Category Archives: Microbial Ecology

August 25, 2017

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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 24, 2017

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Bacterial paleontology of iron formations, gene expression from bacteria and archaea in the Amazon River, indoles promote a “youthful” gene expression profile in their host.

Events and jobs

Podcast: Branding Bacteria – Carla Brown

General microbiome

Preprint: Metabolic Model-Based Analysis of the Emergence of Bacterial Cross-Feeding through Extensive Gene Loss – Colin P McNally – bioRxiv

Pregnancy and early life

Breast Milk Transforming Growth Factor β Is Associated With Neonatal Gut Microbial Composition – Alexandra R Sitarik – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Increased Tryptophan Metabolism is Associated With Activity of Inflammatory Bowel Diseases – Susanna Nikolaus – Gastroenterology

Animal experiments

Indoles from commensal bacteria extend healthspan – Robert Sonowal – PNAS

Plant, root, and soil microbiome

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities – Alessandro Florio – Scientific Reports

Changes in Soil Microbial Community and Its Effect on Carbon Sequestration Following Afforestation on the Loess Plateau, China – Yun Xiang – International Journal of Environmental Research and Public Health

Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island – Giuseppe Concheri – Scientific Reports

Influence of film mulching on soil microbial community in a rainfed region of northeastern China – Wenyi Dong – Scientific Reports

Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE) – Serena Fraraccio – Scientific Reports

Adaptive evolution of rhizobial symbiotic compatibility mediated by co-evolved insertion sequences – Ran Zhao – The ISME Journal

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey – Lu Zhang – FEMS Microbiology Ecology

Water and extremophile microbiome

Predicting blooms of toxic cyanobacteria in eutrophic lakes with diverse cyanobacterial communities – Aleksandra Bukowski – Scientific Reports

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River – Brandon M Satinsky – Frontiers in Marine Science

Probiotics/prebiotics

Protocol for a randomised, placebo-controlled pilot study for assessing feasibility and efficacy of faecal microbiota transplantation in a paediatric ulcerative colitis population: PediFETCh trial – Nikhil Pai – Gastroenterology and Hepatology

More microbes

Bacterial paleontology of the Neoarchean banded iron formations of Karelia and the Kola Peninsula – M M Astafieva – Paleontological Journal

Microbes in the news

Cyborg bacteria covered in solar panels can beat plants at photosynthesis – Angela Chen – The Verge

Gut bacteria influence the brain indirectly, study shows – Maria Cohut – Medical News Today

Scientists uncover two-layer identification among soil bacteria – Amy Wallace – UPI.com

We May Have Just Found The Hormone That Lets Gut Bacteria Talk to The Brain – Peter Duckbill – Science Alert

August 23, 2017

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Human Microbiome

The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women – Aline C. Freitas – Scientific Reports

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy – Heitor S. P. de Souza – Nature Reviews Gastroenterology & Hepatology

Changes in the intestinal microbiota following the administration of azithromycin in a randomised placebo-controlled trial among infants in south India – Edward P. K. Parker – Scientific Reports

High intake of dairy during energy restriction does not affect energy balance or the intestinal microflora compared to low dairy intake in overweight individuals in a Randomized Controlled Trial – Line Quist Bendtsen – Applied Physiology, Nutrition, and Metabolism

Metabolic and functional paths of lactic acid bacteria in plant foods: get out of the labyrinth – Pasquale Filannino –  Current Opinion in Biotechnology

Differences of lung microbiome in patients with clinically stable and exacerbated bronchiectasis – Min Kwang Byun – PLoS ONE

Precision Nutrition: A Review of Personalized Nutritional Approaches for the Prevention and Management of Metabolic Syndrome – Juan de Toro-Martín – Nutrients

 

Animal Microbiome

Soy Improves Cardiometabolic Health and Cecal Microbiota in Female Low-Fit Rats – Tzu-Wen L. Cross – Scientific Reports

Modulatory influence of segmented filamentous bacteria on transcriptomic response of gnotobiotic mice exposed to TCDD – Robert Stedtfeld – Frontiers in Microbiology

Comparative analysis of the gut microbiota composition between captive and wild forest musk deer – Yimeng Li – Frontiers in Microbiology

Modulation of gut microbiome composition and function in experimental colitis treated with Sulphasalazine – Haihui Zheng – Frontiers in Microbiology

Respiratory Commensal Bacteria Corynebacterium pseudodiphtheriticum Improves Resistance of Infant Mice to Respiratory Syncytial Virus and Streptococcus pneumoniae Superinfection – Paulraj Kanmani – Frontiers in Microbiology

 

Pathogen research

Whole-genome sequencing for national surveillance of Shigella flexneri – Marie Anne Chattaway – Frontiers in Microbiology

SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data – Lennard Epping –  BioRxiv

In Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus aureus – Thippeswamy H. Sannasiddappa –  Frontiers in Microbiology

Environmental Microbiology

Alleviation of heavy metal stress in plants and remediation of soil by rhizosphere microorganisms – Jitendra Mishra – Frontiers in Microbiology

From surface to deep-sea: Bacterial distribution to polymetallic nodule fields at 4000 m in the Clarion-Clipperton Zone of the Pacific Ocean – Markus V. Lindh – Frontiers in Microbiology

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation – Shany Ofaim – Frontiers in Microbiology

 

Bioinformatics

Contradictory Results: Low rate of index hopping on the Illumina HiSeq X platform – Tom van der Valk – BioRxiv

Analyzing contentious relationships and outlier genes in phylogenomics – Joseph F. Walker – BioRxiv

Other

Metabolic Reconstruction and Modeling Microbial Electrosynthesis – Christopher W. Marshall – Scientific Reports

Receptor Uptake Arrays For Vitamin B12, Siderophores And Glycans Shape Bacterial Communities – Steven A. Frank – BioRxiv

Diversity of microbiota associated with symptomatic and non-symptomatic bacterial wilt-diseased banana plants determined using 16S rRNA metagenome sequencing – Nurul Shamsinah Mohd Suhaimi – World Journal of Microbiology and Biotechnology

News

Antarctic mystery microbe could tell us where viruses came from – Michael Marshall – New Scientist

Even the Eye Has a Microbiome – Jeff Lyon – JAMA

The Surprising Things Your Microbiome Reveals About You – Ashley Lewis – Readers Digest

Linking mental health and the gut microbiome – MedicalXpress

 

Non-microbiology picks

How to share data for collaboration – Shannon E Ellis – PeerJ preprints

 

August 22, 2017

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Jobs

Postdoctoral Research Fellow in Microbiology/Molecular Ecology : Bremen, Germany (Soil microbial community interactions)

Postdoctoral Training Fellow : London, United Kingdom (M. tuberculosis and immunity)

 

Human Microbiome

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

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli L. Moss – PLoS ONE

Intestinal colonisation patterns in breastfed and formula-fed infants during the first 12 weeks of life reveal sequential microbiota signatures – Harro M. Timmerman  – Scientific Reports

A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy – James Kinross – Scientific Reports

Inflammatory colonic innate lymphoid cells are increased during untreated hiv-1 infection and associated with markers of gut dysbiosis and mucosal immune activation – Stephanie Dilon- JAIDS Journal of Acquired Immune Deficiency Syndromes

The Maternal Infant Microbiome: Considerations for Labor and Birth – Alexis Dunn – MCN, American Journal of Maternal Child Nursing

Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome – Francesco Beghini – The ISME Journal

 

Animal Microbiome

The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition – Limei Chen – Frontiers in Microbiology

Moderate-intensity exercise affects gut microbiome composition and influences cardiac function in myocardial infarction mice – Zuheng Liu – Frontiers in Microbiology  

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life – Christian Milani – The ISME Journal

 

Probiotics

In Vitro Evaluation of the Impact of the Probiotic E. coli Nissle 1917 on Campylobacter jejuni’s Invasion and Intracellular Survival in Human Colonic Cells – Yosra A. Helmy – Frontiers in Microbiology

 

Food Microbiology

Cell surface properties of Lactococcus lactis reveal milk protein binding specifically evolved in dairy isolates – Mariya Tarazanova – Frontiers in Microbiology

 

Pathogen Research

Metagenomic sequencing to replace semi-quantitative urine culture for detection of urinary tract infections: a proof of concept – Victoria A. Janes – BioRxiv

Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches – Viola C. Scoffone –  Frontiers in Microbiology

 

Environmental Microbiome

Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments – Ashleigh R. Currie – Frontiers in Microbiology

Heat Stress Dictates Microbial Lipid Composition along a Thermal Gradient in Marine Sediments – Miriam Sollich – Frontiers in Microbiology

Actinobacterial Rare Biospheres and Dark Matter Revealed in Habitats of the Chilean Atacama Desert – Hamidah Idris – Scientific Reports

A pivotal role for ocean eddies in the distribution of microbial communities across the Antarctic Circumpolar Current – – PLoS ONE

Microbial community analysis of apple rhizosphere around Bohai Gulf – Jihang Jiang – Scientific Reports

From virus isolation to metagenome generation for investigating viral diversity in deep-sea sediments – Cinzia Corinaldesi – Scientific Reports

 

Bioinformatics

PANINI: Pangenome Neighbor Identification for Bacterial Populations – Khalil Abudahab  – BioRxiv

 

 

Non-Microbiology picks

The prehistory of biology preprints: a forgotten experiment from the 1960s – Matthew Cobb – PeerJ preprints

August 21, 2017

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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 18, 2017

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Human Microbiome: Gut

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)

News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology

Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)

 

Human Microbiome: Respiratory tract

Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology

State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)

 

Human Microbiome: Mouth

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports

 

Built microbiome

Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports

 

Animal Microbiome

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports

Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang –  Frontiers in Microbiology

Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology

Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports

Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv

Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia –  Scientific Reports

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)

 

Probiotics, Prebiotics and Synbiotics

Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology

The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal –  Frontiers in Microbiology

Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports

Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology

A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature

 

Pathogen Research

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology

In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science

 

Bioactive compounds

Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology

Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports

 

Bacteriophages

Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa  – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE

 

Soil and Environmental Microbiology

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology

Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)

 

Bioinformatics and Genomics

Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv

Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari –  BMC Bioinformatics

 

Non-microbiology picks

A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science

Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology

Lessons from between the white lines for isolated data scientists – Benjamin S Baumer ​- PeerJ preprints

 

August 17, 2017

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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

 

 

 

August 9, 2017

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Events and jobs

ASM Journals Fellowship – American Society for Microbiology

General microbiome

A mechanistic Individual-based Model of microbial communities – Pahala Gedara Jayathilake – PLoS ONE

Human vaginal microbiome

Group B Streptococcus and the vaginal microbiota – Geoffrey H Rosen – The Journal of Infectious Diseases

Animal experiments

The microbial metabolite desaminotyrosine protects from influenza through type I interferon – Ashley L. Steed – Science

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

Plant, root, and soil microbiome

Microbial Communities as Ecological Indicators of Ecosystem Recovery Following Chemical Pollution – Stéphane Pesce – Microbial Ecotoxicology

Assessment of rhizosphere processes for removing water-borne macrolide antibiotics in constructed wetlands – Yiping Tai – Plant and Soil

Poor-Soil Rhizosphere Enriched with Different Microbial Activities Influence the Availability of Base Elements – Faten Dhaw – Open Journal of Ecology

Water and extremophile microbiome

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure – Man Jae Kwon – PLoS ONE

Built environment

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity – Emma Ransom-Jones – mSphere

Probiotics / prebiotics

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (Gallus gallus domesticus) during Downstream Poultry Processing – Vamsy Priya Guttala – Agricultural Sciences

Lactobacillus casei CCFM419 attenuates type 2 diabetes via a gut microbiota dependent mechanism – Gang Wang – Food & Function

Bioinformatics

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information – Albert Barberán – mSphere

Techniques

Isolation of bacteriophages from air using vacuum filtration technique: An improved and novel method – Bhagyashree Magare – Journal of Applied Microbiology

Microbes in the news

Exploring the Equine Microbiome – Stacey Oke – The Horse

Study: Kitchen sponges carry more bacteria than a toilet – Darren Sweeney – Fox8 Cleveland

August 7, 2017

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General microbiome

Viruses in the 21st Century: From the Curiosity-Driven Discovery of Giant Viruses to New Concepts and Definition of Life – Patrick Forterre, Clinical Infectious Diseases

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities – Arnaud Bridier, Frontiers in Microbiology

Functions and emerging applications of bacteriocins – Michael L Chikindas, Current Opinion in Biotechnology

Pregnancy and early life

Ontogenesis of the Gut Microbiota Composition in Healthy, Full-Term, Vaginally Born and Breast-Fed Infants over the First 3 Years of Life: A Quantitative Bird’s-Eye View – Ravinder Nagpal, Frontiers in Microbiology

Multi-site human microbiome

Profiling of faecal water and urine metabolites among Papua New Guinea highlanders believed to be adapted to low protein intake – Eriko Tomitsuka, Metabolomics

Evidence based selection of probiotic strains to promote astronaut health or alleviate symptoms of illness on long duration spaceflight missions – G.L. Douglas, Beneficial Microbes

Human oral microbiome

Salivary microbiome in non-oral disease: A summary of evidence and commentary – Aneesha Acharya, Archives of Oral Biology

Human gut microbiome

Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction – Yael Litvak, Current Opinion in Microbiology

Role of gut microbiota in idiopathic nephrotic syndrome in children – Kazunari Kaneko, Medical Hypotheses

A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults – Jason R. Anderson, Sleep Medicine

Diarrhea after bariatric procedures: Diagnosis and therapy – Yves M Borbély, World Journal of Gastroenterology

The Intestinal Microbiome and Childhood Obesity – Jessica McCann, Current Pediatrics Reports

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens

Animal experiments

Streptococcus pneumoniae colonization is required to alter the nasal microbiota in cigarette smoke-exposed mice – Pamela Shen, Infection and Immunity

Fenugreek galactomannan and citrus pectin improve several parameters associated with glucose metabolism, and modulate gut microbiota in mice  – Miriam G. Shtriker, Nutrition

Animal microbiome

The B Vitamin Nutrition of Insects: The contributions of diet, microbiome and horizontally-acquired genes – Angela E. Douglas, Current Opinion in Insect Science

Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community – Wei Jin, Current Microbiology

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) – Obed Hernández-Gómez, Frontiers in Microbiology

Microorganisms associated with microscopic insects Megaphragma amalphitanum and Scydosella musawasensis – A. V. Nedoluzhko, Microbiology

Plant, root, and soil microbiome

Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil – Lívia Fabiana Braga, Brazilian Journal of Microbiology

Taxonomic and functional patterns across soil microbial communities of global biomes – Melline Fontes Noronha, Science of The Total Environment

Phylloplane bacteria of Jatropha curcas : diversity, metabolic characteristics and growth promoting attributes towards vigor of maize seedling – Garima Dubey, Canadian Journal of Microbiology

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Root exudates of potato onion are involved in the suppression of clubroot in a Chinese cabbage-potato onion-Chinese cabbage crop rotation – Shaocan Chen, European Journal of Plant Pathology

Isolation, characterization and inter-relationship of Phosphate Solubilizing Bacteria from the Rhizosphere of Sugarcane and Rice – Muhammad Awais, Biocatalysis and Agricultural Biotechnology

Distribution of Rhizosphere and Endosphere Fungi on the First-Class Endangered Plant Cypripedium japonicum – Geun-Hye Gang, Mycobiology

Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest – Guoyong Yan, Ecosphere

Temporal assessment of microbial communities in soils of two contrasting mangroves – Janaina Rigonato, Brazilian Journal of Microbiology

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome – Wu Xiong, Soil Biology and Biochemistry

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce – Apostolos Kalivas, Genomics Data

Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting PseudomonasSpecies Isolated from Sugarcane Rhizosphere – Hai-Bi Li, Frontiers in Microbiology

A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat – Adam Kuzdraliński, Journal of Molecular Microbiology and Biotechnology

Effect of mixed edible bacterial inoculants on the early development of improved cultivars of cocoa (Theobroma cacao L.) in a traditional agroforestry system in northern Oaxaca, Mexico – E. Hipólito-Romero, Argentina Journal of Microbiology

Draft Genome Sequence of Cronobacter sakazakiiGP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato’s Rhizoplane/Rhizosphere Continuum – Hannah R. Chase, Genome Anouncements

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria – Chiun-Kang Hsu, International Journal of Food Microbiology

Water and extremophile microbiome

Assessment upon heterotrophic microalgae screened from wastewater microbiota for concurrent pollutants removal and biofuel production – Liang Shen, Bioresource Technology

Compositions of the Microbial Consortia Present in Biological Sulphate Reduction Processes During Mine Effluent Treatment – Marja Salo, Mine Water and Circular Economy

An underappreciated hotspot of antibiotic resistance: The groundwater near the municipal solid waste landfill – Qing-Lin Chen, Science of The Total Environment

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea – Connor T. Skennerton, mBio

A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia’s Central Queensland, and Heron Island, a nearby fringing platform reef – D.J. Beale, Science of The Total Environment

Glaciers and Ice Sheets As Analog Environments of Potentially Habitable Icy Worlds –  Eva Garcia-Lopez, Frontiers in Microbiology

Changes in microbial community structure in response to changing oxygen stress in column tests of denitrification and selenium reduction – Chiachi Hwang, Mine Water and Circular Economy

Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source – Yingliang Ge, Tropical Journal of Pharmaceutical Research

Microbial community dynamics in aerated biological fluidized bed (ABFB) with continuously increased p-nitrophenol loads – Fangzhou Ji, Process Biochemistry

Food microbiology

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d’Arnad – Ilario Ferrocino, Applied and Environmental Microbiology

The individual contribution of starter and non-starter lactic acid bacteria to the volatile organic compound composition of Caciocavallo Palermitano cheese – Valeria Guarrasi, International Journal of Food Microbiology

Antimicrobial resistance of Lactobacillus spp. from fermented foods and human gut – Qinqin Ma, LWT – Food Science and Technology

Probiotics / prebiotics

Applications of prebiotics in food industry: A review – Vinti Singla,
Food Science and Technology International

Human milk oligosaccharide consumption by probiotic and human-associated bifidobacteria and lactobacilli – Taksawan Thongaram, Journal of Dairy Science

Probiotic properties of Weissella cibaria and Leuconostoc citreum isolated from tejuino – A typical Mexican beverage – Monique Suela Silva, LWT – Food Science and Technology

A Consumer’s Guide for Probiotics: 10 Golden Rules for a Correct Use – Marco Toscano, Digestive and Liver Disease

Bioinformatics

PATRIC as a unique resource for studying antimicrobial resistance – Dionysios A. Antonopoulos, Briefings in Bioinformatics

Techniques

Optimized experimental workflow for tandem mass spectrometry molecular networking in metabolomics – Florent Olivon, Analytical and Bioanalytical Chemistry

Microbes in the news

Taking too many antibiotics to treat eczema may worsen your condition – DR. LESLIE BAUMANN, Miami Herald

August 3, 2017

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The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature