Author Archives: Kiran

February 6, 2018

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General microbiome

Preprint: Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research – IM Velsko – bioRxiv

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas – CM Humphreys – Current Opinion in Biotechnology

 

Human skin microbiome

Individual and household attributes influence the dynamics of the personal skin microbiota and its association network – MHY Leung – Microbiome

 

Human gut microbiome

The intestinal protist Blastocystis is not a common member of the healthy infant gut microbiota in a Westernized country (Ireland) – PD Scanlan – Parasitology

Preprint: When metabolism meets physiology: Harvey and Harvetta – I Thiele – bioRxiv

Connection between BMI related plasma metabolite profile and gut microbiota – F Ottosson – The Journal of Clinical Endocrinology & Metabolism

Animal experiments 

Review: Gut microbiome and depression: what we know and what we need to know – G Winter – Reviews in the Neurosciences

Potential of Lactobacillus plantarum ZDY2013 and Bifidobacterium bifidum WBIN03 in relieving colitis by gut microbiota, immune and anti-oxidative stress – Y Wang – Canadian Journal of Microbiology

Air-Dried Brown Seaweed, Ascophyllum nodosum, Alters the Rumen Microbiome in a Manner That Changes Rumen Fermentation Profiles and Lowers the Prevalence of Foodborne Pathogens – M Zhou – mSphere

Animal microbiome 

Antimicrobial resistance in companion animals – DI Rendle – Equine Veterinary Journal

Plant, root and soil microbiome

Drought neutralises plant–soil feedback of two mesic grassland forbs – EL Fry – Oecologica

Effects of different fertilizers on methane emissions and methanogenic community structures in paddy rhizosphere soil – J Yuan – Science of The Total Environment

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. – L Cortes-Tolalpa – Applied Microbiology and Biotechnology

Microbial Diversity and Community Structure in Agricultural Soils Suffering from 4-year Pb Contamination – A Fengqiu – Canadian Journal of Microbiology

Evidence for species-specific plant responses to soil microbial communities from remnant and degraded land provides promise for restoration – ME Smith – Austral Ecology

Long term effects of Lespedeza bicolor revegetation on soil bacterial communities in Dexing copper mine tailings in Jiangxi Province, China – Z Wu – Applied Soil Ecology

Water microbiome and extremophile

Preprint: Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes – TV Rossum – bioRxiv

Life on Phosphite: A Metagenomics Tale – Y Tapia-Torres – Trends in Microbiology

Biodegradation of n-alkanes on oil-seawater interfaces at different temperatures and microbial communities associated with the degradation. – S Lofthus – Biodegradation

Contrasting the genetic patterns of microbial communities in soda lakes with and without cyanobacterial bloom – AP Andreote – Frontiers in Microbiology

Microbial communities associated with the co-metabolism of free cyanide and thiocyanate under alkaline conditions – L Mekuto – 3 Biotech

Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India – G Mehetre – Archives of Microbiology

Built environment 

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems – M Kokko – Bioresource Technology

Free-living bacteria and potential bacterial pathogens in sewage treatment plants – K Huang – Applied Microbiology and Biotechnology

Crawling-induced floor dust resuspension affects the microbiota of the infant breathing zone – H Hyytiäinen – Microbiome

 

Techniques

Preprint: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – CM Clark – bioRxiv

Preprint: Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction for Klebsiella genomes – RR Wick – bioRxiv

The madness of microbiome: Attempting to find consensus “best practice” for 16S microbiome studies – J Pollock – Applied and Environmental Microbiology

Microbes in the news

The possibilities of microorganisms – The Varsity

New insight into the molecular weapons of the plant microbiome – EurekAlert

Ohio State scientists to send ancient bacteria into space to unlock secrets about life on other planets – The Columbus Dispatch

Workbench for virus design – Phys.org

What does your poo microbiome do? – Phys.org

The Importance of Infants’ Exposure to Microorganisms – The New York Times

Treatment of nitrogen-polluted sediment using marine anammox bacteria – Science Daily

Microbes and the market

Thermo Fisher Scientific Launches Axiom Microbiome Array for Research – Cision PR Newswire

Worldwide Microbiome Sequencing Services Market Driven by Business Overview, Company Profile, Products, Services and Solutions Prediction To 2022 – Facts Week

Non-Microbiology Picks

Chilly Climates, Balancing Acts, and Shifting Pathways: What Happens to Women in STEM Doctoral Programs – M Cabay – Social Sciences

 

February 5, 2018

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A digest full of news for today.

Animal microbiome 

Coexistence of novel gammaproteobacterial and Arsenophonus symbionts in the scale insect Greenisca brachypodii (Hemiptera, Coccomorpha: Eriococcidae) – A Michalik – Environmental Microbiology

Water microbiome

Shift in the microbial community composition of surface water and sediment along an urban river – L Wang – Science of The Total Environment

Techniques

Preprint: Thermoelectric Heat Exchange and Growth Regulation in a Continuous Yeast Culture – A Latorre-Perez – bioRxiv

New colony multiplex PCR assays for the detection and discrimination of vancomycin-resistant enterococcal species – T Nomura – Journal of Microbiological Methods

Microbes in the news

Babies’ infection risk higher if pregnant mums take antibiotics, according to new research – ABC

Monique Keiran: It takes guts to look after yourself – Times Colonist

How tumours develop where these gut bacteria thrive – Deccan Chronicle

Bacteria that causes leprosy is mutating into something even more dangerous – Joe

The microbiome has been called the forgotten organ — and it could hold the ‘next paradigm shift in science and medicine’ – Infosurhoy

Superbugs – Our destiny of doom – The Sentinel-Echo

Johnson & Johnson Innovation to Explore the Role of Microbiome in Sleep – Sleep Review

Historic Fort Myers Billy’s Creek has been ‘frighteningly’ polluted for at least 15 years – News-Press

It’s not just planes — airports also crawling with germs, study says – The Seattle Times

January 28, 2018

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A preprint on the gut microbiome of few tribal groups in the Himalayan region; association between vaginal microbiota and HIV;   an integrative approach that encompasses  metatranscriptomics & fatty acid profiling to study the rumen microbiome during feeding;   environmental adaptation shapes the gut microbiota of Rhesus macaques;   microbiome of cactus rhizosphere;   news about uBiome; antibiotics;  and many more articles for today’s digest!

General microbiome

Review: Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome – S Sandoval-Motta – Archives of Medical Research

Multi-site human microbiome

The nasal microbiome mirrors and potentially shapes olfactory function – K Koskinen – Scientific Reports

Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls – Y Qiao – Scientific Reports

Human respiratory microbiome

Pseudomonas aeruginosa Biofilms: Host Response and Clinical Implications in Lung Infections – NM Maurice – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Analysis of the skin mycobiome in adult patients with atopic dermatitis – SH Han – Experimental Dermatology

Human vaginal microbiome

Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study – RS McClelland – The Lancet

Prevalence of vaginal microorganisms among pregnant women according to trimester and association with preterm birth – K-A Son – Obstetrics & Gynecology Science

Human gut microbiome

Preprint: Gut microbiome transition across a lifestyle gradient in Himalaya – AR Jha – bioRxiv

Physical exercise, gut, gut microbiota, and atherosclerotic cardiovascular diseases – J Chen – Lipids in Health and Disease

Therapeutic Opportunities in Intestinal Microbiota–Virus Interactions – V Monedero – Trends in Biotechnology

Almond Consumption and Processing Affects the Composition of the Gastrointestinal Microbiota of Healthy Adult Men and Women: A Randomized Controlled Trial. – HD Holscher – Nutrients

Effects of Ampicillin on the Gut Microbiome of an Adult Male as Determined by 16S rRNA V4 Metagenomics Sequencing and Greengenes Bioinformatics Suite – K Anukam – Journal of Advances in Microbiology

Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis – EJ Laserna-Mendieta – Journal of Crohn’s and Colitis

The Role of Bacteria, Probiotics and Diet in Irritable Bowel Syndrome – A Harper – Foods

Animal experiments 

Preprint: Inter- and intra-domain functional redundancy in the rumen microbiome during plant biomass degradation – A Soellinger – bioRxiv

Gut microbiome may contribute to insulin resistance and systemic inflammation in obese rodents: a meta-analysis. – N Jiao – Physiological Genomics

Protective effect of rosmarinic acid and carnosic acid against streptozotocin-induced oxidation, glycation, inflammation and microbiota imbalance in diabetic rats. – J Ou -Food & Function

Glucocorticoids Drive Diurnal Oscillations in T Cell Distribution and Responses by Inducing Interleukin-7 Receptor and CXCR4 – A Shimba – Immunity

Review: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – TT Nguyen – Journal of Psychiatric Research

Animal microbiome 

Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment – J Zhao – Microbial Ecology

Opinion: Mission Accomplished? We Need a Guide to the ‘Post Release’ World of Wolbachia for Aedes-borne Disease Control – SA Ritchie – Cell

Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster – KL Adair – The ISME Journal

In silico identification, characterization and expression analysis of attacin gene family in response to bacterial and fungal pathogens in Tenebrio molitor – YH Jo – Entomological Research

Plant, root and soil microbiome

Editorial special issue: the soil, the seed, the microbes and the plant – EB Nelson – Plant and Soil

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid – Y Zhang – Current Microbiology

The effects of road building on arbuscular mycorrhizal fungal diversity in Huangshan Scenic Area – A Yang – World Journal of Microbiology & Biotechnology

The role of species turnover in structuring bacterial communities in a local scale in the cactus rhizosphere – VN Kavamura – Plant and Soil

p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions – X Zhou – Biology and Fertility of Soils

Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition – M Unterseher – Mycological Progress

Identification, synthesis and regulatory function of the N-acylated homoserine lactone signals produced by Pseudomonas chlororaphis HT66 – H Peng – Microbial Cell Factories

Building Bioeconomy in Agriculture: Harnessing Soil Microbes for Sustaining Ecosystem Services – R Rengalakshmi – Towards a Sustainable Bioeconomy: Principles, Challenges and Perspectives

Competitive traits are more important than stress-tolerance traits in a cadmium-contaminated rhizosphere: a role for trait theory in microbial ecology – JL Wood – Frontiers in Microbiology

Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential as an Inoculant – E Megías – Genome Announcements

Copper Bioleaching in China: Review and Prospect – S Yin – Minerals

Water microbiome and extremophiles 

Core promoter information content correlates with optimal growth temperature – AA Aptekmann – Scientific Reports

Food microbiology

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening – M Olvera-García – Applied Microbiology and Biotechnology

Phages and viruses

Review: Phage or foe: an insight into the impact of viral predation on microbial communities – L Fernández – The ISME Journal

Techniques

Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity – KJ Hoegler – Journal of Molecular Evolution

Microbes in the news

uBiome, the Leader in Microbial Genomics, Launches SmartGut and SmartJane Microbiome Test Kits in Canada – Daily Telescope

Niki Bezzant: A gutsful of good health – NZ Herald

How Phenylbutazone, Firocoxib Affect Horses’ Gut Microbiota – the Horse

Botulinum-type toxins jump to a new kind of bacteria – Science Daily

‘Forgotten’ antibiotic offers hope against worst superbugs – Digital Journal

Detect The Level Of Bacteria In Food With This Smartphone-Based System – Wonderful Engineering

When bad bugs jump from farm to bedside – Hutch News

January 27, 2018

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A Saturday digest with lots of fun and weird news of microbiome!
Events and jobs

Adjunct Faculty- Biology, Microbiology, Anatomy & Physiology – St. Louis Community College in Missouri – USA

General microbiome

A Case of Recurrent Pasteurella Bacteremia in an Immunocompetent Patient with No Animal Bite. – F Zarlasht – The American Journal of Case Reports

Pregnancy and early life

Lipopolysaccharide-induced maternal inflammation induces direct placental injury without alteration in placental blood flow and induces a secondary fetal intestinal injury that persists into adulthood. – EM Fricke – American Journal of Reproductive Immunology

Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants – RD Zwittink – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach – FM Borges – Current Microbiology

Review: Dietary practices and FODMAPs in South Asia: Applicability of the low FODMAP diet to patients with irritable bowel syndrome – SP Hewawasam – Journal of Gastroenterology and Hepatology

Animal experiments 

Preprint: Mono-Association with Lactobacillus plantarum Disrupts Intestinal Homeostasis in adult Drosophila. – D Fast – bioRxiv

Beneficial effects of Rifaximin in post-infectious irritable bowel syndrome mouse model beyond gut microbiota – Y Jin –  Journal of Gastroenterology and Hepatology

Plant, root and soil microbiome

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves. – EJ Canter – Ecology

Purple corn-associated rhizobacteria with potential for plant growth promotion – A Castellano-Hinojosa – Journal of Applied Microbiology

Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease – OY de Assis Costa – PLoS One

Biosynthetic and antimicrobial potential of actinobacteria isolated from bulrush rhizospheres habitat in Zhalong Wetland, China – Y Li – Archives of Microbiology

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil – M Pacwa-Płociniczak – Water, Air and Soil Pollution

Water microbiome and extremophile 

Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids – H Bestová – Oecologia

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide –  A Nishihara – J-Stage

Food microbiology

Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing – HNJ Shangpliang – Scientific Reports

Phages and viruses

Preprint: Diversity and evolution of the emerging Pandoraviridae family – M Legendre – bioRxiv

Microbes in the news

Explore the human microbiome in new Delaware natural history museum exhibit – Delaware Public Media

Thoroughness of panel called into question – Delta Optimist

When DNA Went Mobile Some Archaea Jumped Out of the Hot Tub – GEN News

Scientists find 10 new defense systems used by bacteria – Science News

ASTRONAUTS LIVING IN SPACE CAN EAT BACTERIA THAT FEED ON HUMAN WASTE – Newsweek

A Never-Before-Seen Virus Was Just Found in the Sea, and It Kills Bacteria – Inverse Science

Bacteria block transmission of Zika and Dengue viruses – Medical Xpress

First annual thesis competition held at JMU – The Breeze

Microbiome research refines HIV risk for women – EurekAlert

Shimmery bacteria plus a canvas equals art, briefly – Chicago Tribune

BACTERIA THAT HITCH RIDES ON TOOTHBRUSHES, DIAPERS AND OTHER PLASTIC POLLUTION ARE KILLING CORAL REEFS – Newsweek

 

January 21, 2018

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A light reading for Sunday!
Events and jobs

Professor (Chairperson), Department of Microbiology and Immunology (MIC) – The Uniformed Services University of the Health Sciences – Bethesda, Maryland

Postdoc in Intestinal Microbiology and Ecology – The National Food Institute (DTU Food) – Denmark

SCIENCE INQUIRY LECTURE: “FLYING” BACTERIA AS POTENTIAL RAINMAKERS – APRIL 18, 2018; 7:00PM – 8:30PM – HAGER AUDITORIUM, Montana 

General microbiome

Review: Bacterial RNA Biology on a Genome Scale – Jens Hör  – Molecular Cell

Multi-site human microbiome

Epigenetics, microbiota, and intraocular inflammation: New paradigms of immune regulation in the eye – Xiaofeng Wen – Progress in Retinal and Eye Research

Human skin microbiome

The role of fatty acids and their endocannabinoid-like derivatives in the molecular regulation of appetite – Renger F. Witkamp – Molecular Aspects of Medicine

Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair – Jonathan L. Linehan – Cell

Propionibacterium acnes Strains Differentially Regulate the Fate of Th17 Responses in the Skin – Emmanuel Contassot – Journal of Investigative Dermatology

Human gut microbiome

P038 FECAL MICROBIOTA TRANSPLANT (FMT) FOR IMMUNO-CHECKPOINT INHIBITOR-INDUCED COLITIS (ICI-C) IN A 50 YEAR OLD FEMALE WITH BLADDER CANCER – Yinghong Wang – Gastroenterology

P110 STEROID-RESISTANCE AND STEROID-DEPENDENCE IN INFLAMMATORY BOWEL DISEASE CAN BE LINKED WITH GUT MICROBIOTA COMPOSITION CHANGES – Natalia Danilova – Gastroenterology

P069 LOW FAT DIET IMPROVES QUALITY OF LIFE AND CHANGES THE MICROBIOME IN A CATERED, CROSS-OVER DESIGN INTERVENTION OF UC PATIENTS WITH QUIESCENT DISEASE: RESULTS OF A PILOT STUDY – Matthew C. Phillips  – Gastroenterology

Animal experiments 

The family Coriobacteriaceae is a potential contributor to the beneficial effects of Roux-en-Y gastric bypass on type 2 diabetes – Haijun Liu – Surgery for Obesity and Related Diseases

P039 FECAL MIRNAS SHAPE THE INTESTINAL MICROBIOTA – Emilie Viennois – Gastroenterology

P125 TLR4 ACTIVATION UPREGULATES EXPRESSION OF OXIDATIVE ENZYMES: IMPLICATIONS FOR INTESTINAL TUMORIGENESIS AND LUMINAL MICROBIOTA – Juan F. Burgueno – Gastroenterology

Effect of live yeast supplementation on gastric ecosystem in horses fed a high-starch diet – Samy Julliand – Livestock Science

The symbiont Lactobacillus plantarum causes intestinal pathogenesis in adult Drosophila. – David Fast – bioRxiv

Plant, root and soil microbiome

Distinct responses of soil bacterial and fungal communities to changes in fertilization regime and crop rotation – Chao Ai – Geoderma

Microbial degradation of poly(ε-caprolactone) in a coastal environment – Miwa Suzuki – Polymer Degradation and Stability

Shifts in prokaryotic communities under forest and grassland within a tropical mosaic landscape – Sergio E. Morales – Applied Soil Ecology

Food microbiology

Polyphasic identification of Penicillia and Aspergilli isolated from Italian grana cheese – Simone Decontardi – Food Microbiology

Phages and viruses

Bacteriophages as modulator for the human gut microbiota: Release from dairy food systems and survival in a dynamic human gastrointestinal model – Meike Samtlebe – LWT

Techniques

Metagenomic analysis uncovers strong relationship between periodontal pathogens and vascular dysfunction in American Indian population – Prathik K Vijay Kumar – bioRxiv

P168 WHERE WILL FECAL MICROBIOTA TRANSPLANTATION FIT IN THE TREATMENT ALGORITHMS FOR CROHN’S DISEASE AND ULCERATIVE COLITIS: A SYNTHESIS OF COMPLETED, ONGOING AND FUTURE TRIALS – Yiran Song – Gastroenterology

Microbes in the news

The Prehistoric Bacteria That Helped Create Our Cells Billions of Years Ago – Mental Floss

IIT Delhi develops a novel platform to test drug sensitivity in bacteria – The Hindu

Scientists Unlock Key Information About the World’s Soil Microbes – Yale Environment 360

January 20, 2018

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Our Saturday digest has microbes associated with oesophageal region; sore throat; aphids, stingless bees; common carps, Italian cheeses and many more!

General microbiome

Bipartite network analysis of gene sharings in the microbial world – Eduardo Corel –

FEMS Microbiology Ecology

Is the impact of starvation on the gut microbiota specific or unspecific to anorexia nervosa? A narrative review based on a systematic literature search – Isabelle Mack – Current Neuropharmacology

Pregnancy and early life

Association between sn-2 fatty acid profiles of breast milk and development of the infant intestinal microbiome – Teimin Jiang – Food and Function

Multi-site human microbiome

The microbiology and treatment of human mastitis. – A Angelopoulou – Medical Microbiology and Immunology

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – PLoS Pathogens

Analysis of the tonsillar microbiome in young adults with sore throat reveals a high relative abundance of Fusobacterium necrophorum with low diversity – T. Preskott Atkinson – PLoS One

Human gut microbiome

Diet Affects Gut Microbiota and Modulates Hospitalization Risk Differentially In an International Cirrhosis Cohort – JS Bajaj – Hepatology

Emerging Insights into the Esophageal Microbiome – M May – Current Treatment Options in Gastroenterology

Analysis of gut microbiota diversity and auxiliary diagnosis as a biomarker in patients with schizophrenia: A cross-sectional study –  Y Shen – Schizophrenia Research

Animal experiments 

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – PLoS One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition & Food Research

Sequential BMP7/TGF-β1 signaling and microbiota instruct mucosal Langerhans cell differentiation. – Tal Capucha – Journal of Experimental Medicine

A host-pathogen interaction screen identifies ada2 as a mediator of Candida glabrata defences against reactive oxygen species – I Kounatidis – bioRxiv

Animal microbiome 

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Common cuckoos (Cuculus canorus) affect the bacterial diversity of the eggshells of their great reed warbler (Acrocephalus arundinaceus) hosts  – Nikoletta Geltsch – PLoS One

Stingless Bee Larvae Require Fungal Steroid to Pupate. – Camila R. Paludo – Scientific Reports

Plant, root and soil microbiome

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Draft Genome Sequence of Bacillus subtilis 2C-9B, a Strain with Biocontrol Potential against Chili Pepper Root Pathogens and Tolerance to Pb and Zn – Claudia Y. Muñoz-Moreno – Genome Announcements

Biotic elicitation of ginsenoside metabolism of mutant adventitious root culture in Panax ginseng – Kim-Cuong Le – Applied Microbiology and Biotechnology

Streptomyces AcH 505 triggers production of a salicylic acid analogue in the fungal pathogen Heterobasidion abietinum that enhances infection of Norway spruce seedlings – Nadine Keilhofer – Antonie van Leeuwenhoek

Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria – AS Sánchez-López – International Journal of Molecular Sciences

Extreme rainfall affects assembly of the root-associated fungal community – CJ Barnes – The New Phytologist

Abrupt burial imparts persistent changes to the bacterial diversity of turbidite-associated sediment profiles. – BK Harrison – Geobiology

Review: Fungal-Mediated Solid Waste Management: A Review –  A Jain – Mycoremediation and Environmental Sustainability

The PEG-responding desiccome of the alder microsymbiont Frankia alni – K Ghedira – Scientific Reports

Composition of pelagic microbial communities in Mediterranean coastal aquatic ecosystems under extreme drought conditions – N Àvila –  Estuarine, Coastal and Shelf Science

Water microbiome and extremophile 

What color should glacier algae be? – Roman J dial – FEMS Microbiology Ecology

Microbial Community Structure of Sea Spray Aerosols at Three California Beaches – Katherine Graham – FEMS Microbiology Ecology

The early conversion of deep-sea wood falls into chemosynthetic hotspots revealed by in situ monitoring – Dimitri Kalenitchenko – Scientific Reports

Microbial communities and their predicted metabolic functions in a desiccating acid salt lake – Elena Zaikova – Extremophiles

Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome – A Kumar – Seminars in Cell & Developmental Biology

Built environment 

Composition and role of the attached and planktonic microbial communities in mesophilic and thermophilic xylose-fed microbial fuel cells – Paolo Dessi – RSC Advances

Food microbiology

Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses – Fabrizia Tittarelli – Microbial Genomics

Application of molecular tools to elucidate the microbiota of seafood – Paloma Almeida Rodrigues – Journal of Applied Microbiology

Review: Recent Past, Present, and Future of the Food Microbiome – Francesca De Filippis – Annual Review of Food Science and Technology

Extracellular Enzyme Composition and Functional Characteristics of Aspergillus niger An-76 Induced by Food Processing Byproducts and Based on Integrated Functional-omics – L Liu – Journal of Agricultural and Food Chemistry

Changes in microbial communities and quality attributes of white muscle and dark muscle from common carp (Cyprinus carpio) during chilled and freeze-chilled storage – Q Li – Food Microbiology

Phages and viruses

Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – BG Blasdel – bioRxiv

Single-cell transcriptional dynamics of flavivirus infection – F Zanini – bioRxiv

Techniques

A distance-based approach for testing the mediation effect of the human microbiome – J Zhang – Bioinformatics

ReprDB and panDB: minimalist databases with maximal microbial representation – W Zhou – Microbiome

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria – B LaSarre – bioRxiv

Microbes in the news 

WEBINAR REVIEW: IMMUNO-ONCOLOGY AND THE MICROBIOME – Taconic

Scientists Peek Inside The ‘Black Box’ Of Soil Microbes To Learn Their Secrets – npr

Broadways Nursing Home: Legionella bacteria found in plumbing – BBC

Agros refuses Troodos water after coliform bacteria found – Cyprus Mail Online

Strange Weather Triggered Bacteria That Killed 200,000 Endangered Antelope – npr

Bacterial biofilm cellulose found to differ from plant cellulose – Phys.org

This is what happens to your gut when you go on a juice cleanse – Well and Good

New Course in Virus Hunting – SDSU NewsCenter

December 25, 2017

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A short digest today covering the human oral and gut microbiome, animal experiments, animal microbiome, plant, root and soil microbiome, techniques and news. At last we also have some “Lab stock fun picks”. Merry Christmas!!

 

Human oral microbiome

The oral microbiome-the relevant reservoir for acute pediatric appendicitis? – C Blod – International Journal of Colorectal Disease

 

 

Human gut microbiome

Intestinal microbiome analysis revealed dysbiosis in sickle cell disease – SH Lim – American Journal of Hematology

 

Animal experiments 

Fermented Soybean Meal Increases Lactic Acid Bacteria in Gut Microbiota of Atlantic Salmon (Salmo salar). – N Catalán – Probiotics and Antimicrobial Proteins

 

Animal microbiome 

The Combined Effect of Temperature and Host Clonal Line on the Microbiota of a Planktonic Crustacean. – KE Sullam – Microbial Ecology

 

Plant, root, and soil microbiome

Grey relational analysis for evaluating the effects of different rates of wine lees-derived biochar application on a plant-soil system with multi-metal contamination. – M Xu – Environmental Science and Pollution Research International

http://Transcriptomic responses of catalase, peroxidase and laccase encoding genes and enzymatic activities of oil spill inhabiting rhizospheric fungal strains. – MD Asemoloye – Environmental Pollution

Augmentation with potential endophytes enhances phytostabilization of Cr in contaminated soil. – MT Ahsan – Environmental Science and Pollution Research International

 

 

Techniques

Strain profiling and epidemiology of bacterial species from metagenomic sequencing – D Albanese – Nature Communications

Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme – K Kumar – Journal of Cellular Biochemistry

 

Microbes in the news

Cooking a turkey? Here’s how to make sure you avoid getting food poisoning – thejournal.ie

How the US military killed an Irishman in San Fran with germ warfare – Irish Central

How to avoid getting sick from flying – keep clean, stay hydrated and try to get a window seat – South China Morning Post

It’s getting real tough to ‘ESKAPE’ hospital-acquired infections – Indian Express

 

Lab stock funny picks (source: Shutterstock)

My magnifying glass is more powerful than the microscope

stock-photo-male-doctor-working-in-the-lab-on-virus-vaccine-748941127

 

Sometimes I try to incorporate the additive model of primary colours in my research: Red, Green , Blue!!

stock-photo-male-doctor-working-in-the-lab-on-virus-vaccine-740000146

 

Seems some one has finally been able to culture virus on a solid (agar) medium..

stock-photo-a-scientist-holding-a-petri-dish-with-virus-and-bacteria-cells-79142374

 

Do you see what I see?

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December 18, 2017

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In today’s short post we have included the “Lab stock photo fun” at the end of this post. A couple of more arriving shortly during  Christmas!!

General microbiome

Phylogenetic and Phenotypic Characterization of the Energy-taxis Receptor Aer in Pseudomonas – SC Booth – bioRxiv

Interleukin-18: Biological properties and role in disease pathogenesis – G Kaplanski – Immunological Reviews

Animal experiments 

Selenium nanoparticles in poultry feed modify gut microbiota and increase abundance of Faecalibacterium prausnitzii –  S Gangadoo – Applied Microbiology and Biotechnology

Phages and viruses

Prophages and Growth Dynamics Confound Experimental Results with Antibiotic-Tolerant Persister Cells. – A Harms – mBio

Techniques

Phylofactorization – a graph partitioning algorithm to identify phylogenetic scales of ecological data – AD Washburne – bioRxiv

Microbes in the news

Bacteria see etchings, and die – Cosmos

Rejected antibiotic candidate likely to get new chance for producing bacteria killers: study – Xinhuanet

For the New Year, resolve to treat your gut bugs right – Lexington Herald Leader

This is how dirty your money is – Channel NewsAsia

Before hosting Christmas, get rid of these germy spots in your home – Local 8 now

ASU scientists discover gut bacteria in bees spread antibiotic-resistant genes to each other – ASU Now

Lab stock photo fun

When  the colour of the solution matches that of my gloves!

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When my samples are at the same spot on the petridish and have similar patterns..

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When good things happen with completely filled-up test tubes..

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December 17, 2017

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General microbiome

Disease tolerance: concept and mechanisms – JL McCarville – Current Opinion in Immunology

Enterohemorrhagic Escherichia coli outwits hosts through sensing small molecules – KM Carlson-Banning – Current Opinion in Microbiology

 

Pregnancy and early life

Breastfeeding-associated microbiota in human milk following supplementation with Lactobacillus rhamnosus GG, Lactobacillus acidophilus La-5, and Bifidobacterium animalis subspecies lactis Bb-12 – MR Simpson – Journal of Dairy Science

 

 

Human skin microbiome

Dietary control of skin lipid composition and microbiome – KS Moestrup – Journal of Investigative Dermatology

 

 

Human gut microbiome

Modeling metabolism of the human gut microbiome – S Magnúsdóttir – Current Opinion in Biotechnology

Importance of microbial defence systems to bile salts and mechanisms of serum cholesterol reduction – H Šárka – Biotechnology Advances

 

Animal experiments 

Growth performance, nutrient digestibility, fecal microbiota and fecal noxious gas emission in weaning pigs fed high and low density diet with and without protected organic acid blends – SD Upadhaya – Animal Feed Science and Technology

 

Animal microbiome 

Host gut-derived probiotic bacteria promote hypertrophic muscle progression and upregulate growth-related gene expression of slow-growing Malaysian Mahseer Tor tambroides – Md Asaduzzaman – Aquaculture Reports

 

Plant, root and soil microbiome

Biochar alters microbial community and carbon sequestration potential across different soil pH – Y Sheng – Science of The Total Environment

Growth and extended survival of Escherichia coli O157:H7 in soil organic matter – G NandaKafle – bioRxiv

 

Water and extremophile microbiome 

Review: People, pollution and pathogens – Global change impacts in mountain freshwater ecosystems – DS Schmeller – Science of The Total Environment

 

 

Techniques

Mapping mutational effects along the evolutionary landscape of HIV envelope – HK Haddox – bioRxiv

 

Microbes in the news

Would You Put Honey In Your Vagina For A Yeast Infection? – Alternative Daily

Charge-Switchable Nanozymes for Bioorthogonal Imaging of Biofilm-Associated Infections – ACS Nano

Microbiome Sequencing Services Market Forecast To 2018 With Key Companies Profile, Supply, Demand, Cost Structure, And SWOT Analysis – Miltech PR Distribution

Synthetic Biologics CEO On Pipeline Advances And The Microbiome – Scrip

November 26, 2017

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Events and jobs

Microbiology Technician – Companion Animal Clinic – Midwestern University – Glendale, AZ

 

General microbiome

Biogas from slaughterhouse wastewater anaerobic digestion is driven by the archaeal family Methanobacteriaceae and bacterial families Porphyromonadaceae and Tissierellaceae – CE Granada – Renewable Energy

Ferrosenescence: the iron age of neurodegeneration? – A Sfera – Mechanisms of Ageing and Development

 

Pregnancy and early life

Intestinal Microbiota Composition in Sudden Infant Death Syndrome and Age-Matched Controls – LEX Leong – The Journal of Pediatrics

 

Multi-site human microbiome

Chapter: Microbiome – M Dewar – Bladder

 

Human respiratory microbiome

Bacterial microbiota of the nasal passages across the span of human life – L Bomar – Current Opinion in Microbiology

 

 

Human gut microbiome

Review: Aging and Parkinson’s Disease: Inflammaging, neuroinflammation and biological remodeling as key factors in pathogenesis – V Calabrese – Free Radical Biology and Medicine

 

Animal experiments 

The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses – L de Sordi – Cell Host and Microbe

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform – J Kim – Gut Pathogens

Influences of quorum-quenching probiotic bacteria on the gut microbial community and immune function in weaning pigs  – J Kim – Animal Science Journal

Dietary inclusion of xylanase improves growth performance, apparent total tract nutrient digestibility, apparent ileal digestibility of nutrients and amino acids and alters gut microbiota in growing pigs – KY Lee – Animal Feed Science and Technology

Age, sex, and TNF associated differences in the gut microbiota of mice and their impact on acute TNBS colitis – AJ Kozik – Experimental and Molecular Pathology

 

Animal microbiome 

Comparative analysis of gut bacterial communities of green turtles (Chelonia mydas) pre-hospitalization and post-rehabilitation by high-throughput sequencing of bacterial 16S rRNA gene – MS Ahasan – Microbiological Research

Innate immune responses to metabolic stress can be detected in rumen fluids – E Trevisi – Research in Veterinary Science

Molecular characterization and potential sources of aqueous humor bacterial contamination during phacoemulsification with intraocular lens implantation in dogs – LCC Lacerda – Veterinary Microbiology

 

Plant, root, and soil microbiome

Anaerobic microsites have an unaccounted role in soil carbon stabilization – M Keiluweit – Nature Communications

The rhizosphere and root exudates of maize seedlings drive plasmid mobilization in soil – H Zhu – Applied Soil Ecology

Review: AMF: The future prospect for sustainable agriculture – S Basu – Physiological and Molecular Plant Pathology

Review: Modified mycotoxins: An updated review on their formation, detection, occurrence, and toxic effects – L Freire – Food and Chemical Toxicology

 

 

Food microbiology

Colonic fermentation of polyphenolics from Sea buckthorn (Hippophae rhamnoides) berries: Assessment of effects on microbial diversity by Principal Component Analysis – S Attri – Food Research International

Review: Yeast and yeast derivatives in feed additives and ingredients: Sources, characteristics, animal responses, and quantification methods – GC Shurson – Animal Feed Science and Technology

 

Probiotics / prebiotics

Turning Fruit Juice Into Probiotic Beverages – ALF Pereira – Fruit Juices

Probiotics in Newborns and Children – MW Lenfestey – Pediatric Clinics of North America

 

Phages and viruses

The gut virome of the protochordate model organism, Ciona intestinalis subtype A – BA Leigh – Virus Research

DDX3 is exploited by Arenaviruses to suppress type I interferons and favor their replication – ME  Loureiro – bioRxiv

MVP: a microbe–phage interaction database  – NL Gao – Nucleic Acids Research

Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host – J Zheng – Current Opinion in Virology

 

Bioinformatics

Deciphering the Effects of Microbiome on Plants Using Computational Methods – MS Khan – Plant Bioinformatics

Application of Bioinformatics in Understanding of Plant Stress Tolerance – J Upadhyay – Plant Bioinformatics

 

Techniques

Monitoring microbial communities using light sheet fluorescence microscopy – R Parthasarathy – Current Opinion in Microbiology

Precise and simultaneous enumeration of multiplex pathogens using multiplex polymer chain reaction coupled with a novel quantitative capillary electrophoresis – C Liu – Sensors and Actuators B: Chemical

Biomarkers of antibiotic resistance genes during seasonal changes in wastewater treatment systems  – Y-N Jiao – Environmental Pollution

 

Microbes in the news

The End is Nigh — Will Biology Doom Us or Save Us? – Labiotech.eu

Study: Common food preservative harms ‘good’ gut bacteria – The Maui News

Why you should NEVER eat off your plate after a fly lands on it: Insects’ legs and wings are teeming with bacteria from rotting carcasses and faeces – Daily Mail Online