Category Archives: Techniques

March 8, 2018

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A wide range of interesting articles today: the use of fungi communities in the production of gold nanoparticles, a link between dysbiosis of the oral microbiome and rheumatoid arthritis, a diet low in PKU decreases fecal butyrate, the bacterial diet of  C. elegans alters their proteome, and a functional metagenomic study of the gut microbiome of the giant panda.

Events and jobs

Postdoctoral Associate – School of Medicine/Surgery – University of Pittsburgh Health Sciences

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General microbiome

Review: Understanding the microbiome – Mark Buchanan – Nature Physics

Pregnancy and early life

Conference Proceedings: Biology and Science of Human Milk – Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space – Rob Knight – Human Milk Science

PrePrint: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T. Brown – bioRxiv

Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis – Martin Glatz – PLOSone

Human oral microbiome

*Dysbiotic subgingival microbial communities in periodontally healthy patients with rheumatoid arthritis – Isabel Lopez-Oliva – Arthritis and Rheumatology

Human gut microbiome

*Phenylketonuric diet negatively impacts on butyrate production – E. Verduci – Nutrition, Metabolism and Cardiovascular Diseases

Review: Microbiotes et rhumatismes inflammatoires – Matthias Jarlborg – Revue Medicale Suisse

Gut Microbiome Composition Predicts Infection Risk during Chemotherapy in Children with Acute Lymphoblastic Leukemia – Hana Hakim – Clinical Infectious Diseases

PrePrint: American Gut: an Open Platform for Citizen-Science Microbiome Research – Daniel McDonald – bioRxiv

Review: Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis: a role for bifidobacteria and lactobacilli? – Borja Sánchez – Gastroenterology and Hepatology

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Animal microbiome

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls – Zhenming Zhou – Applied Microbiology and Biotechnology

*Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda (Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation – Wei Guo – Frontiers in Microbiology

*The C. elegans Proteome Response to Naturally Associated Microbiome Members of the Genus Ochrobactrum – Liam Cassidy – Proteomics

16S rRNA gene sequencing reveals effects of photoperiod on cecal microbiota of broiler roosters – Jun Wang – PeerJ

The Drosophila melanogaster Gut Microbiota Provisions Thiamine to Its Host – David R. Sannino – mBio

Host and aquatic environment shape the amphibian skin microbiome but effects on downstream resistance to the pathogen Batrachochytrium dendrobatidis are variable – Andrea J. Jani – Frontiers in Microbiology

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOSone

Plant, root, and soil microbiome

Impact of wastewater effluent containing aged nanoparticles and other components on biological activities of the soil microbiome, Arabidopsis plants, and earthworms – Jia Liu – Environmental Research

Dissertation: The influence of intraspecific variation in host plants on arthropod and fungal endophyte communities – Joshua G. Harrison – University of Nevada

Soil Microbiology Research in the Coming Decades: Translational Research Opportunities – Tapan Kumar Adhya – Advances in Soil Microbiology: Recent Trends and Future Prospects

Divergence of dominant factors in soil microbial communities and
functions in forest ecosystems along a climatic gradient – Zhiwei Xu – Biogeosciences

Climate, but not trait, effects on plant–soil feedback depend on mycorrhizal type in temperate forests – Jonathan A. Bennett – Ecosphere

Arbuscular Mycorrhiza Alleviates Restrictions to Substrate Water Flow and Delays Transpiration Limitation to Stronger Drought in Tomato – Michael Bitterlich – Frontiers in Plant Science

Ecological responses to forest age, habitat, and host vary by mycorrhizal type in boreal peatlands – Peter G. Kennedy – Mycorrhiza

Microbial Ecology

Holobionts and their hologenomes: Evolution with mixed modes of inheritance – Karen Luisa Haag – Genetics and Molecular Biology

Resistome

PrePrint: Conjugation factors controlling F-plasmid antibiotic resistance transmission – Hanna Alalam – bioRxiv

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense – Malcolm James Horsburgh – bioRxiv

Bioinformatics

PrePrint: MetaWRAP – a flexible pipeline for genome-resolved metagenomic data analysis
– Gherman V Uritskiy – bioRxiv

Biotechnology

*Green synthesis of gold nanoparticles by thermophilic filamentous fungi – Zsófia Molnár – Scientific Reports

Techniques

Evaluation of magnetic cellulose bead-based DNA extraction from faecal materials for high-throughput bacterial community analyses – Tanzila Afrin – Applied Entomology and Zoology

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Microbes in the news

How extremophiles flourish in stressful environments – Science Daily

Does a Microbiome Exist in the Womb? – Medical News Bulletin

IBS and the Developing Microbiome – David Carreon – Modern Medicine Network

Bacteria and Art

Finding Art in the Gut, and Other Unexpected Places – Patrician Olsen – The New York Times

This Psychedelic Art Made from Moldy Food Is Tripping Us Out – Artist Felix Kalmenson proves decay can be gorgeous – Anna Marks – Vice

Artist to offer presentation on ‘Living Light’ exhibit March 5 at MCC – Daily Herald

March 4, 2018

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Events and jobs

Phd position in antimicrobial resistance development in biofilm communities – University of Leuven

Professor in Microbiome/Microbiota-Host Interactions – University of Alabama

Microbiology Lab Scientist – Lyneer Staffing

General microbiome

Impact of Brazilian microbiome for boosting agriculture, animal husbandry and human being: a book review – Arthur Prudêncio de Araujo Pereira, Journal of Cleaner Production

Are animals a source of Stenotrophomonas maltophiliain human infections? Contributions of a nationwide molecular study – Aurélie Jayol, European Journal of Clinical Microbiology & Infectious Diseases

The organization of bacterial genomes: Towards understanding the interplay between structure and function – Daan J.W. Brocken, Current Opinion in Systems Biology

Pregnancy and early life

Selective maternal seeding and environment shape the human gut microbiome – Katri Korpela, Genome Research

Ecological Shifts of Supragingival Microbiota in Association with Pregnancy – Wenzhen Lin, Frontiers in Cellular and Infectious Microbiology

Human respiratory microbiome

Impaired diversity of the lung microbiome predicts progression of idiopathic pulmonary fibrosis – Youhei Takahashi, Respiratory Research

Human gut microbiome

Methanogens in humans: potentially beneficial or harmful for health – Prem Prashant Chaudhary, Applied Microbiology and Biotechnology

Gut microbiota alterations and dietary modulation in childhood malnutrition – The role of short chain fatty acids – Ceyda Tugba Pekmez, Clinical Nutrition

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A. Rosa, Microbiome

Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic Development – Keaton Stagaman, mSystems

A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies – Bruno K. Rodiño-Janeiro, Advances in Therapy

Characterizing the metabolic phenotype of intestinal villus blunting in Zambian children with severe acute malnutrition and persistent diarrhea – Marta Farràs, PLOS one

Animal experiments

Differences in gut microbiota composition in finishing Landrace pigs with low and high feed conversion ratios – Zhen Tan, Antonie van Leeuwenhoek

Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice – Ling Xiao, Scientific Reports

TRIM31 Deficiency Is Associated with Impaired Glucose Metabolism and Disrupted Gut Microbiota in Mice – Jing Cheng, Frontiers in Physiology

Animal microbiome

Quantitative prediction of shrimp disease incidence via the profiles of gut eukaryotic microbiota – Jinbo Xiong, Applied Microbiology and Biotechnology

Bioturbation activity of three macrofaunal species and the presence of meiofauna affect the abundance and composition of benthic bacterial communities – Élise Lacoste, Marine Environmental Research

Spatial Organization of the Gastrointestinal Microbiota in Urban Canada Geese – Sergei V. Drovetski, Scientific Reports

Skin microbiomes of California terrestrial salamanders are influenced by habitat more than host phylogeny – Alicia K. Bird, Frontiers in Microbiology

Plant, root, and soil microbiome

Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions – Antonietta Mello, Frontiers in Microbiology

Micro-decomposer communities and decomposition processes in tropical lowlands as affected by land use and litter type – Valentyna Krashevska, Oecologia

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Size-Controlled Production of Gold Bionanoparticles Using the Extremely Acidophilic Fe(III)-Reducing Bacterium, Acidocella aromatica – Intan Nurul Rizki, Minerals

Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similismediated by Pseudomonas fluorescens pf36 – Deqiang Chen, Applied Microbiology and Biotechnology

The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting – Xiangyun Zang, Biotechnology for Biofuels

Diversity and contributions to nitrogen cycling and carbon fixation of soil salinity shaped microbial communities in Tarim Basin – Min Ren, Frontiers in Microbiology

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling – Ruben López-Mondéjar, The ISME Journal

Soil bacterial community shifts driven by restoration time and steppe types in the degraded steppe of Inner Mongolia – Minjie Yao, CATENA

One-time phosphate fertilizer application to grassland columns modifies the soil microbiota and limits its role in ecosystem services – Israel Ikoyi, Science of The Total Environment

Enumeration of Culturable Endophytic Bacterial Population of Different Lycopersicum esculentum L. Varieties – Monika Singh, International Journal of Current Microbiology and Applied Sciences

Isolation and Characterization of Methanol Utilizing Microorganisms from Leguminous Crops – Umang Ahlawat, International Journal of Current Microbiology and Applied Sciences

Isolation of Mercury-Resistant Fungi from Mercury-Contaminated Agricultural Soil – Reginawanti Hindersah, Agriculture

Root-associated fungi shared between arbuscular mycorrhizal and ectomycorrhizal conifers in a temperate forest – Hirokazu Toju, Frontiers in Microbiology

Antagonistic Potential and Molecular Characterization of Trichoderma spp. against Rhizoctonia solani Infecting Ghost Pepper in Manipur, India – Khedarani Koijam, International Journal of Current Microbiology and Applied Sciences

Isolation of Biocontrol (Bacterial) Agents from Chickpea (Cicer arietinum linnaeus) – S. Vijaya Kumar, International Journal of Current Microbiology and Applied Sciences

Potentiality of Native Pseudomonas spp. in Promoting Sugarcane Seedling Growth and Red Rot (Colletotrichum falcatum went) Management – P. Kishore Varma, International Journal of Current Microbiology and Applied Sciences

Interactions between isolates of the fungus Beauveria bassiana and Zea mays – Aimee McKinnon, Lincoln University (thesis)

Metagenome Sequencing of Prokaryotic Microbiota from Two Hypersaline Soils of the Odiel Salt Marshes in Huelva, Southwestern Spain – Blanca Vera-Gargallo, Genome Anouncements

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau – Yunfu Gu, Scientific Reports

Water and extremophile microbiome

Survival of Listeria monocytogenes and Staphylococcus aureus in Synthetic Brines. Studying the Effects of Salt, Temperature and Sugar through the Approach of the Design of Experiments – Antonio Bevilacqua, Frontiers in Microbiology

Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov. – Hiroyuki D. Sakai,  International Journal of Systematic and Evolutionary Microbiology

Distinct Osmoadaptation Strategies in the Strict Halophilic and Halotolerant Bacteria Isolated from Lunsu Salt Water Body of North West Himalayas – Shivani Vaidya, Current Microbiology

Archaeal Viruses from High-Temperature Environments – Jacob H. Munson-McGee, Genes

Strategies of adaptation of microorganisms of the three domains of life to high salt concentrations – Nina Gunde-Cimerman, FEMS Microbiology Reviews

Tertiary treatment and dual disinfection to improve microbial quality of reclaimed water for potable and non-potable reuse: A case study of facilities in North Carolina – Emily S. Bailey, Science of The Total Environment

The Early Earth Geochemical and Isotope Record of Serpentinizing Environments from Archean Stichtite (Mg6Cr2(OH)16[CO3] · 4H2O) – Erik B. Melchiorre, Precambrian Research

Process performance and population dynamics of ammonium tolerant microorganisms during co-digestion of fish waste and manure – Linn Solli, Renewable Energy

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – I.A. Vasiliadou, Science of The Total Environment

Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu, Bioresource Technology

Pretreatment of saline antibiotic wastewater using marine microalga – Xueqing Shi, Bioresource Technology

Bioinformatics

Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9Agene of Clostridium thermocellum – Wolfgang H. Schwarz, World Journal of Microbiology and Biotechnology

Techniques

Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench – Wei-Kai Wu, Journal of the Formosan Medical Association

The Application of Omics Data to the Development of AOPs – Mary T. McBride, A Systems Biology Approach to Advancing Adverse Outcome Pathways for Risk Assessment

From correlation to causation: analysis of metabolomics data using systems biology approaches – Antonio Rosato, Metabolomics

Application of ensemble deep neural network to metabolomics studies – Taiga Asakura, Analytica Chimica Acta

Genome-reconstruction for eukaryotes from complex natural microbial communities – Patrick T West, Genome Research

Microbes in the news

Magnetic bacteria cause a stir – Christian Harding, Chemistry World

Federal Panel Passes Antibiotic-Resistant Bacteria Resolutions – Troy Brown, MedScape

Dangerous bacteria found in raw milk from Pennsylvania dairy – Coral Beach, Food Safety Network

 

March 3, 2017

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Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.

Events and jobs

Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology

Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University

General microbiome

Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports

Human oral microbiome

Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry

Human vaginal microbiome

Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv

Human gut microbiome

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome

Animal experiments

Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv

Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv

Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition

Animal microbiome

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express

Water and extremophile microbiome

Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv

Microbes in space

Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv

Phages and viruses

Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science

Bioinformatics

Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv

Techniques

Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome

Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome

Microbes in the news

Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science

Most Viruses And Bacteria Fall From The Sky – Astrobiology Web

Microbes on the market

Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks

Science, career, and publishing

Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv

Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv

March 2, 2018

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Events and jobs

Enter our ‘scientist at work’ photo contest – Nature

General microbiome

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

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

Animal experiments 

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

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

Animal microbiome 

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

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

Plant, root, and soil microbiome

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

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

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

Water microbiome and extremophile 

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

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

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

Built environment 

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

Phages and viruses

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

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

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

Techniques

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

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

Microbes in the news

Biofilm Replaces Plastic Packaging in this Dutch Supermarket Aisle – Futurism

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

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

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

More than soap scum: Learning about biofilms – Silive

7 Startups Treating Disease Using the Microbiome – Nanalyze

ATM keypads, restaurant menus full of bacteria – News3Channel

Non-microbiology picks

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

 

March 1, 2018

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Quite a few articles on viruses today: The identification of human-like hormones in viral genomes that can bind to human and murine receptors; identification of multiple Antarctic sea-ice bacteriophages that are only active in the cold; bacterial immunity loss explains bacteria/phage co-existence; and the plans for a global virome project.

Pregnancy and early life

The microbiome and metabolome of pre-term infant stool is personalized, and not driven by health outcomes including necrotizing enterocolitis and late-onset sepsis -Stephen Wandro – bioRxiv

Review: Relationships Between Perinatal Interventions, Maternal-Infant Microbiomes, and Neonatal Outcomes – Gregory Valentine – Clinics in Perinatology

Human respiratory microbiome

Review: The Respiratory Microbiome in COPD – Orla O’Carroll – COPD – An Update in Pathogenesis and Clinical Management

Human vaginal microbiome

Bacterial identification of the vaginal microbiota in Ecuadorian pregnant teenagers: an exploratory analysis – Ana María Salinas – PeerJ

Human gut microbiome

Dissertation: Multi-Omic Analysis of Complex Microbial Communities in Gastrointestinal Lavage Fluid and their Association with Pancreatic Ductal Adenocarcinoma – Brittany Ferguson-Williams – University of South Alabama

Gut microbiota diversity according to dietary habits and geographical provenance – Bruno Senghor – Human Microbiome Journal

Intestinal microbiota, metabolome and gender dimorphism in autism spectrum disorders – Rafail I.Kushak – Research in Autism Spectrum Disorders

Review: A gut feeling: Microbiome-brain-immune interactions modulate social and affective behaviors – Kristyn E.Sylvia – Hormones and Behavior

Gorillibacterium timonense sp. nov. and Vitreoscilla massiliensis sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients – Sokhna Ndongo – New Microbes and New Infections

«Collinsella provencensis» sp. nov., «Parabacteroides bouchesdurhonensis» sp. nov., and «Sutterella seckii» sp. nov., three new bacterial species identified from human gut microbiota – Niokhor Dione – New Microbes and New Infections

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Animal experiments

Gastrointestinal colonisation and systemic spread of Candida albicans in mice treated with antibiotics and prednisolone – Michiyo Kobayashi-Sakamoto – Microbial Pathogenesis

Effects of non-purified and semi-purified commercial diets on behaviors, plasma corticosterone levels, and cecum microbiome in C57BL/6J mice – Atsushi Toyoda – Neuroscience Letters

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice – Chen Li – The Kaohsiung Journal of Medical Sciences

Immunization with intestinal microbiota-derived Staphylococcus aureus and Escherichia coli reduces bacteria-specific recolonization of the intestinal tract – Julio Adrián Garfias-López – Immunology Letters

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis – Joel R.Wilmore – Cell Host & Microbe

Animal microbiome

Effects of glyphosate herbicide on the gastrointestinal microflora of Hawaiian green turtles (Chelonia mydas) Linnaeus – Ronald P.Kittle – Marine Pollution Bulletin

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows – Lee James Opdahl – Microorganisms

Microbial community dynamics during rearing of black soldier fly larvae (Hermetia illucens) and its impact on exploitation potential – Jeroen De Smet – Applied and Environmental Microbiology

Urea nitrogen induces changes in rumen microbial and host metabolic profiles in dairy cows – D.Jin – Livestock Science

Air Microbiome

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states – Tina Šantl-Temkiv – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Shrub encroachment is associated with changes in soil bacterial community composition in a temperate grassland ecosystem – Xingjia Xiang – Plant and Soil

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau – Peng Dang – Science of The Total Environment

Characterization of halotolerant, pigmented, plant growth promoting bacteria of groundnut rhizosphere and its in-vitro evaluation of plant-microbe protocooperation to withstand salinity and metal stress – Avishek Banik – Science of The Total Environment

Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths – Tessa Camenzind – FEMS Microbiology Ecology

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau – Peng Dang – Science of The Total Environment

Plant growth-promoting rhizobacteria inoculation and nitrogen fertilization increase maize (Zea mays L.) grain yield and modified rhizosphere microbial communities – Luciana P. Di Salvo – Applied Soil Ecology

Review: Understanding the impact of soil sodicity on mycorrhizal symbiosis: Some facts and gaps identified from cotton systems – Samieh Eskandari – Applied Soil Ecology

Morphological, biochemical and molecular characterization of culturable epilithic and endolithic bacteria from rocks of Ayubia (Murree), lower Himalaya, Pakistan – I. Khan –
Applied Ecology and Environmental Research

Impact of sugarcane bagasse-derived biochar on heavy metal availability and microbial activity: A field study – Chengrong Nie – Chemosphere

Water and extremophile microbiome

Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors – Kai-Hui Liu – Extremophiles

Marine microbes in 4D — using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health – Pier Luigi Buttigieg – Current Opinion in Microbiology

The future of genomics in polar and alpine cyanobacteria – Nathan A M Chrismas – FEMS Microbiology Ecology

Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors – Kai-Hui Liu – Extremophiles

Actinobacterial community structure in the Polar Frontal waters of the Southern Ocean of the Antarctica using Geographic Information System (GIS): A novel approach to study Ocean Microbiome – P. Sivasankar – Data in Brief

Review: Actinobacterial community structure in the Polar Frontal waters of the Southern Ocean of the Antarctica using Geographic Information System (GIS): A novel approach to study Ocean Microbiome – P. Sivasankar – Data in Brief

Microbial Ecology

Symbiosis in the microbial world: from ecology to genome evolution – Jean-Baptiste Raina – Biology Open

Dissertation: Understanding Microbial Community Dynamics in High-Solids Lignocellulolytic Systems Using Bioinformatics Tools – Joshua Thomas Claypool – University of California, Davis

Review: Uncultivated microbes—in need of their own nomenclature? – Aharon Oren – The ISME Journal

Resistome

Diverse and abundant antibiotic resistance genes from mariculture sites of China’s coastline – Quanxin Gao – Science of The Total Environment

Evaluation of resistance gene transfer from heat-treated Escherichia coli – Laëtitia Le Devendec – International Journal of Food Microbiology

Phages and viruses

*The Global Virome Project – Dennis Carroll – Science

*Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions – Emrah Altindis – PNAS

*The first known virus isolates from Antarctic sea ice have complex infection patterns – Anne-Mari Luhtanen – FEMS Microbiology Ecology

*Immune loss as a driver of coexistence during host-phage coevolution
Jake L Weissman – The ISME Journal

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries – Steven Shave – PLOSone

Metabolomics

A quantitative metabolomics study of bacterial metabolites in different domains – Fanyi Zhong – Analytica Chimica Acta

Waste and Pollution

Ferric sulfate and proline enhance heavy-metal tolerance of halophilic/ halotolerant soil microorganisms and their bioremediation potential for spilled-oil under multiple stresses – Dina M. Al-Mailem – Frontiers in Microbiology

The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants – Ziyan Wei – Science of The Total Environment

Techniques

Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets – Bashir Sajo Mienda – Future Medicine

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Microbes in the news

Microbiota-gut-brain axis is at epicenter of new approach to mental health – Mary Ann Leibert – EurekAlert

Dietary Advice Based on the Bacteria in Your Gut – Charles Wallace – The Wall Street Journal

The silent microbiome crisis – Tobias Rees – The Washington Post

C-sections and gut bacteria increase risk of childhood obesity – Medical Press

Researchers film bacteria using melee combat to steal antibiotic resistance genes – Phys.org

February 23, 2018

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This Friday: A nice set of papers focused in pathogens such as Salmonella and C. difficile, several papers about soil/root microbiome and more…

Human Microbiome

Review: Skin microbiota and human 3D skin models – Franziska Rademacher – Experimental Dermatology

News and Views: Gut microbiota: Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD – Aonghus Lavelle – Nature Reviews Gastroenterology & Hepatology

Letter: Concomitant resolution through fecal microbiota transplantation of Clostridium difficile and OXA-48-producing Klebsiella pneumoniae –  Giovanni Bruno – Infectious Diseases

Oral cholera vaccination promotes homing of IgA+ memory B cells to the large intestine and the respiratory tract – M van Splunter – Mucosal Immunology

Review: Signalling from the periphery to the brain that regulates energy homeostasis – Ki-Suk Kim – Nature Reviews Neuroscience

Research Highlight: Colorectal cancer: Bacterial biofilms and toxins prompt a perfect storm for colon cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Research Highlight: Metabolism: The small intestine — a new player in fructose metabolism – Ivone Leong – Nature Reviews Endocrinology

Akkermansia muciniphila-derived extracellular vesicles influence gut permeability through the regulation of tight junctions – Chaithanya Chelakkot – Experimental & Molecular Medicine

 

Animal Microbiome / Animal Experiments

Effects of a galacto-oligosaccharide-rich diet on fecal microbiota and metabolite profiles in mice – W. Cheng – Food and Function

Impact of oral fidaxomicin administration on the intestinal microbiota and susceptibility to Clostridium difficile colonization in mice – N. J. Ajami – Antimicrobial Agents and Chemotherapy

Interplay between gut microbiota and p66Shc affects obesity-associated insulin resistance – Stefano Ciciliot – The FASEB Journal

CD Obesity-Prone Rats, but not Obesity-Resistant Rats, Robustly Ferment Resistant Starch Without Increased Weight or Fat Accretion – Diana Obanda – Obesity

Dietary live yeast and increased water temperature influence the gut microbiota of rainbow trout – David Huyben – Journal of Applied Microbiology

Remodeling of the Candida glabrata cell wall in the gastrointestinal tract affects the gut microbiota and the immune response – Rogatien Charlet – Scientific Reports

Absence of receptor guanylyl cyclase C enhances ileal damage and reduces cytokine and antimicrobial peptide production during oral Salmonella Typhimurium infection – Shamik Majumdar – Infection and Immunity

Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato – Kelly Brener-Raffalli – Microbiome

Chitin Oligosaccharide Modulates Gut Microbiota and Attenuates High-Fat-Diet-Induced Metabolic Syndrome in Mice – Junping Zheng – Marine Drugs

Targeting the PXR–TLR4 signaling pathway to reduce intestinal inflammation in an experimental model of necrotizing enterocolitis – Kezhen Huang – Pediatric Research

Hypoglycemic and hypolipidemic effect of S-allyl-cysteine sulfoxide (alliin) in DIO mice – Baiqiang Zhai –  Scientific Reports

 

Human Pathogens

Clostridioides (Clostridium) difficile infection: current and alternative therapeutic strategies – Fernando Gil – Future Medicine

Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins – Elizabeth J. Klemm – mBio

Metronidazole-Loaded Polyethyleneimine and Chitosan-Based Liquid Crystalline System for Treatment of Staphylococcal Skin Infections – Francesca Damiani Victorelli –  Journal of Biomedical Nanotechnology

Cost-Effectiveness of Competing Treatment Strategies for Clostridium difficile Infection: A Systematic Review – Phuc Le – Infection Control & Hospital Epidemiology

 

Food Microbiome

Antibiotic Resistance Genetic Markers and Integrons in White Soft Cheese: Aspects of Clinical Resistome and Potentiality of Horizontal Gene Transfer –  Ana Caroline L. de Paula – Genes

Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation – Xiao-Na Pang – Scientific Reports

 

Plant and Environmental Microbiomes

Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation – Wafa Hassen – Frontiers in Microbiology

Indigenous Pseudomonas spp. Strains from the Olive (Olea europaea L.) Rhizosphere as Effective Biocontrol Agents against Verticillium dahliae: From the Host Roots to the Bacterial Genomes – Carmen Gómez-Lama Cabanás – Frontiers in Microbiology

Preprint: Network hubs in root-associated fungal metacommunities – Hirokazu Toju – BioRxiv

Preprint: Microbial Treatment of Soil Contaminated with Spent engine Oil / Biotreatment of Soil Contaminated with Spent Engine by Microorganisms – Abiodun A. Ayandele – BioRxiv

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses – Michael Hemkemeyer – Frontiers in Microbiology

Peatland Acidobacteria with a dissimilatory sulfur metabolism – Bela Hausmann – The ISME Journal

Systemic Homeostasis in Metabolome, Ionome, and Microbiome of Wild Yellowfin Goby in Estuarine Ecosystem – Feifei Wei – Scientific Reports

 

Microbes in General

Review: Ethanolamine Utilization in Bacteria – Karan Gautam Kavala – mBio

Review: The Genome-Scale Integrated Networks in Microorganisms – Tong Hao – Frontiers in Microbiology

 

February 21, 2018

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Events and jobs

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

General microbiome

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

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

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

Human reproductive or urinary microbiome

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

Human respiratory microbiome

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

Human gut microbiome

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

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

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

Animal microbiome

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

Food microbiology

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

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

Phages and viruses

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

Bioinformatics

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

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

Techniques

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

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

Microbes in the news

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

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

Earthquakes follow wastewater disposal patterns in southern Kansas

Ultra-processed foods ‘linked to cancer’

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

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

Poor fitness linked to weaker brain fiber, higher dementia risk

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

Fewer Infants Died In States That Allowed Affordable Care Act

February 19, 2018

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Events and jobs

Research Technician I – University at Buffalo

General microbiome

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

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

Nasal microbiome

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

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

Pregnancy and early life

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

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

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

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

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

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

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

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

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

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

Oral microbiome

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

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

Animal experiments

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

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

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

Animal microbiome

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

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

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

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

Plant, root, and soil microbiome

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

Water and extremophile microbiome

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

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

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

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

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

Food microbiology

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

Probiotics/Prebiotics

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

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

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

Bioinformatics

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

Techniques

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

February 18, 2018

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Quite a few articles with alerts from today and the day before. Many interesting articles on microbe/microbe and microbe-host interactions, enjoy!

Events and jobs
Senior Bioinformatician – Host Microbiota Interactions – Wellcome Trust Sanger Institute

Postdoctoral Fellow – ‘Microbiome of intestinal tract cancers’ – Centre for Molecular and Biomolecular Informatics (CMBI)

Department Chair – Department of Microbiology and Immunology – College of Veterinary Medicine Cornell University, Ithaca, New York

Associate Scientist- Microbiology – Aerotek, Los Angeles, CA

Multi-site human microbiome
Differential contributions of specimen types, culturing, and 16S – Lone Heimann Larsen – Journal Of Clinical Microbiology

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females – Yu-Feng Huang – BMC Medical Genomics

Human oral microbiome
Bacterial microleakage at the abutment-implant interface, in vitro study. – Carlos Larrucea – Clinical Implant Dentistry And Related Research

Comparison of Oropharyngeal Microbiota from Children with Asthma and Cystic Fibrosis. – Sébastien Boutin – Mediators Of Inflammation

Human vaginal microbiome
Review: Cervicovaginal Microbiota and Reproductive Health: The Virtue of Simplicity. – Melis N Anahtar – Cell Host & Microbe

Human gut microbiome
The effect of Clostridium butyricum on symptoms and fecal microbiota in diarrhea-dominant irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. – Yi-Yuan Sun – Scientific Reports

Association of gut microbial communities with plasma lipopolysaccharide-binding protein (LBP) in premenopausal women – Jessica S Citronberg – ISME

Microbiota Accessible Carbohydrates Suppress Clostridium difficile in a Murine Model – Andrew J Hryckowian – bioRxiv

Review: Gut Microbiota-Based Therapies for Irritable Bowel Syndrome. – Emily K Stern – Clinical And Translational Gastroenterology

Review: A neuroscience perspective of the gut theory of Parkinson’s disease. – Lisa M Smith – The European Journal Of Neuroscience

Microbial-microbial/host interactions
Interactions between predation and disturbances shape prey communities. – Canan Karakoç – Scientific Reports

Elevated success of multispecies bacterial invasions impacts community composition during ecological succession. – Damian W Rivett – Ecology Letters

Competition in biofilms between cystic fibrosis isolates of Pseudomonas aeruginosa is driven by R-pyocins – Olubukola Oluyombo – bioRxiv

Linking associations of rare low-abundance species to their environments by association networks – Tatiana V. Karpinets – Frontiers in Microbiology

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease. – Denise N Bronner – Cell Host & Microbe

Goblet cell associated antigen passages are inhibited during Salmonella typhimur/cium infection to prevent pathogen dissemination and limit responses to dietary antigens. – Devesha H Kulkarni – Mucosal Immunology

Animal experiments
Cytosolic and secreted peptidoglycan-degrading enzymes in Drosophila respectively control local and systemic immune responses to microbiota – Bernard Charroux – Cell Host & Microbe

Differences in the intestinal microbiota between uninfected piglets and piglets infected with porcine epidemic diarrhea virus. – Mei-Zhou Huang – Plos One

Rumen-protected methionine during the peripartal period in dairy cows and its effects on abundance of major species of ruminal bacteria. – Mohamed K Abdelmegeid – Journal Of Animal Science And Biotechnology

Impact of Chestnut and Quebracho Tannins on Rumen Microbiota of Bovines. – Juan María Díaz Carrasco – Biomed Research International

Starvation influences the microbiota assembly and expression of immunity-related genes in the intestine of grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – Aquaculture

Animal microbiome
The Dynamic Distribution of Small-Tail Han Sheep Microbiota across Different Intestinal Segments. – Hao Zhang – Frontiers In Microbiology

Microbiome assembly of avian eggshells and their potential as transgenerational carriers of maternal microbiota. – H Pieter J van Veelen – The Isme Journal

Plant, root, and soil microbiome
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts. – Stefanie Maier – The Isme Journal

Long-term use of cover crops and no-till shift soil microbial community life strategies in agricultural soil. – Radomir Schmidt – Plos One

Genome mining of Streptomyces scabrisporus NF3 reveals symbiotic features including genes related to plant interactions. – Corina Diana Ceapă – Plos One

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments – Liana T. Burghardt – PNAS

Microbial Flora Associated with the Halophyte- – Fehmida Bibi – Frontiers In Microbiology

Root growth improvement of mesquite seedlings and bacterial rhizosphere and soil community changes are induced by inoculation with plant growth-promoting bacteria and promote restoration of eroded desert soil – Cristina Galaviz – Land Degradation and Development

Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions – Marketa Polivkova – Applied Soil Ecology

Succession of the functional microbial communities and the metabolic functions in maize straw composting process – Huawei Wei – Bioresource Technology

Rhizospheric microbial communities are driven by Panax ginseng at different growth stages and biocontrol bacteria alleviates replanting mortality – Linlin Dong – Acta Pharmaceutica Sinica B

Review: Soil protists: a fertile frontier in soil biology research. – Stefan Geisen – Fems Microbiology Reviews

Water and extremophile microbiome
Composition and Activity of Microbial Communities along the Redox Gradient of an Alkaline, Hypersaline, Lake. – Christian F Edwardson – Frontiers In Microbiology

Phosphorus Solubilizing and Releasing Bacteria Screening from the Rhizosphere in a Natural Wetland – Ying Cao – Water

Effects of water flow on submerged macrophyte-biofilm systems in constructed wetlands – Bing Han – Scientific Reports

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities – Eric M Bottos – bioRxiv

Metagenomic exploration of soils microbial communities associated to Antarctic vascular plants – Marco A. Molina-Montenegro – PeerJ Preprints

Built environment
Liquid co-substrates repower sewage microbiomes – Justus Hardegen – bioRxiv

Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas – Edina Szekeres – Environmental Pollution

Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers – Huan Li – Water Research

Review: A review on the applications of microbial electrolysis cells in anaerobic digestion. – Zhengsheng Yu – Bioresource Technology

Probiotics / prebiotics / antibiotics
Tacrolimus concentration to dose ratio in solid organ transplant patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. – Michael H Woodworth – Transplant Infectious Disease : An Official Journal Of The Transplantation Society

Techniques
Functional imaging of the interaction between gut microbiota and the human host: A proof-of-concept clinical study evaluating novel use for 18F-FDG PET-CT. – Ben Boursi – Plos One

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

How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories? – Elisabeth Nagy – Clinical Microbiology and Infection

Microbes in the news
A trip to ‘the poopy lab’ in the interest of drug development – Eric Boodman – STAT News

Probe provides rapid lung investigation – Pallab Ghosh – BBC News

February 16, 2018

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Happy Lunar New Year of the Dog!

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

Jobs

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

General microbiology

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

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

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

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

Human gut microbiome

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

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

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

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

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

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

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

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

Animal experiments

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

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

Animal microbiome

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

Plant, root and soil microbiome

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

Food microbiology

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

Phages and viruses

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

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

Technology

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

Microbes in the news

Surgeon sets new frontiers in battle against bacteria! – WBWire

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

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

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

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

Monitoring bacteria on whale skin – EurekAlert

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

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

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

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

Microbes on the market

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

Scientific Communication and Education

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