November 2, 2017

 

Second day of November we have quite a few job offers, nice set of microbiome news, two reviews in “gut microbiome” sector. Two (personal) highlights today would be the Thomas J. Browning’s  paper about phytoplankon nutrient co-limitation and Luke R. Thompson’s paper about The Earth Microbiome Project. Enjoy…

Events and jobs

Research Technician, University of York, UK

Postdoctoral Researcher – Molecular Microbiologist, University of Oxford, Oxford, UK

Bioinformatics Postdoc, Max Planck Institute for Infection Biology, Berlin, Germany

Microbiology Postdoctoral Scholar,  The University of California, Berkeley, California, US

Bioinformatics Analyst, Ares Genetics GmbH, Vienna, Austria

Assistant Professor of Microbiology, The University of Alabama in Huntsville, Huntsville, Alabama, US

Tenure-track Assistant Professor of Microbiology, Miami University, Miami, Ohio, US

Tenure Track Assistant Professor in Microbiology, The University of British Columbia, Vancouver,  Canada

General microbiome

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU – Theresa Hoelscher – bioRxiv

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival – Matthew Z. Tien – bioRxiv

Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility – Anthony Piro – bioRxiv

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – Robert M Cooper – eLIFE

A communal catalogue reveals Earth’s multiscale microbial diversity Luke R. Thompson – Nature

Human gut microbiome

Rapid Assessment of Microbiota Changes in Individuals with Autism Spectrum Disorder Using Bacteria-derived Membrane Vesicles in Urine – Yunjin Lee – Experimental Neurobiology

Review: Dietary and microbial metabolites in the regulation of host immunity – Jun Kunisawa – frontiers in Microbiology

Review: Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics – Mingqian He – Cell & Bioscience

Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study – Tomomi Minato – PLOS One

Animal experiments

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – Kalie F. Beckers – PLOS One

Cecal Microbiota in Broilers Fed with Prebiotics – Dany Mesa – Frontiers in Genetics

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice – Nobuhiro Nakamoto – Cell Reports

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – Majdi Masarwi – The Journal of Nutritional Biochemistry

Animal microbiome 
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella – Valeria Mereghetti -Insect Science

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon – Evan P. Starr – bioRxiv

Water and extremophile microbiome 

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria) – Jeffrey R. Johansen – PLOS One

Study of Microbial diversity in Ganga river water sample by the use of Metagenomics technique – Jamilah Ali Ahmed Zaed – Journal of Pharmacognosy and Phytochemistry

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – Miye Kwon – Environmental Microbiology

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(VI) in groundwater – Dianxin Li – RSC Advances

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone – Steven J. Hallam – Scientific Data

Synechococcus plasticity under environmental changes – Cristiana Callieri – FEMS Microbiology Letters

Nutrient co-limitation at the boundary of an oceanic gyre – Thomas J. Browning -Nature

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake – Junyi Zhang – Science of The Total Environment

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions – Dexin Fang – Bioresource Technology

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus — Jessika Füssel – Science Advances

Food microbiology

Characterization of Enterococcal Community Isolated from an Artisan Istrian Raw Milk Cheese: Biotechnological and Safety Aspects – Mirna Mrkonjic Fuka – Food Technology and Biotechnology

Probiotics / prebiotics
Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? – Yolande Bertin – PLOS One

Bioinformatics

MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota – Evgenii I Olekhnovich – Bioinformatics

Techniques

Quantification of diverse virus populations in the environment using the polony method – Nava Baran – Nature Microbiology

Microbes in the news 

Microbiome Link with Colorectal Cancer Drug Toxicity Points to Predictive Tests and Prevention – Genetic Engineering and Biotechnology News

Gut bacteria composition could predict toxicity of chemotherapy drugs in cancer patients – News Medical

Versatile marine bacteria could be an influence on global warming, scientists discover – Science Daily

By 2100, climate change could alter key microbial interactions in the ocean  – Phys Org

Microbes on the market 

Symbiotix Biotherapies Receives $5 Million in Institutional Financing to Advance its Development of Molecular Therapeutics that Modulate Regulatory T Cell Activity

Tina’s (non)microbiology picks 

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology – Amy G. Briggs – Journal of Microbiology & Biology Education

Announcing the winner of this year’s ‘Dance Your Ph.D.’ contest – John Bohannon – Science

 

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October 2, 2017

This Monday we have quite short digest with interesting review from K. Rosenthal about microbial single cell analysis,  T. K. Hattenrath-Lehmann tells us about microbes associated with harmful algal blooms while G. Chen demonstrates mutualistic interaction between bacteria in anaerobic mixed culture. Enjoy your reading.

Events and jobs

Tenure Track Faculty Position in Microbial Systems/Synthetic Biology, Chestnut Hill, Massachusetts

General microbiome

Review: Beyond the bulk: disclosing the life of single microbial cells  – Katrin Rosenthal – FEMS Microbiology Reviews

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture – Gao Chen – Environmental Microbiology

Human skin microbiome

Antisepsis of the skin before spinal surgery with povidone iodine-alcohol followed by chlorhexidine gluconate-alcohol versus povidone iodine-alcohol applied twice for the prevention of contamination of the wound by bacteria – S. Patrick – The Bone & Joint Journal

Human nearly-sterile sites 

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation – E Xiao – Stem Cell Research & Therapy

Human gut microbiome

Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells – Cláudia Mara Lara Melo Coutinho –  Microbial Pathogenesis

Animal experiments

Changes in the microbiota cause genetically modified Anopheles to spread in a population – Andrew Pike – Science

Plant, root, and soil microbiome

Impact of spatial organization on a novel auxotrophic interaction among soil microbes – Xue Jiang – bioRxiv

Novel archaeal thermostable cellulases from an oil reservoir metagenome – Anna Lewin – AMB Express

Periodically spilled-oil input as a trigger to stimulate the development of hydrocarbon-degrading consortia in a beach ecosystem – Kai Zhang – Scientific Reports

Water and extremophile microbiome 

Identification of unique microbiomes associated with harmful algal blooms caused by Alexandrium fundyense and Dinophysis acuminata -Theresa K.Hattenrath-Lehmann – Harmful Algae

Metagenomic insights into zooplankton-associated bacterial communities – Daniele De Corte – Environmental Microbiology

Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community – Anyi Hu – Environmental Microbiology

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars – Alexandra Pontefract – Frontiers in Microbiology

Bioinformatics

SAMSA2: A standalone metatranscriptome analysis pipeline – Samuel T. Westreich – bioRxiv

Microbes in the news 

Oral sex spreading unstoppable bacteria

 

September 15, 2017

Events and jobs

 
Assistant or Associate Professor – Microbiology/Infectious Disease, Farmington, US

 
General microbiome

 
Review: Human microbiota in aging and infection: A review – Elisavet Stavropoulou  – Critical Reviews in Food Science and Nutrition

 

Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis – Erin P. Price – PLOS

 
Pregnancy and early life

 
The relation between cesarean birth and child cognitive development – Cain Polidano – Scientific Reports

 

Simultaneously Monitoring Immune Response and Microbial Infections During Pregnancy through Plasma cfRNA Sequencing – Wenying Pan – Clinical Chemistry

 
Human respiratory microbiome

 
Oral microbiomeTooth Be Told, Genetics Influences Oral Microbiome – Emily R. Davenport – Cell Host & Microbe

 
Host Genetic Control of the Oral Microbiome in Health and Disease – Andres Gomez – Cell Host & Microbe

 

Human nearly-sterile sites 

 

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing – Beili Sun – BioMed Research International

 

Review: Microbiota-Derived Uremic Retention Solutes: Perpetrators of Altered Nonrenal Drug Clearance in Kidney Disease – Alexander J. Prokopienko – Expert Review of Clinical Pharmacology

 

Human gut microbiome

 
Microbial metabolites as mimickers of human molecules – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

 
The intestinal microbiota regulates body composition through NFIL3 and the circadian clock – Yuhao Wang – Science

 
The Landscape of Type VI Secretion across Human Gut Microbiomes Reveals Its Role in Community Composition – Adrian J. Verster – Cell Host & Microbe

 
Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity – Annelies Geirnaert – Scientific Reports

 
Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota – Eric J. de Muinck –  mSystems
Review: Microbiota and neurodegenerative diseases – Moira Marizzonip – Current Opinion in Neurology

 
Effect of cytomegalovirus and Epstein–Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals – Gianella Sara – AIDS

 
Systematic Review and Meta-analysis: Fecal Microbiota Transplantation for Treatment of Active Ulcerative Colitis – Narula Neeraj – Inflammatory Bowel Diseases

 
Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka – FEMS Microbiology Ecology

 
Quantity and source of dietary protein influence metabolite production by gut microbiota and rectal mucosa gene expression: a randomized, parallel, double-blind trial in overweight humans – Martin Beaumont – The American Journal of Clinical Nutrition
Analysis of Mucosa-Associated Microbiota in Colorectal Cancer – Kehan Xu – Medical Science Monitor

 
Animal experiments 

 
Short-term dietary methionine supplementation affects one-carbon metabolism and DNA methylation in the mouse gut and leads to altered microbiome profiles, barrier function, gene expression and histomorphology – Isabelle R. Miousse – Genes & Nutrition

 
Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – mSystems

 
Development of a Stable Lung Microbiome in Healthy Neonatal Mice – Matea Kostric – Microbial Ecology

 

Animal microbiome

 

Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas – Qi Wu  – Proceedings of the Royal Society of London B

 
Plant, root, and soil microbiome

 
Soil microbial community responses to acid exposure and neutralization treatment – Doyun Shin – Journal of Environmental Management

 
Spatial patterns of hypolithic cyanobacterial diversity in Northern Australia –  Keith Christian – Ecology & Evolution

 

Food microbiology

 

Short-Term Intake of a Fructose-, Fat- and Cholesterol-Rich Diet Causes Hepatic Steatosis in Mice: Effect of Antibiotic Treatment – Annette Brandt – Nutrients

 
Overview of craft brewing specificities and potentially associated microbiota – Lindsey Rodhouse – Critical Reviews in Food Science and Nutrition

 

Probiotics / prebiotics
Isolation of probiotic piliated Lactobacillus rhamnosus strains from human faecal microbiota using SpaAantiserum-based colony immunoblotting – Zhen-quan Yang – Journal of Microbiology and Biotechnology

 

Phages and viruses
CRISPR-based Herd Immunity Limits Phage Epidemics in Bacterial Populations – Pavel Payne – bioRxiv

 
Bioinformatics
A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome – Imane Allali – BMC Microbiology

 
Minimizing mixing intensity to improve the performance of rice straw anaerobic digestion via enhanced development of microbe-substrate aggregates – Moonkyung Kim – Bioresource Technology

 
Long term effects of cerium dioxide nanoparticles on the nitrogen removal, micro-environment and community dynamics of a sequencing batch biofilm reactor – Yi Xu – Bioresource Technology

 

Microbes in the news 
NIPGR scientists identify bacteria that can devour fungi

 
Are Genes to Blame for Cavity-causing Bacteria?

 
Microbes on the market (news about biotech companies)

 
Newly Launched CoreBiome Touts Microbiome ‘Profiling’ Services

 
Inventor converts waste plastics to fertilizer, fuel

 
Science, publishing, and career

 
The hundred most-cited publications in microbiota of diabetes research: A bibliometric analysis – Jiaxing Tian – Medicine

August 31, 2017

Today we have a lot of interesting job offers, a lot of news, many papers from Nature’s Scientific Reports and several reviews from Immunological Reviews and to mention each time more and more papers dealing with wastewater treatments. Enjoy your (still) summer microbiome reading.

Events and jobs

Laboratory Manager (Microbiology), Sydney, Australia

Algae Technician, MBD Energy Limited, Townsville 

PhD position: Synthetic Microbiology/Biotechnology, Germany

PhD position (m/f) in the field of microbiota-host interaction in laying hens, Germany

PhD position in the field of microbial ecology of the fowl gastrointestinal tract,  Germany

Post-Doctoral Research Associate, King’s College London , UK

Synthetic Biologist / Geneticist: Ginkgo Bioworks, Boston, MA

General microbiome

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA – Mark Kowarsky – PNAS

Maintenance of microbial cooperation mediated by public goods in single and multiple traits scenarios – Özhan Özkaya – Journal of Bacteriology

Pregnancy and early life

The oral microbiome and adverse pregnancy outcomes – Charles M Cobb – International Journal of Women’s Health

Human respiratory microbiome

The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci – Sanjay K. Shukla –  PLOS One

Sphenoid sinus microbiota in pituitary apoplexy: a preliminary study – Gavin J. Humphreys – Pituitary

Oral microbiology

Review: Studying the human oral microbiome: challenges and the evolution of solutions – Angela ML Benn – Australian Dental Journal

Human vaginal microbiome

The human vaginal microbial community – Mario Vaneechoutte – Research in Microbiology

Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women – Benjamin J. Callahan – PNAS

Comparison of vaginal microbiota sampling techniques: cytobrush versus swab – Anita Mitra – Scientific Reports

Human nearly-sterile sites 

Dominance of ST131 Escherichia coli carrying blaCTX-M in patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial –  Patrick Harris – bioRxiv

Temporal Stability and Composition of the Ocular Surface Microbiome – Jerome Ozkan – Scientific Reports

Human gut microbiome

Review:Interactions between bile salts, gut microbiota, and hepatic innate immunity – Kristin Schubert – Immunological Reviews

Review:Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes – Thomas Clavel – Immunological Reviews

Review: Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease – Joseph M. Pickard – Immunological Reviews

Gut microbiota and chronic kidney disease: implications for novel mechanistic insights and therapeutic strategies – Wei Pan –  International Urology and Nephrology

Ecophylogenetics Reveals the Evolutionary Associations between Mammals and their Gut Microbiota – Christopher Andrew Gaulke -bioRxiv

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses – Leonardo Mancabelli –  Scientific Reports

Influence of gut microbiota on neuropsychiatric disorders – María Carmen Cenit – World Journal of Gastroenterology

Fecal microbiota transplantation for Clostridium difficile infection in patients with ileal pouches – Nan Lan – Gastroenterology Report

The Intestinal Microbiome in Infectious Diseases: The Clinical Relevance of a Rapidly Emerging Field – Vanessa C Harris – Open Forum Infectious Diseases

A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota – Ashok K. Sharma – Scientific Reports

Animal experiments

Metagenomic Analysis of Cecal Microbiome Identified Microbiota and Functional Capacities Associated with Feed Efficiency in Landrace Finishing Pigs – Zhen Tan – Frontiers in Microbiology

Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract – Janina A. Krumbeck – Environmental Microbiology

Animal microbiome

High Spatial and Temporal Variations of Microbial Community along the Southern Catfish Gastrointestinal Tract: Insights into Dynamic Food Digestion – Zhimin Zhang – Frontiers in Microbiology

Unraveling the gut microbiome of the long-lived naked mole-rat – Tewodros Debebe – Scientific Reports

Plant, root, and soil microbiome

Effects of cationic surfactant on the bioaccumulation of polycyclic aromatic hydrocarbons in rice and the soil microbial community structure – Ni Ni – RSC Advances

The impact of adsorption on the exposure assessment of Bacillus thuringiensis in the water-sediment system: a mathematical model approach – Stefano Cervelli – Biology and Fertility of Soils

Phylogenetic diversity and antagonistic traits of root and rhizosphere pseudomonads of a bean from Iran for controlling Rhizoctonia solani – Vahid Keshavarz-Tohid – Research in Microbiology

Petroleum Contamination and Plant Identity Influence Soil and Root Microbial Communities While AMF Spores Retrieved from the Same Plants Possess Markedly Different Communities – Bachir Iffis – Frontiers in Microbiology

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Microbial communities with distinct denitrification potential in spruce and beech soils differing in nitrate leaching – Jiří Bárta – Scientific Reports

The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China – Wei Z – PLOS One

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence – Y. Colin – Scientific Reports

Water and extremophile microbiome 

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping – Katherine R. M. Mackey – Frontiers in Microbiology

Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland – Wenkai Yan – Frontiers in Microbiology

Microbial community structure and diversity within hypersaline Keke Salt Lake environments – Rui Han – Canadian Journal of Microbiology

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities – Bennett S. Lambert –  Nature Microbiology

Anaerobic methanotrophic communities thrive in deep submarine permafrost – Matthias Winkel – bioRxiv

Microbial communities in peatlands along a chronosequence on the Sanjiang Plain, China – Xue Zhou – Scientific Reports

Microbial communities in marine sediments modify success of an invasive macrophyte – Paul E. Gribben – Scientific Reports

Built environment 

Novosphingobium clariflavum sp. nov., isolated from a household product plant –  Xin Zhang – International Journal of Systematic and Evolutionary Microbiology

Probiotics / prebiotics

Bifidobacterium longum W11: an antibiotic-resistant probiotic – Francesco Di Pierro – Nutrafoods

Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice – Hongqi Chen – Molecular Medicine Reports

Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Probiotics administration following sleeve gastrectomy surgery: A randomized double-blind trial – S Sherf-Dagan – International Journal of Obesity

Phages and viruses

Infection with purified Piscine orthoreovirus demonstrates a causal relationship with heart and skeletal muscle inflammation in Atlantic salmon – Øystein Wessel  – PLOS One

HPeV-3 predominated among Parechovirus A positive infants in the summer of 2013-2014 in Queensland, Australia – Donna M. McNeale – bioRxiv

Review: A bacteriophages journey through the human body – Jeremy J. Barr – Immunological Reviews

Mouse hepatitis virus nsp14 exoribonuclease activity is required for resistance to innate immunity – James Brett Case – bioRxiv

Bioinformatics

microPop: Modelling microbial populations and communities in R – Helen Kettle – Methods in Ecology and Evolution

Biotechnology

Biodegradation of mono-, di- and trifluoroacetate by microbial cultures with different origins – Diogo A.M. Alexandrino – New Biotechnology

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community – Man Zhou – Biotechnology for Biofuels

Wastewater microbiology

Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment – Hebin Liang – RSC Advances

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment – Yaohui Bai – Applied Microbiology and Biotechnology

Techniques

A Comparison of Methods to Analyze Aquatic Heterotrophic Flagellates of Different Taxonomic Groups – Alexandra Jeuck – Protist

Fast and Simple Tool for the Quantification of Biofilm-Embedded Cells Sub-Populations From Fluorescent Microscopic Images – Mikhail Bogachev – bioRxiv

Microbes in the news 

Gut bacteria that “talk” to human cells may lead to new treatments

Gut Microbiome Differences in REM Sleep Behavior Disorder, Parkinson’s, and Healthy Controls

Scientists Made Music From the Human Microbiome, and It’s Seriously Cool

Over 50% of Bacteria and Viruses inside Human Body are Unknown to Science

August 25, 2017

Highlight of the day goes to Anna Karenina principle on microbiomes by J.R. Zaneveld as a Perspective in Nature Microbiology: “When healthy our microbiomes look alike, but when stressed each one of us has our own microbial snowflake”.

Events and jobs

Food Microbiology Microscopist II, EMSL Analytical, Inc. ,Cinnaminson, NJ 

Research Associate, University of Bristol – School of Biochemistry

General microbiome

Perspectives: Stress and stability: applying the Anna Karenina principle to animal microbiomes – Jesse R. Zaneveld – Nature Microbiology

Sugar metabolism of the first thermophilic Planctomycetes Thermogutta terrifontis: comparative genomic and transcriptomic approache – Alexander Elcheninov – bioRxiv

Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species – Evgeni Bolotin –  Frontiers in Microbiology

Pregnancy and early life

Early gut mycobiota and mother-offspring transfer – Kasper Schei -Microbiome

Oral Microbiology

Genetic influences on the human oral microbiome – Brittany A. Demmitt – BMC Genomics

 

Human gut microbiome

Beyond gut feelings: how the gut microbiota regulates blood pressure – Francine Z. Marques – Nature Reviews Cardiology

Animal microbiome 

Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone – Stephanie L. Bond – BMC Microbiology

Plant, root, and soil microbiome

Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations – Zainab Abdulrahman Beiruti – Environmental Microbiology

Water and extremophile microbiome

Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary – Brett G. Enos – bioRxiv

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments – Nina Dombrowski –  Microbiome

Prey range and genome evolution of Halobacteriovorax marinus predatory bacteria from an estuary – Brett G. Enos – bioRxiv

Bacteria-induced mixing in natural waters – T. Sommer – Geophysical Research Letters

Food microbiology

Unraveling the correlation between microbiota succession and metabolite changes in traditional Shanxi aged vinegar – Zhiqiang Nie – Scientific Reports

Microbes in the news

Space travel microbes turn urine into polymers

Is The Secret To A Healthier Microbiome Hidden In The Hadza Diet?

IBM: Your Computer Can Help Scientists Study Connection Between Body Bacteria and Autoimmune Diseases

 

August 21, 2017

New Microbiome Digest and many many interesting articles: metagenome analysis as a powerful tool for enzyme bioprospecting, application of DGGE on oral bacterial community; labeling of prokaryotic mRNA in live cells with FISH-TAMB…
While in non-microbiology picks read and join very interesting project Scientist Selfies. This project explores how scientists use Instagram and how scientists’ IG posts can potentially change public perceptions of scientists’.

Events and jobs

Postdoc position for Cell Factory Construction, Novozymes, Denmark

IBS-Nature Conference on Frontiers in Genome Engineering

General microbiome

Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer – Frances Tran – Scientific Reports

Review: Archaea Are Interactive Components of Complex Microbiomes – Christine Moissl-Eichinger – Trends in Microbiology

 

Pregnancy and early life

Human Milk Oligosaccharides Exhibit Antimicrobial and Antibiofilm Properties against Group B Streptococcus – Dorothy L. Ackerman – ACS Infectious Diseases

Review: Development of the gut microbiota in infancy and its impact on health in later life – Masaru Tanaka –  Allergology International

Maternal microbiomes in preterm birth: Recent progress and analytical pipelines – Lindsay A. Parnell – Seminars in Perinatology

Oral microbiology

Application of denaturing gradient gel electrophoresis to the analysis of bacterial communities associated with asymptomatic and symptomatic pericoronitis –  Xin Zhang – Journal of Oral and Maxillofacial Surgery

 

 

Human gut microbiome

Review: Food contact materials and gut health: Implications for toxicity assessment and relevance of high molecular weight migrants – Ksenia J. Groh – Food and Chemical Toxicology

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota – Clémence Defois – Frontiers in Microbiology

Animal experiments

AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut – Kevin Cadwell – BMC Genomics

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Rebecca A. Ober – Veterinary Microbiology

Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks – Kirsty Dougal – Frontiers in Microbiology

Animal microbiome

Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness – Suyeon Kim – LWT – Food Science and Technology

Diet and gut microbiota of two supralittoral amphipods Orchestia montagui and Talitrus saltator living in different microhabitats – Khaled F.A. Abdelrhman – Estuarine, Coastal and Shelf Science

Gut microbiome analysis as a tool for developing new probiotic products – Daniel Ramón – Journal of Biotechnology

Review: Human genetic variation and the gut microbiome in disease – Andrew Brantley Hall – Nature Reviews  Genetics

Plant, root, and soil microbiome

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems – Madangchanok Imchen – Scienfic Reports

Microbial community structure and function respond more strongly to temporal progression than to the application of slurry in an Irish grassland – Aaron Fox – Applied Soil Ecology

Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens – John B. Bruce – Evolution

Water and extremophile microbiome

Differences in temperature and water chemistry shape distinct diversity patterns in thermophilic microbial communities – Cecilia M. Chiriac –  Applied nad Environmental Microbiology

Planococcus ruber sp. nov., isolated from a polluted farmland soil sample – Xu Wang – International Journal of Systematic and Evolutionary Microbiology

Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka – Andrey V. Mardanov – Antonie van Leeuwenhoek

Aura-biomes are present in the water layer above coral reef benthic macro-organisms – Kevin Walsh – PeerJ

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov – Jiro F Mori – The ISME

Food microbiology

Restoration of GABA production machinery in Lactobacillus brevis by accessible carbohydrates, anaerobiosis and early acidification – Qinglong Wu – Food Microbiology

Development of non-pathogenic bacterial biofilms on the surface of stainless steel which are inhibitory to Salmonella enterica – Yoonbin Kim – Food Microbiology

 

Bioinformatics

Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting – Aravind Madhavan –  Applied Biochemistry and Biotechnology

Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process – Karolina Elżbieta Kaczor-Urbanowicz – Bioinformatics

Biotechnology

Biogas production from brewery spent grain as a mono-substrate in a two-stage process composed of solid-state anaerobic digestion and granular biomass reactors – Mario Panjičko – Journal of Cleaner Production

Revealing sludge and biofilm microbiomes in membrane bioreactor treating piggery wastewater by non-destructive microscopy and 16S rRNA gene sequencing – Tomohiro Inaba – Chemical Engineering Journal

Techniques

Characterization of syntrophic Geobacter communities using ToF-SIMS – Wenchao Wei – Biointerphases

Labeling of prokaryotic mRNA in live cells using fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB) – Rachel Harris – bioRxiv

Microbes in the news

No guts no glory: Harvesting the microbiome of athletes

Oil-eating bacteria help sea life thrive

Tina’s (non-microbiology) picks

 Research project “To Selfie or Not to Selfie” – How Can Scientists Foster Public Trust on Instagram? 

Is there enough transparency in #peerreview? Join the debate #PeerRevWk17

August 17, 2017

After two days of holidays on Microbiome Digest, today our blog is a bit longer with many papers in the part of water, soil and gut microbiome. Moreover, check new tools which can be used to deal with microbiome data (MicrobiomeDB and MetaMeta) and some interesting news about microbes in the “Microbes in the news” section. Enjoy the summer (in the lab or on the beach) while reading what is new in microbial world.

Events and jobs

Quality Control Manager, Microbiology, Technical Operations, Marlborough, Massachusetts, US

Assistant/Associate Professor – Microbiology and Immunology (Job ID #83258), Chicago, US

General microbiome

A macroecological theory of microbial biodiversity – William R. Shoemaker – Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms – Jonathan Friedman – Nature Ecology & Evolution

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla – Eric Becraft – bioRxiv

Review: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life – Anja Spang – Science

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria – Arnauld Vinçon-Laugier – Frontiers in Microbiology

Advances in the analysis of “less-conventional” human body fluids: an overview of the ce- and hplc-ms applications in the years 2015–2017 – Monica Di Venere – Electrophoresis

Pregnancy and early life

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly A.Lackey – Journal of Microbiological Methods

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants – Danping Zhu – Scientific Reports

Multi-site human microbiome

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid –  Philipp Kirstahler – bioRxiv

Oral microbiome

Oral microbial community assembly under the influence of periodontitis – Hongju Chen – PLOS One

Subgingival Microbiome of Gingivitis in Chinese Undergraduates – Ke Deng – Chinese Journal of Dental Research

Human skin microbiome

Review: What is new in the pathophysiology of acne, an overview – B. Dréno – Journal of the European Academy of Dermatology and Venerology

The Role of the Skin and Gut Microbiome in Psoriatic Disease – Di Yan – Current Dermatology Reports

Human vaginal microbiome

The Vaginal Microbiome and its Potential to Impact Efficacy of HIV Pre-exposure Prophylaxis for Women –  Jennifer Velloza – Current HIV/AIDS Reports

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment – Cornelia Gottschick – Microbiome

 

Human gut microbiome

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – bioRxiv

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska- Gut Pathogens

Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism –  Wenzhen Ji – Molecular Medicine Reports

Brain-gut-microbiota axis and mental health – Timothy G. Dinan – Psychosomatic Medicine

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells – Mei San Tang – Inflamatory Bowel Diseases

Gut microbiome response to short-term dietary interventions in reactive hypoglycemia subjects – Sara Quercia –  Diabetes Metabolism Research and Reviews

The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces – Donjete Statovci –  Frontiers in Immunology

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects – Elena Buelow – Microbiome

Future prospect of faecal microbiota transplantation as a potential therapy in asthma – Y Kang  – Allergologia et Immunopathologia

Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients With Rheumatoid Arthritis – Annalisa Pianta – Arthritis & Rheumatology

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska – Gut Pathogens

The impact of age and gut microbiota on Th17 and Tfh cells in K/BxN autoimmune arthritis – Fei Teng – Arthritis Research & Therapy

Amoxapine Demonstrates Incomplete Inhibition of β-Glucuronidase Activity from Human Gut Microbiota – Wei Yang –  SLAS Discovery

Animal experiments 

Role of intestinal microbiome in American ginseng-mediated colon cancer protection in high fat diet-fed AOM/DSS mice –  C.-Z. Wang –  Clinical and Translational Oncology

The influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens – Zifeng Han – Infection and Immunity

Animal microbiome 

Microbiota of little penguins and short-tailed shearwaters during development – Meagan L. Dewar – PLOS One

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLOS One

Brief Communication: Climate warming reduces gut microbiota diversity in a vertebrate ectotherm – Elvire Bestion – Nature Ecology & Evolution

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Andrea Springer – Ecology and Evolution

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLOS One

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community – Marcus J. Pennington – Scientific Reports

Plant, root, and soil microbiome

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach – Thanyaporn Ruangdech – Agriculture and Natural Resources

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient – Eric J. Chapman – European Journal of Soil Biology

Bacteria from the rhizosphere and tissues of As-hyperaccumulator Pteris vittata and their role in arsenic transformation – Yong-HeHan – Chemosphere

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize – LinChen – Pedosphere

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates – Yanglei Yi – Frontiers in Microbiology

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants – Anna C. Santamans – PLOS One

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China – Guangyu Li – International Journal of Environmental Research and Public Health

Microbial volatile compounds alter the soil microbial community – Jun Yuan –  Environmental Science and Pollution Research

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G. Marshall – Marine Genomics

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils – Ruo-Nan Wu – Microbial Ecology

Biophysical processes supporting the diversity of microbial life in soil – Robin Tecon – FEMS Microbiology Reviews

Water and extremophile microbiome 

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond – Patrick J. Kearns – Aquatic Microbial Ecology

Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques –  Samuel Bryson – Thesis, Oregon State University

Effects of alkali types on waste activated sludge (WAS) fermentation and microbial communities – Xiaoling Li – Chemosphere

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern –  María José León –  International Journal of Systematic and Evolutionary

Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis – Emad I. Hussein – Microbiology Open

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters – Dahe Zhao – Applied Microbiology and Biotechnology

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing – M Jongman – Journal of Applied Microbiology

Report: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga – Haim Treves – Current Biology

The effects of morphology and neighbouring seaweeds on macroalgal microbiota – Thesis, The University of British Columbia

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system – Jing-Zhe Jiang – PLOS One

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre – Stephanie A. Sommer – Molecular Ecology

Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem – Mohd Ezhar Mohd Noor –  bioRxiv

The organizing effects of elevated CO2 on competition among estuarine primary producers – Craig S. Young – Scientific Reports

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation – Mamoru Oshiki – Genome Announcements

Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology

Early photosynthetic eukaryotes inhabited low-salinity habitats – Patricia Sánchez-Baracaldo – PNAS

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs – Sunita J.Varjani – Bioresource Technology

Probiotics / prebiotics

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure – Gurjeet Kaur – Journal of Proteomics

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Phages and viruses

Phage in urban wastewater have the potential to disseminate antibiotic resistance – Gayathri Upeksha Gunathilaka – International Journal of Antimicrobial Agents

Bioinformatics

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments – Francislon Silva de Oliveira – bioRxiv

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling – Vitor C. Piro – Microbiome

A bioarchitectonic approach to the modular engineering of metabolism – Cheryl A. Kerfeld – Philosophical Transactions of the Royal Society B

Techniques

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems – Joanne B. Emerson – Microbiome

A Note: A simple methodology to collect culturable bacteria from feces of Anopheles darlingi (Diptera: Culicidae) – Andrelisse Arruda – Journal of Microbiological Methods

Biotechnology

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks – Keaton Larson – Environmental Science & Technology

Microbial communities as biosensors for monitoring urban environments – Fangqiong Ling – Microbial Biotechnology

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Review: Purification and reuse of non-point source wastewater via Myriophyllum-based integrative biotechnology: A review – Liu F – Bioresource Technology

Improvements in algal lipid production: a systems biology and gene editing approach –  Avik Banerjee – Critical Reviews in Biotechnology

Microbes in the news 

Scientists Make Food From Bacteria, Water, Electricity, and a Whole Lot of Patience

Are you lonesome tonight? Why we, like Elvis, turn to food for comfort

Scientists See Bacteria Responding Electrically to Physical Stimuli for the First Time

Killing bacteria by hacking plastics with silver and electricity

Human Gut Microbes May Help Suppress MS, New Research Suggests 

Unexpected Microbial Life in Glacial Clay Could Offer Antibiotic Solutions