – Journal of Antimicrobial Chemotherapy

 

Bioinformatics

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach – Loo Wee Chia – Antonie van Leeuwenhoek

Biotechnology

*A 3D intestinal tissue model supports Clostridioides difficile germination, colonization, toxin production and epithelial damage – Lamyaa Shaban – Anaerobe

Design of synthetic bacterial communities for predictable plant phenotypes – Sur Herrera Paredes – PLOS Biology

Harnessing a Methane-Fueled, Sediment-Free Mixed Microbial Community for Utilization of Distributed Sources of Natural Gas – Jeffrey J. Marlow – Biotechnology and Bioengineering

Dissertation: Microbial Communities Involved in Carbon Monoxide and Syngas Conversion to Biofuels and Chemicals – Sofia Victoria Esquivel Elizondo – Arizona State University

 

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Microbes in the news

This Vibrant Bacteria Could Be Used to “Grow” Paint – Meilan Solly – Smithsonian

Bacteria-eaters to prevent food poisoning? Phages eliminate Yersinia from food – Science Daily

A ‘Grueling and Grotesque’ Biohacking Experiment – Kate McLean – The Atlantic

 

February 21, 2018

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Events and jobs

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

General microbiome

[editorial] Systems biology of the human microbiome – BP Bernabé, L Cralle, JA Gilbert – Current Opinion in Biotechnology, 2018

[pre-print] Growth tradeoffs produce complex microbial communities without direct interactions – Michael Manhart – bioRxiv

Exploring the Multifaceted Role of Microbes in Pharmacology – Mitali Mishra – Microbial Biotechnology

Human reproductive or urinary microbiome

Seminal bacterial composition in patients with obstructive and non-obstructive azoospermia – Houyang Chen – Experimental and Therapeutic Medicine

Human respiratory microbiome

Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 – Jose A. Romero-Espinoza – PLOS One

Human gut microbiome

[pdf[ Phytochemicals that influence gut microbiota as prophylactics and for the treatment of obesity and inflammatory diseases – Lucrecia Carrera-Quintanar – Hindawi

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis – F Bishehsari – Genes

A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease – Pedro Gonçalves – Inflammatory Bowel Diseases

Animal microbiome

Differential microbial communities of omnivorous and herbivorous cattle in Southern China – Susanna K.P. Lau – Computational and Structural Biotechnology Journal

The gills of reef fish support a distinct microbiome influenced by host-specific factors – Zoe A. Pratte – Applied and Environmental Microbiology

Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758) – Jaison H. Cuartas – PeerJ

Plant, root, and soil microbiome

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Structural and metabolic diversity of rhizosphere microbial communities of Phragmites karka in a tropical coastal lagoon – Pratiksha Behera – Applied Soil Ecology

Responses of soil microbial communities to a short-term application of seaweed fertilizer revealed by deep amplicon sequencing – Mingpeng Wang – Applied Soil Ecology

[pdf] The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery – Roberta Fulthorpe – Frontiers in Ecology and Evolution

Microbes and Their Role in Drought Tolerance of Agricultural Food Crops – Rout George Kerry – Microbial Biotechnology

Microscopic and Metagenomic Analyses of Peltigera ponojensis (Peltigerales, Ascomycota) – Linda E. Graham – International Journal of Plant Sciences

Frankia Diversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity of Frankia Populations in Corresponding Rhizosphere Soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

High frequency cropping of pulses modifies soil nitrogen level and the rhizosphere bacterial microbiome in 4-year rotation systems of the semiarid prairie – Chantal Hamel – Applied Soil Ecology

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Water and extremophile microbiome

Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts – James C. Wallace – PLOS One

Linking the effect of antibiotics on partial-nitritation biofilters: performance, microbial communities and microbial activities – Alejandro Gonzalez-Martinez – Frontiers in Microbiology

The effect of epiphytic macroinvertebrates on microbial communities in different types of macrophyte-dominated shallow lakes – Tomasz Mieczan –  Knowl. Manag. Aquat. Ecosyst

Watershed-induced limnological and microbial status in two oligotrophic Andean lakes exposed to the same climatic scenario – Alex Echeverría-Vega – Frontiers in Microbiology

** A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil) – Danyelle Toyama – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier – Xiukun Wu – Brazilian Journal of Microbiology

Food microbiology

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation – Haizhou Li – PLOS One

Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry – Ramya Sree Boddu – Microbial Biotechnology

Phages and viruses

[pre-print] THEA: A novel approach to gene identification in phage genomes – Katelyn McNair – bioRxiv

Bioinformatics

* [pdf] Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models – Aeriel Belk – Genes

COREMIC: a web-tool to search for a niche associated CORE MICrobiome – Richard R. Rodrigues – PeerJ

Techniques

Isotope fractionation in biogas allows direct microbial community stability monitoring in anaerobic digestion – Jo De Vrieze – Environmental Science & Technology

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples – Rishi Mahajan – Molecular Biology Reports

Microbes in the news

These Bacteria Eat Toxic Metal, ‘Poop’ Gold Nuggets – Live Science

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Earthquakes follow wastewater disposal patterns in southern Kansas

Ultra-processed foods ‘linked to cancer’

Promising cancer vaccine would use patient’s own cells to train the immune system

Does GMO corn increase crop yields? 21 years of data confirm it does—and provides substantial health benefits

Poor fitness linked to weaker brain fiber, higher dementia risk

Low cigarette consumption and risk of coronary heart disease and stroke: meta-analysis of 141 cohort studies in 55 study reports

Fewer Infants Died In States That Allowed Affordable Care Act

February 20, 2018

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In today’s digest you can read: about advantages of Atomic Force Microscopy in studying of oral microbiota in the paper by S. S. Salavadhi; about gut microbiome association with Type 1 diabetes in the paper by J.A. Mullaney; about influence of steroids on the gut microbiota in the review by M.J Tetel and about the ability of Synechococcus cyanobacteria to dynamically change their pigment content to match the ambient light color, in the paper by T. Grébert. These are of course just a few of many interesting articles today. Enjoy!

Events and jobs

MS graduate position: Amoeba microbiome, Conway, Arkansas, US

Research Fellow in Cell Biology – Microscopy, Warwick, UK

PhD Student, ROYAL NIOZ-TEXEL, Texel, the Netherlands

General microbiome

Review: A new piece in the microbiome puzzle – Lindsay J. Pike – Nature Reviews Microbiology

The importance of resolving biogeographic patterns of microbial microdiversity – Alexander B Chase – Microbiology Australia

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession – Rüdiger Ortiz-Álvarez – the ISME Journal

Pregnancy and early life

Infant formulae supplemented with prebiotics: Are they better than unsupplemented formulae? An updated systematic review – Agata Skórka – British Journal of Nutrition

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions – Patricia Iozzo – Frontiers in Nutrition

Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring – Hein M. Tun – JAMA Pediatrics

Multi-site human microbiome

A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms – Kiren Gill – International Urogynecology Journal

Oral microbiome

Atomic force microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis – Shyam Sunder Salavadhi – Journal of Indian Society of Periodontology

Human gut microbiome

Review: Steroids, stress and the gut microbiome-brain axis – M. J. Tetel – Journal of Neuroendocrinology

Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients – Zhao Fuya – Thyroid

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean Michael Kearney – bioRxiv

Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-cell Receptor-positive Cells and Pathogenesis of Cholestatic Liver Disease – Dana Tedesco – Gastroenterology

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota – Jane A. Mullaney – BMC Microbiome

Animal experiments

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes – Arianna Buccioni – BioMed Research International

Long-Term Treatment with Green Tea Polyphenols Modifies the Gut Microbiome of Female Sprague-Dawley Rats – Jincheng Wang – The Journal of Nutritional Biochemistry

Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor – Erica E. Alexeev – The Americn Journal of Pathology

Interrelations between the rumen microbiota and production, behavioral, rumen-fermentation, metabolic, and immunological attributes of dairy cows – M. Schären – Journal of Diary Science

Animal microbiome

Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kešnerová – PLOS One

Plant, root, and soil microbiome

Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection – Jana A. Hassan – Plant Direct

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.) – Ting Gao – Archives of Microbiology

The soil microbiome — from metagenomics to metaphenomics – Janet K Jansson – Current Opinion in Microbiology

Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source – Richard Paul Jacoby – Molecular Plant-Microbiome Interactions

A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing Nalidixic acid, a synthetic antibiotic – Nidhi Arora – Journal of Applied Microbiology

High microbial diversity promotes soil ecosystem functioning – Pierre-Alain Maron – Applied and Environmental Microbiology

Water and extremophile microbiome 

Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS – Christos Gougoulias – Environmental Microbiology Reports

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea – E. J. Fleming – Applied and Environmental Microbiology

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria – Théophile Grébert – PNAS

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning – Zhili He – mBio

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium – Yael Tzubari – the ISME Journal

Cryptophyta as major bacterivores in freshwater summer plankton – Vesna Grujcic – the ISME Journal

Phages and viruses

The impact of bacteriophages on phyllosphere bacterial abundance and composition – Norma M. Morella – Molecular Ecology

Microbes in the news 

Guts and gory: vampire bats need bacteria to digest blood

Using mutant bacteria to study how changes in membrane proteins affect cell functions

February 19, 2018

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Events and jobs

Research Technician I – University at Buffalo

General microbiome

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation – Ji Lu, bioRxiv

Oncologists tap the microbiome in bid to improve immunotherapy outcomes – Asher Mullard, Nature Reviews Drug Discovery

Nasal microbiome

Establishment of the Nasal Microbiota in the first 18 Months of Life – Correlation with Early Onset Rhinitis and Wheezing – Le Duc Huy Ta, Journal of Allergy and Clinical Immunology

The nasal microbiome in chronic rhinosinusitis: analyzing the effects of atopy and bacterial functional pathways in 111 patients – Mahboobeh Mahdavinia, Journal of Allergy and Clinical Immunology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela S. A. Goltsman, bioRxiv

Human vaginal microbiome

Microbiota changes impact on sexually transmitted infections and the development of pelvic inflammatory disease – Nathalie Loeper, Microbes and Infection

Human gut microbiome

Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis – Katsuyoshi Matsuoka, Digestive Diseases and Sciences

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review – Simon D. Goldenberg, Infectious Diseases and Therapy

Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections – Tiffany Wang, Open Forum Infectious Diseases

Fecal microbiota transplantation for severe complicated C. difficile colitis in a patient with acquired immunodeficiency syndrome – P. Martínez-Ayala, Revista de Gastroenterología de México

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD – Robert P Hirten, bioRxiv

The impact of a helminth-modified microbiome on host immunity – Tara P. Brosschot &
Lisa A. Reynolds, Mucosal Immunology

Depression and obesity: evidence of shared biological mechanisms – Yuri Milaneschi, Molecular Psychiatry

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation – Juliana Durack, Nature Communications

Roux-en-Y Gastric-Bypass and sleeve gastrectomy induces specific shifts of the gut microbiota without altering the metabolism of bile acids in the intestinal lumen – Henri Duboc, International Journal of Obesity

Effects of ewe’s milk yogurt (whole and semi-skimmed) and cow’s milk yogurt on inflammation markers and gut microbiota of subjects with borderline-high plasma cholesterol levels: a crossover study – Noemí Redondo, European Journal of Nutrition

Impact of food additives on the gut-brain axis – Mary K. Holder, Physiology & Behavior

Gut microbiota injury in allogeneic haematopoietic stem cell transplantation – Yusuke Shono, Nature Reviews Cancer

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

Gut Microbiomics—A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation – Amy Zhang, Journal of Heredity

Oral microbiome

Host defense against oral microbiota by bone-damaging T cells – Masayuki Tsukasaki, Nature Communications

Beyond Streptococcus mutans: clinical implications of the evolving dental caries aetiological paradigms and its associated microbiome – N. Philip, BDJ

Animal experiments

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages – Xiaofeng Zhao, Frontiers in Microbiology

Microbiota in fermented feed and swine gut – Cheng Wang, Applied Microbiology and Biotechnology

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract – Carl J. Yeoman, Scientific Reports

Animal microbiome

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure – Kieran A. Bates, Nature Communications

The effect of cadmium exposure on diversity of intestinal microbial community of Rana chensinensis tadpoles – Danyang Mu, Ecotoxicology and Environmental Safety

A new cell extraction method reveals hemolymph microbiome of three aquatic invertebrates – Xinxu Zhang, Applied Microbiology and Biotechnology

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition – Ting Jia, Scientific Reports

Plant, root, and soil microbiome

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health – Jia Zhao, PLOS One

Water and extremophile microbiome

Seasonal dynamics of tetracycline resistance gene transport in the Sumas River agricultural watershed of British Columbia, Canada – Patricia L. Keen, Science of The Total Environment

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde – Ana Paula Semedo-Aguiar, bioRxiv

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities – Adam C. Mumford, Applied and Environmental Microbiology

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation – Bing Li, Applied and Environmental Microbiology

Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river – Xianlei Cai, AMB Express

Food microbiology

Nitrogen removal enhancement using lactic acid fermentation products from food waste as external carbon sources: performance and microbial communities – Jialing Tang, Bioresource Technology

Probiotics/Prebiotics

Advances in Probiotic Regulation of Bone and Mineral Metabolism – Laura R. McCabe, Calcified Tissue International

Prebiotics as functional food ingredients preventing diet-related diseases – A. Florowska, Food and Function

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalisgastrointestinal in vitro resistance in petit-suisse – Marina Padilha, Food and Function

Bioinformatics

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses – Tomáš Větrovský, Bioinformatics

Techniques

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children – Nan Zhang, Chinese Medical Journal

February 16, 2018

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Happy Lunar New Year of the Dog!

Today’s Digest contains many news pieces, and also features a major paper on strain tracking post fecal microbiota transplantation, a review on antibacterial proteins shaping the intestinal microbiota, and a call for action to build communities for bioinformatics programming.

Jobs

Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

General microbiology

Book chapter: Agro-industrial Lignocellulosic Waste: An Alternative to Unravel the Future Bioenergy – Nidhi V. Maheshwari – Biofuels: Greenhouse Gas Mitigation and Global Warming

Review: Evolutionary Mechanisms Shaping the Maintenance of Antibiotic Resistance – Paulo Durão et al. – Trends in Microbiology

A single amino acid change in the response regulator PhoP acquired during Yersinia pestis evolution affects PhoP target gene transcription and polymyxin B susceptibility – Fukuto HS et al. – Journal of Bacteriology

Validated measurements of microbial loads on environmental surfaces in intensive care units before and after disinfecting cleaning – H. Frickmann et al. – Journal of Applied Microbiology

Human gut microbiome

Review: Proceedings of the 2017 ASPEN Research Workshop—Gastric Bypass: Role of the Gut – Ajay Kumar Jain et al. – Journal of Parenteral & Enteral Nutrition

A Phase 1 Study in Healthy Subjects to Assess the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of Multiple Oral Doses of DS-2969b, a Novel GyrB Inhibitor – Vandell AG et al. – Antimicrobial Agents and Chemotherapy

* Antibacterial Weapons: Targeted Destruction in the Microbiota – Benoit Chassaing and Eric Cascales – Trends in Microbiology

Perspective: How to train your microbiome to eat broccoli – Sam H. Au – Science Translational Medicine

* Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation – Christopher S. Smillie – Cell Host & Microbe

Press: Model of fecal transplantation predicts which bacteria will flourish – Medical Xpress

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn et al. – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo et al. – bioRxiv

Animal experiments

Extracellular cholesterol oxidase production by Streptomyces aegyptia, in vitro anticancer activities against rhabdomyosarcoma, breast cancer cell-lines and in vivo apoptosis – Noura El-Ahmady El-Naggar et al. – Scientific Reports

Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats – Carla Raquel Fontana et al. – Clinical and Experimental Dental Research

Animal microbiome

Preprint: Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria – Ines Silva Pais et al. – bioRxiv

Plant, root and soil microbiome

Removal of metals and their pools in plant in response to plant diversity in microcosms of floating constructed wetlands – Wenjuan Han et al. – Ecological Engineering

The Sesamum indicum rhizosphere associated bacterium: A source of Antifungal compound – Renu Chaudhary et al. – Current Topics in Medicinal Chemistry

Intensifying rotations increases soil carbon, fungi, and aggregation in semi-arid agroecosystems – Steven T. Rosenzweig et al. – Agriculture, Ecosystems & Environment

Impact of oxytetracycline and bacterial bioaugmentation on the efficiency and microbial community structure of a pesticide-degrading biomixture – Víctor Castro-Gutiérrez et al. – Environmental Science and Pollution Research

Indigenous endophytic seed bacteria promote seedling development and defend against fungal disease in browntop millet (Urochloa ramosa L.) – S.K. Verma and J.F. White – Journal of Applied Microbiology

Water and extremophile microbiome

Halophilic starch degrading bacteria isolated from Sambhar Lake, India, as potential anode catalyst in Microbial fuel cell: A promising process for saline water treatment – Ankisha Vijay et al. – Bioresource Technology

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges – Indu Shekhar Thakur et al. – Bioresource Technology

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro et al. – ISME

Neobodonids are dominant kinetoplastids in the global ocean – Olga Flegontova et al. – Environmental Microbiology

Food microbiology

Review: Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes – The way towards global harmonisation and data exchange – StefanieLüth et al. – Trends in Food Science & Technology

Phages and viruses

Book chapter: Tick-Borne Viruses and Host Skin Interface – Mária Kazimírová et al. – Skin and Arthropod Vectors

Preprint: The virome of Drosophila suzukii, an invasive pest of soft fruit – Nathan C Medd et al. – bioRxiv

Technology

Microfluidics-based liquid chromatography/mass spectrometry multiple reaction monitoring approach for the relative quantification of Burkholderia cenocepacia secreted virulence factors – Sofie Depluverez et al. – Rapid Communications in Mass Spectrometry

Microbes in the news

Surgeon sets new frontiers in battle against bacteria! – WBWire

The effect of antibacterials on the skin – Zoe Diana Draelo – Dermatology Times

Donor, Recipient Strain Analyses Offer Fecal Transplant Engraftment Clues – Genome Web

Australian Scientist Gets $1 Million to See if Probiotics Can Help Children with CF – Carolina Henriques – Cystic Fibrosis News Today

Do probiotics work? Answers to this and other gut-wrenching questions – Joanna Clay – USC News

Monitoring bacteria on whale skin – EurekAlert

Bacteria Hidden Under Our Feet May Be a New Weapon Against Superbugs – Kristin Houser – Futurism

Which probiotic is right for you? These are the exact bacteria strains to look for – Emily Laurence – Well and Good

How can we harness the power of bacteria-killing viruses? – Claire O’Connell – Sillcon Republic

Manipulating gut bacteria may cut obesity, diabetes risk – The Peninsula

Microbes on the market

Carbiotix launches world’s lowest cost microbiome test – Nathan Gray – Nutra Ingredients

Scientific Communication and Education

* Preprint: Building a local community of practice in scientific programming for Life Scientists – Sarah L.R. Stevens et al. – bioRxiv

 

February 15, 2018

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An especially interesting article on engineered bacteria in the treatment of colon cancer today: Chun Loong Ho and colleagues engineered an E. coli strain to bind to colon cancer cells and constitutively secrete an enzyme that can turn dietary derived glucosinolates (from cruciferous vegetables) into cancer fighting isothiocynates. Mice exposed to carcinogens and fed both the engineered bacteria and broccoli developed fewer and smaller colorectal tumors than exposed mice who were fed 1) neither bacteria or brocoli, 2) only bacteria, or 3) only broccoli.  Engineered probiotics anyone?

Also : A cultured community developed from wastewater that can reduce the greenhouse gas N2O to N2 and help mitigate global warming; the majority of Daphnia microbiomes are not passed from parent to offspring but absorbed from the surrounding environment; and the impacts of CRISPR-Cas9 selection pressure on phage evolution.

Events and jobs

Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

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General microbiome

Review: The genome, microbiome and evolutionary medicine – Robert C. Brunham – cmaj

Pregnancy and early life

Survey of Staphylococcus aureus in a general pediatric population and focus on isolates with three clinically relevant toxin-encoding genes – Anne Filleron – World Journal of Pediatrics

Human skin microbiome

Review: Impact of Skin Microbiome on Attractiveness to Arthropod Vectors and Pathogen Transmission – Niels O. Verhulst – Skin and Arthropod Vectors

Human gut microbiome

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers – Xi Mei Zhang – Biomedical and Environmental Sciences

The microbiome in chronic kidney disease patients undergoing hemodialysis and peritoneal dialysis – Liliana Simões-Silva – Pharmacological Research

Review: Intestinal Microbiome Shifts, Dysbiosis, Inflammation, and Non-alcoholic Fatty Liver Disease – Emma T. Saltzman – Frontiers in Microbiology

Does Low-Protein Diet Influence the Uremic Toxin Serum Levels From the Gut Microbiota in Nondialysis Chronic Kidney Disease Patients? – Ana Paula Black – Journal of Renal Nutrition

The Effect of Oligofructose-Enriched Inulin on Faecal Bacterial Counts and Microbiota-Associated Characteristics in Celiac Disease Children Following a Gluten-Free Diet: Results of a Randomized, Placebo-Controlled Trial – Natalia Drabińska – Nutrients

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo – bioRxiv

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Animal experiments

Influence of Eimeria falciformis Infection on Gut Microbiota and Metabolic Pathways in Mice – Guangping Huang – Infection and Immunity

The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance – Teizo Yoshimura – The Journal of Immunology

Animal microbiome

*Good Daphnia parents do not control the offspring microbiome – Angela E. Douglas – Journal of Animal Ecology

Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens – Sanjay Kumar – PLOSone

Review: The Microbial Zoo in the C. elegans Intestine: Bacteria, Fungi and Viruses – Hongbing Jiang – Viruses

Effects of parental care on resource allocation into immune defense and buccal microbiota in mouthbrooding cichlid fishes – Isabel S. Keller – Evolution

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats – Guido Bonthond – PeerJ

Effect of ginkgo extract supplementation on in vitro rumen fermentation and bacterial profiles under different dietary conditions – Seongjin Oh – Animal Science Journal

Review: Animal host–microbe interactions – Bethany J. Hoye – Journal of Animal Ecology

Plant, root, and soil microbiome

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium – Xin Wang – Journal of Soils and Sediments

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters – Emine Gozde Ozbayram – Microorganisms

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community – Felix Moronta-Barrios – Microorganisms

Water and extremophile microbiome

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro – The ISME Journal

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea – Jin Zhou – Microbial Ecology

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea – Yuzhi Wu – Extremophiles

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system – Caroline Souffreau – Environmental Microbiology

Chemical and Microbial Quality of Groundwater in Siloam Village, Implications to Human Health and Sources of Contamination – John Ogony Odiyo – International Journal of Environmental Research and Public Health

Microbial Ecology

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies – Mari Pent – Environmental Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Resistome

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes – Wenguang Xiong – BMC Microbiome

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Probiotics / prebiotics

Effect of VSL#3 Probiotic in a Patient with Glycogen Storage Disease Type Ia and Irritable Bowel Disease-like Disease – Miguel Carnero-Gregorio – Probiotics and Antimicrobial Proteins

New Insight into Biofilm Formation Ability, the Presence of Virulence Genes and Probiotic Potential of Enterococcus sp. Dairy Isolates – Nikola Popović – Frontiers in Microbiology

Effectiveness and Safety of a Probiotic-Mixture for the Treatment of Infantile Colic: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial with Fecal Real-Time PCR and NMR-Based Metabolomics Analysis – Maria Elisabetta Baldassarre – Nutrients

Fecal Microbiome Transplants

Long-term follow-up of the effects of fecal microbiota transplantation in combination with soluble dietary fiber as a therapeutic regimen in slow transit constipation – Xueying Zhang – Science China Life Sciences

Bioinformatics

Identification of fungi in shotgun metagenomics datasets – Paul D. Donovan – PLOSone

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies – Ahmed A. Metwally – BMC Microbiome

Biotechnology

*Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention – Chun Loong Ho – Nature Biomedical Engineering

*Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9 – Pan Tao – Science Advances

Waste and Pollution

*Life on N2O: deciphering the ecophysiology of N2O respiring bacterial communities in a continuous culture – Monica Conthe – The ISME Journal

Metagenomic analysis of microbial community and function involved in cd-contaminated soil – Gang Feng – BMC Microbiology

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Microbes in the news

Humpback microbiome linked to seasonal, environmental changes – Phys.org

 

February 12, 2018

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A rich Digest to start your work week. Highlights include a review in Lancet cautionary about precision nutrition, an NIH metagenome FTP site, and a sampling of songbirds that reveals high prevalence of antibiotic resistant bacteria.

Events

Intellectual Property x The Microbiome – SF Bay Area Microbiome Meetup

General microbiology

Expanding our Understanding of the Role of the Microbiome in Health and Disease – Rob Knight – Archives of Medical Research

* NIH Metagnome FTP site

* The Ecosystem Services of Animal Microbiomes – E.A. McKenney et al. – Molecular Ecology

Preprint: Experimental Evolution of Cell Shape in Bacteria – Paul Richard Yulo et al. – bioRxiv

Human skin microbiome

In vitro: Yeasts from skin colonization are able to cross the acellular dermal matrix – Isabele Carrilho Jarros et al. – Microbial Pathogenesis

Human vaginal microbiome

Review: Immunology of the Uterine and Vaginal Mucosae – Jordan Z. Zhou et al. – Trends in Immunology

Human gut microbiome

The Role of Diet in the Treatment of Irritable Bowel Syndrome : A Systematic Review – Rajdeep Singh et al. – Gastroenterology Clinics of North America

Review: Metabolic Surgery : Weight Loss, Diabetes, and Beyond – Manan Pareek et al. – Journal of the American College of Cardiology

Review: Environmental Noise and the Cardiovascular System – Thomas Münzel et al. – Journal of the American College of Cardiology

The effects of synbiotic supplementation on insulin resistance/sensitivity, lipid profile and total antioxidant capacity in women with gestational diabetes mellitus: a randomized double blind placebo controlled clinical trial – Zohoor Nabhani et al. – Diabetes Research and Clinical Practice

* Precision nutrition for prevention and management of type 2 diabetes – Dong D Wang and Frank B Hu – The Lancet Diabetes & Endocrinology

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids – Cholsoon Jang et al. – Cell Metabolism

Review: Therapeutic implications of the gastrointestinal microbiome – Purna C Kayshap and Eamonn MM Quigley – Current Opinion in Pharmacology

Risk factors for Clostridium difficile infection in intestinal transplant recipients during the first year post transplant – Luis Guzman et al. – Transplant Infectious Disease

Metabolomics

Review: Advances in computational metabolomics and databases deepen the understanding of metabolisms – Hiroshi Tsugawa – Current Opinion in Biotechnology

Animal experiments

Rat: Onion quercetin monoglycosides alter microbial activity and increase antioxidant capacity – Katarzyna Grzelak-Błaszczyk et al. – The Journal of Nutritional Biochemistry

Preview: Cultivating a Relationship with Gut Bacteria – Catherine E. Schretter and Sarkis K. Mazmanian – Cell Metabolism

Effect of two seaweed polysaccharides on intestinal microbiota in mice evaluated by illumina PE250 sequencing – Zhongshan Zhang et al. – International Journal of Biological Macromolecules

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice – Li Wang et al. – Journal of Food Science

Animal microbiome

* Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments – Diana L. Carter et al. – Science of The Total Environment

Effects of chlorogenic acids-enriched extract from Eucommia ulmoides leaves on growth performance, stress response, antioxidant status and meat quality of lambs subjected or not to transport stress – H.W. Liu et al. – Animal Feed Science and Technology

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets – M. Lorenzo de Arriba et al. – The Veterinary Journal

Horse: The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins – L.E. Peachey et al. – International Journal for Parasitology

The effects singular or combined administration of fermentable fiber and probiotic on mucosal immune parameters, digestive enzyme activity, gut microbiota and growth performance of Caspian white fish (Rutilus frisii kutum) fingerlings – Ali Taheri Mirghaed et al. – Fish & Shellfish Immunology

Diagnostics and Treatments in Chronic Diarrhea and Weight Loss in Horses – Olimpo Oliver-Espinosa – Veterinary Clinics: Equine Practice

Plant, root and soil microbiome

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community – Luciana D’Acunto et al. – Agriculture, Ecosystems & Environment

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome – Franck Stefani et al. – Scientific Reports

Water and extremophile microbiome

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis – Renxin Zhao et al. – Water Research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH – Raquel Quatrini and D Barrie Johnson – Current Opinion in Microbiology

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control – Pan Ji et al. – Microbiome

Food microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts et al. – Food Microbiology

Modelling the growth of Listeria monocytogenes in Mediterranean fish species from aquaculture production – Araceli Bolívar et al. – International Journal of Food Microbiology

Prebiotic in fruit juice: processing challenges, advances, and perspectives – Thatyane Vidal Fonteles and Sueli Rodrigues – Current Opinion in Food Science

Technology

Multi-omics approach to elucidate the gut microbiota activity. Metaproteomics and metagenomics connection – Maria Guirro et al. – Electrophoresis

Microbes in the news

Can Your Gut Protect You Against Cancer? – Michelle Schoffro Cook – Care2

Millions of Mosquitoes to Be Released in Florida for Good Cause – Inside Edition

Using Special UV Light in Public Spaces Could Kill Flu Viruses, Bacteria – Jakob Nielson – Apex Tribune

 

February 10, 2018

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Check out the Environmental Microbiology * The New Microscopy themed issue from
Events and jobs from Current Opinion in Microbiology! Other highlights include bioinformatic and wet lab techniques, including fecal water preparation for metabolomics and SMRT, as well as a new version of Kraken with k-mer coverage (KrakenHLL)!

Jobs and events
PhD scholarships in Microbiome Synthetic Biology – Danmarks Tekniske Universitet

Human respiratory microbiome
Dysbiosis of inferior turbinate microbiota is associated with high total IgE levels in allergic rhinitis patients – Dong-Wook Hyun – Infection and Immunity

Human skin microbiome
Epidermal lipid composition, barrier integrity and eczematous inflammation are associated with skin microbiome configuration  – Hansjörg Baurecht – Journal of Allergy and Clinical Immunology

Human oral microbiome
Presence of archaea and selected bacteria in infected root canal system – Ewa Brzezińska-Błaszczyk – Canadian Journal of Microbiology

Human gut microbiome
Review: Understanding the Microbiome: Emerging Biomarkers for Exploiting the Microbiota for Personalized Medicine against Cancer – Meenakshi Rajpoot – Seminars in Cancer Biology

Animal microbiome
Exploring virulence of new and less studied species of Metarhizium spp. from Brazil for two-spotted spider mite control – Thiago Castro – Experimental and Applied Acarology

Plant, root, and soil microbiome
Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum – Myung Hwan Lee – Journal of Biotechnology

Effects of rhizosphere interactions of grass interspecies on the soil microbial properties during the natural succession in the Loess Plateau – Chao Zhang – European Journal of Soil Biology

Degradation of polycyclic aromatic hydrocarbons in soil mesocosms by microbial/plant bioaugmentation: Performance and mechanism – Fan-xin Kong – Chemosphere

The influence of tree species on soil properties and microbial communities following afforestation of abandoned land in northeast China – Na Yang – European Journal of Soil Biology

Diversity of the bacterial microbiome in the roots of four Saccharum species: S. spontaneum, S. robustum, S. barberi, and S. officinarum – Meng Dong – Frontiers in Microbiology

Water and extremophile microbiome
Current Opinion in Microbiology has a themed issue called Environmental Microbiology * The New Microscopy with many articles of interest, some including:

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea – Jiyoung Lee – Ocean Science Journal

The effect of temperature on the microbial communities of peak biogas production in batch biogas reactors – Guangliang Tian – Renewable Energy

The Effects of Antibiotics on Microbial Community Composition in an Estuary Reservoir during Spring and Summer Seasons – Zheng Xu – Water

Built environment
Review: Advances in concrete materials for sewer systems affected by microbial induced concrete corrosion: A review – Cyrill Grengg – Water Research

Microbial interactions
Comparative study on nutrient depletion-induced lipidome adaptations in Staphylococcus haemolyticus and Staphylococcus epidermidis – Yu Luo – Scientific Reports

The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp – Hung-Yu Liao – Journal of Hazardous Materials

Probiotics / prebiotics / antibiotics
Evolutionary trajectories to amoxicillin-clavulanic acid resistance in Escherichia coli are affected by growth media – Alasdair TM Hubbard – biorXiv

Bioinformatics
ComPAS: Community Preserving Sampling for Streaming Graphs – Sandipan Sikdar – arXiv

KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts – Florian P Breitwieser – bioRxiv

Techniques
Efficient non-cytotoxic fluorescent staining of halophiles – Ivan Maslov – Scientific Reports

Metabonomic Evaluation of Fecal Water Preparation Methods: The Effects of Ultracentrifugation – Sandi Yen – Current Metabolomics

SMRT-Cappable-seq reveals complex operon variants in bacteria – Bo Yan – bioRxiv

Microbes in the news
Are Hand Dryers Actually Full of Bacteria? A Viral Photo Doesn’t Tell the Whole Story – Maggie Astor – New York Times

Bacteria-infected mosquitoes might be good thing for Miami – Jennifer Kay – ABC News
Miami releases bacteria-infected mosquitoes to help fight Zika virus – KGUN9

UV Light That Is Safe for Humans but Bad for Bacteria and Viruses – GEN News

Stanford Global Health awards seed funding to nine projects – Stanford Medicine News Center

Microbes on the market
Seres Therapeutics Inc. (MCRB) Settles Into New 52-Week Low on February 08 Session – Equities.com

Tiffany’s other picks
Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain – Sylvie Janssens – mSystems

 

February 9, 2018

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Transcriptomics in wildlife, skin microbiota, phages and a lot more for today’s digest!

Events and jobs

MEDICAL LABORATORY TECHNOLOGIST – Florida Hospital – Orlando, USA

Assistant Professor in Metagenomics and Bioinformatics, tenure-track position – Kansas State University – Manhattan, USA

General microbiome

Review: Linking the Gut Microbiota to Bone Health in Anorexia Nervosa – NC Aurigemma – Current Osteoporosis Reports

Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System – AE Kates – Infection Control & Hospital Epidemiology

Tumour-associated and non-tumour-associated microbiota: Addendum – B Flemer – Gut Microbes

Preprint: An Escherichia coli nitrogen starvation response is important for mutualistic coexistence with Rhodopseudomonas palustris – AL McCully – bioRxiv

 

Human skin microbiome

Nature-oriented daycare diversifies skin microbiota in children – no robust association with allergies. – J Lehtimäki – Pediatric Allergy and Immunology

Epidermal lipid composition, barrier integrity and eczematous inflammation are associated with skin microbiome configuration – H Baurecht – The Journal of Allergy & Clinical Immunology

 

Human gut microbiome

Review: Pathophysiology of Functional Gastrointestinal Disorders: A Holistic Overview – G Holtmann – Karger

Preprint:  Stronger connectivity of the resident gut microbiome lends resistance to invading bacteria – CM Herren – bioRxiv

Animal experiments 

Enteric Immunity : Happy Gut, Healthy Animal – CCL Chase – Veterinary Clinics of North America: Food Animal Practice

Influence of changes in the intestinal microflora on the immune function in mice – S Kishida – Journal of Veterinary Medical Science

In Vivo Assessment of Resistant Starch Degradation by the Caecal Microbiota of Mice Using RNA-Based Stable Isotope Probing—A Proof-of-Principle Study – E Herrmann – Nutrients

Animal microbiome 

A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations – LJ Campbell – Molecular Ecology

The bacterial community associated with the sheep gastrointestinal nematode parasite Haemonchus contortus – G Sinnathamby – PLoS One

Mucus glycosylation and immunity, and bacterial microbiota associated to the skin of experimentally ulcered gilthead seabream (Sparus aurata). – ST Tapia-Paniagua – Fish & Shellfish Immunology

Modulation of gut microbiota by dietary supplementation with tuna oil and algae oil alleviates the effects of D-galactose-induced ageing – H Zhang – Applied Microbiology and Biotechnology

Probiotic treatment during neonatal age provides optimal protection against experimental asthma through the modulation of microbiota and T cells: Neonatal exposure to probiotics prevents asthma – CFCG Nunes – International Immunology

Plant, root and soil microbiome

Activating biochar by manipulating the bacterial and fungal microbiome through pre-conditioning. – AK Jaiswal – New Phytologist

 

Food microbiology

Growth potential of Listeria monocytogenes in twelve different types of RTE salads: impact of food matrix, storage temperature and shelf life – M Ziegler – bioRxiv

Phages and viruses

Lysogeny is prevalent and widely distributed in the murine gut microbiota – M-S Kim – The ISME Journal

Preprint: A T7 phage factor required for managing RpoS in Escherichia coli  – A Tabib-Salazar – bioRxiv

Preprint: Genotypic and phenotypic diversity within the neonatal HSV-2 population – LN Akhtar – bioRxiv

Techniques

Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis – R Khan – PLoS One

Microbes in the news

Reality check: Are hand dryers in public bathrooms full of bacteria and fungi? – Global News

Consider skipping orange juice in the morning  – Channel NewsAsia

‘Dozens of bacteria:’ After 2 days, snow is no longer safe to eat, study reveals  – Fox6 Now

Termites’ unique gut ‘factory’ key to global domination – Phys.org

Bacteria persist as stowaways – Innovations Report

Genomic Analysis Finds Hospital Plumbing Harbors Antibiotic Resistant Bacteria – Genome Web

Skin microbiome announces agenda – Cosmeticsdesign.com

TIPS ON BECOMING A CLINICAL MICROBIOLOGY LABORATORY DIRECTOR – ASM