Category Archives: Phages and viruses

June 8, 2018

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A short Digest today with primarily preprints. A policy piece on diabetic patient care in the UK, Wolbachia strains never found before in Anopheles mosquitoes, and fecal pollution contributing to antibiotic resistant genes in waste water.

Jobs

Postdoctoral Fellowship in Microbiome Data Science – Johns Hopkins University

General microbiology

Preprint: DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth – Emily Sarah Melzer et al. – bioRxiv

Preprint: Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA – David G Welkie et al. – bioRxiv

Preprint: The fungal-specific Hda2 and Hda3 proteins regulate morphological switches in the human fungal pathogen Candida albicans – Misty Peterson et al. – bioRxiv

Preprint: Chance and pleiotropy dominate genetic diversity in complex bacterial environments – Lianet Noda-Garcia et al. – bioRxiv

Preprint: Molecular basis for the evolution of species-specific hemoglobin capture by pathogenic Staphylococcus – Jacob E Choby et al. – bioRxiv

Antibiotic resistance

Preprint: Comparison of trimethoprim-sulfamethoxazole versus ciprofloxacin monotherapy in Stenotrophomonas maltophilia bloodstream infections in children – Ahu Aksay et al. – bioRxiv

Preprint: The reduced prevalence of macrolide resistance in Mycoplasma pneumoniae clinical isolates from pediatric patients in Beijing in 2016 – Xiu jun Tian et al. – bioRxiv

Preprint: The key lethal effect existed in the antibacterial behavior of short, medium, and long chain fatty acid monoglycerides on Escherichia coli – Song Zhang et al. – bioRxiv

Human oral microbiome

Preprint: The stress hormone cortisol induces virulence in the oral microbiome – Ana Emilia Duran-Pinedo et al. – bioRxiv

Human gut microbiome

** Policy: Diabetes UK nutrition guidelines: reinforcing the foundations of diabetes care – Mark Greener – Practical Diabetes

Animal microbiome

** Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Preprint: The effect of susceptible and resistant potato cultivars on bacterial communities in the tuberosphere of potato in soil suppressive or conducive to common scab disease – Marketa Sagova-Mareckova et al. – bioRxiv

Preprint: Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit – Peter McAtee et al. – bioRxiv

Water and extremophile microbiome

** Preprint: Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments – Antti Karkman et al. – bioRxiv

Phages and viruses

Preprint: Adomaviruses: an emerging virus family provides insights into DNA virus evolution – Nicole L Welch et al. – bioRxiv

Preprint: Epstein-Barr Virus May Contribute to Central Nervous System Involvement in HIV-positive Individuals – Tommaso Lupia et al. – bioRxiv

Bioinformatics

Preprint: PorSignDB: a database of in vivo perturbation signatures for dissecting clinical outcome of PCV2 infection – Nicolaas Van Renne et al. – bioRxiv

 

June 5, 2018

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A model to study the effect of horizontal gene transfer on maintaining equilibrium in microbial communities, antimicrobial tolerance in brewery biofilms, the sperm whale microbiota.

General microbiome

Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities – Yuhang Fan – Journal of Theoretical Biology

Human gut microbiome

Review: Carcinogenesis as a Result of Multiple Inflammatory and Oxidative Hits: a Comprehensive Review from Tumor Microenvironment to Gut Microbiota – Floriana Morgillo – Neoplasia

Animal experiments

Extrathymically Generated Regulatory T Cells Establish a Niche for Intestinal Border-Dwelling Bacteria and Affect Physiologic Metabolite Balance – Clarissa Campbell – Immunity

Animal microbiome

Pre-print: Microbiome interaction networks and community structure from lab-reared and field-collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus mosquito vectors – Shivanand Hegde – bioRxiv

Pre-print: Metagenomics reveals diet-specific specialization in fungus gardens of grass- and dicot-cutter ants – Lily Khadempour – bioRxiv

Occurrence of anthropozoonotic parasitic infections and faecal microbes in free-ranging sperm whales (Physeter macrocephalus) from the Mediterranean Sea – Carlos Hermosilla – Parasitology Research

Plant, root, and soil microbiome

Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom) – Seung-Yoon Oh – Journal of Microbiology

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area – Katie M McGee – Microbial Ecology

Water and extremophile microbiome

Pre-print: Competition and Synergy Between Prochlorococcus and Synechococcus Under Ocean Acidification Conditions – James Jeffrey Morris – bioRxiv

Quantifying the Relative Contributions of Environmental Sources to the Microbial Community in an Urban Stream under Dry and Wet Weather Conditions – Darshan Baral – Applied and Environmental Microbiology

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

Food microbiology

Competitive inter-species interactions underlie the increased antimicrobial tolerance in multispecies brewery biofilms – Ilse Parijs – ISME Journal

Phages and viruses

Influence of gut microbiome on mucosal immune activation and SHIV viral transmission in naive macaques – Yongjun Sui – Mucosal Immunity

Techniques

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds? – Vaibhav Diwan – Journal of Microbiological Methods

June 1, 2018

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Happy June! A rich Digest today featuring evolution of antibiotic resistant Enterobacter, a review on links between gut microbiota and gastrointestinal cancers, and functional variation in the gut microbiome of wild Drosophila populations. Enjoy!

General microbiology

Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities – Manuel Kleiner et al. – PNAS

Commentary: The need for independent research on the health effects of glyphosate-based herbicides – Philip J. Landrigan and Fiorella Belpoggi – Environmental Health

Antibiotic resistance

** Genomic and Geographic Context for the Evolution of High-Risk Carbapenem-Resistant Enterobacter cloacae Complex Clones ST171 and ST78 – Angela Gomez-Simmonds, Medini K. Annavajhala and Zheng Wang et al. – mBio

Doctoral thesis: Implementation of an Antibiotic Stewardship Program for Urinary Tract Infections – Michel, Kaysha Pollyanna – Wilmington University

Preprint: Disrupting folate metabolism alters the capacity of bacteria in exponential growth to develop persisters to antibiotics – Jasmine Morgan et al. – bioRxiv

Pregnancy and early life

Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison – C. Quin et al. – Scientific Reports

Human skin microbiome

The microbiota of traumatic, open fracture wounds is associated with mechanism of injury – Casey Bartow‐McKenney et al. – Wound Repair and Regeneration

Human gut microbiome

Review: Gut nutrient sensing and microbiota function in the control of energy homeostasis – Gilles Mithieux – Current Opinion in Clinical Nutrition and Metabolic Care

Gut Microbiota: FFAR Reaching Effects on Islets – Medha Priyadarshini et al. – Endocrinology

Pathophysiology of diverticular disease – Kathleen M. Schieffer et al. – Expert Review of Gastroenterology & Hepatology

** Review: Gut microbiota-mediated inflammation in obesity: a link with gastrointestinal cancer – Patrice D. Cani & Benedicte F. Jordan – Nature Reviews Gastroenterology & Hepatology

Combining amplicon sequencing and metabolomics in cirrhotic patients highlights distinctive microbiota features involved in bacterial translocation, systemic inflammation and hepatic encephalopathy – Valerio Iebba et al. – Scientific Reports

Human gut-microbiome-brain axis

Review: Recognizing Depression from the Microbiota–Gut–Brain Axis – Shan Liang et al. – International Journal of Molecular Sciences

Review: Microbiota‐gut‐brain axis: Interaction of gut microbes and their metabolites with host epithelial barriers – Y. Bhattarai – Neurogastroenterology & Motility

Animal experiments

Enterobacter cloacae administration induces hepatic damage and subcutaneous fat accumulation in high-fat diet fed mice – Anniina Keskitalo et al. – PLoS One

Mouse: Intestinal microbiota enhances pancreatic carcinogenesis in preclinical models – Ryan M Thomas et al. – Carcinogenesis

Consumption of transglycosylated starch down-regulates expression of mucosal innate immune response genes in the large intestine using a pig model – Barbara U. Metzler-Zebeli et al. – British Journal of Nutrition

N-Acetyl-Cysteine Alleviates Gut Dysbiosis and Glucose Metabolic Disorder in High-Fat Diet-Induced Mice – Junping Zheng et al. – Journal of Diabetes

The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiome – Qixing Mao and Fabiana Manservisi et al. – Environmental Health

Animal microbiome

Insights into the gut microbiota of freshwater shrimp and its associations with the surrounding microbiota and environmental factors – Yanting Zhao et al. – Journal of Microbiology and Biotechnology

Bacterial Microbiota Assemblage in Aedes albopictus Mosquitoes and Its Impacts on Larval Development – Xiaoming Wang et al. – Molecular Ecology

Cockroach: The role of gut microbiota in the regulation of standard metabolic rate in female Periplaneta americana – Paul A. Ayayee et al. – PeerJ

Preliminary Analysis of the Proteome of Exhaled Breath Condensate in Bottlenose Dolphins (Tursiops truncatus) – Bergfelt, Don R et al. – Aquatic Mammals

** Functional variation in the gut microbiome of wild Drosophila populations – Alyssa Bost et al. – Molecular Ecology

Plant, root and soil microbiome

Book chapter: Genomic Identification and Analysis of Specialized Metabolite Biosynthetic Gene Clusters in Plants Using PlantiSMASH – Satria A. Kautsar et al. – Plant Chemical Genomics

Compositional and abundance changes of nitrogen-cycling genes in plant-root microbiomes along a salt marsh chronosequence – Miao Wang et al. – Antonie van Leeuwenhoek

Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing – Cheng Han et al. – Journal of Applied Microbiology

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza et al. – Scientific Reports

Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion – R. Krishnamoorthy et al. – 3 Biotech

Water and extremophile microbiome

Bacterial Communities Changes during Food Waste Spoilage – Shanghua Wu et al. – Scientific Reports

Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting – Caihong Song et al. – Bioresource Technology

Exploratory Study of Archaebacteria and their Habitat in Underground, Opencast Coal Mines and Coal Mine Fire Areas of Dhanbad – D. Mukherjee et al. – Journal of the Geological Society of India

Book chapter: A Practical Guide to Studying the Microbiology of Karst Aquifers – Olivia S. Hershey et al. – Karst Water Environment

Phages and viruses

Responses of intestinal virome to silver nanoparticles: safety assessment by classical virology, whole-genome sequencing and bioinformatics approaches – Kuppan Gokulan and Aschalew Z Bekele et al. – International Journal of Nanomedicine

Technology

In silico design of novel proton-pump inhibitors with reduced adverse effects – Xiaoyi Li et al. – Frontiers of Medicine

Preprint: Diagnosing Bacterial Vaginosis with a Novel, Clinically-Actionable Molecular Diagnostic Tool – Joseph P Jarvis et al. – bioRxiv

Bioinformatics

PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens – Burdukiewicz Michał et al. – Environmental Microbiology Reports

Microbes in the news

Robert Chapkin on Relationships Between the Gut Microbiome, Diet, and Colorectal Cancer – Cancer Network

What are bacteria doing in the bladder? – Gregor Reid – Nature Reviews Urology

May 29, 2018

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Today we have an interesting review discussing the best practices for performing a microbiome study by R. Knight, “Microbial wars” – a brief overview on microbial competition by M.A. Bauer. Check many other interesting papers, particularly “crowded” section of Soil microbes, while in news you can read how scientists tested bacteria’s power to boost broccoli growth in space. Enjoy!

General microbiome

Review: Best practices for analysing microbiomes – Rob Knight – Nature Reviews Microbiology

Microbial wars: Competition in ecological niches and within the microbiome – Maria A. Bauer – Microbial Cell

Review: Concepts and Methods to Access Novel Antibiotics from Actinomycetes – Joachim J. Hug  – Antibiotics

 

 

Human gut microbiome

Gut Microbiota and Human Health: Insights From Ecological Restoration – Matthew R. Orr – The Quarterly Review of Biology

Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota – Ruairi C. Robertson – Microbiome

Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation – Seong Ran Jeon – Current Infectious Disease Reports

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species – Melhem Bilen – Microbiome

Animal experiments

Gut microbes contribute to variation in solid organ transplant outcomes in mice – Christine M. McIntosh – Microbiome

Animal microbiome 

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota – Fanshu Xiao – Current Microbiology

Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration – Mohamed Zeineldin – Microbial Pathogenesis

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain – Alejandro M. Labella – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Effects of genetically modified Burkholderia pyrrocinia JK-SH007E1 on soil microbial community in poplar rhizosphere – L. He – Forest Pathology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Short-term transcriptional response of microbial communities to N-fertilization in a pine forest soil – Michaeline B.N. Albright – Applied and Environmental Microbiology

Spatial structuring of soil microbial communities in commercial apple orchards – Greg Deakin – Applied Soil Ecology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Effects of winter snowpack and nitrogen addition on the soil microbial community in a temperate forest in northeastern China – Guoyong Yan – Ecological Indicators

Responses of soil bacterial communities to Conyza canadensis invasion with different cover classes along a climatic gradient* – Congyan Wang – CLEAN Soil Water

Shifts in microbial community structure and soil nitrogen mineralization following short-term soil amendment with the ammonifier Bacillus amyloliquefaciens DT – Cai Hui – International Biodeterioration & Biodegradation

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China – Xiaoyan Sun – Environmental Science and Pollution Research

Enhancer assisted-phytoremediation of mercury-contaminated soils by Oxalis corniculata L., and rhizosphere microorganism distribution of Oxalis corniculata L. – Zhongchuang Liu – Ecotoxicology and Environmental Safety

Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata – Abanoub E. Wanees – Genome Announcements

Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L.)  – Dandi Hou – Environmental Pollution

Elevated CO2 increases the abundance but simplifies networks of soybean rhizosphere fungal community in Mollisol soils – Zhenhua Yu – Agriculture, Ecosystems & Environment

Suppression of Alternaria blight disease and plant growth promotion of mustard (Brassica juncea L.) by antagonistic rhizosphere bacteria – R. Sharma – Applied Soil Ecology

Water and extremophile microbiome

Salipaludibacillus halalkaliphilus sp. nov., a moderately haloalkaliphilic bacterium from a coastal-marine wetland – Mohammad Ali Amoozegar – International Journal of Systematic and Evolutionary Microbiology

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia – Amjad B. Khalil – BioMed Research International

Seasonal dynamics of bacterioplankton community in a large, shallow, highly dynamic freshwater lake – Zhaoyu Kong – Canadian Journal of Microbiology

Sediment microbial communities influenced by cool hydrothermal fluid migration – Laura A. Zinke – Frontiers in Microbiology / Extreme Microbiology

Microbial interactions with dissolved organic matter drive carbon dynamics and community succession’ – Xiaoqin Wu – Frontiers in Microbiology / Microbiological Chemistry and Geomicrobiology

Metabolites change of Scenedesmus obliquus exerted by AgNPs – Pu Wang – Journal of Environmental Sciences

Built environment

Cultivable microbial diversity associated with cellular phones – Rashmi Kurli – Frontiers in Microbiology / Systems Microbiology

Food microbiology

A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods – Marios Mataragas – Food Microbiology

Phages and viruses

Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs – Qiang Wang – Science of The Total Environment

Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States – Qi Chen – Virology Journal

Bioinformatics

Evaluating the use of diversity indices to distinguish between microbial communities with different traits – Sergey Feranchuka – Research in Microbiology

Taxonomic and functional compositions impacted by the quality of metatranscriptomic assemblies – Maggie Lau – Frontiers in Microbiology – Microbiological Chemistry and Geomicrobiology

Biotechnology

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples – Zhichao Zhou – Applied Microbiology and Biotechnology

Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides – Yanan Wang – Biotechnology for Biofuels

Review: A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications – Izzah Shahid – Environmental Sustainability

Microbes in the news

Could we work together with our bacteria to stop infection?

Scientists test bacteria’s power to boost broccoli growth in space

May 27, 2018

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Pharmacobiomics, liver-microbiome axis, starvation effect on gut microbiota of shrimp,  influence of gut microbiome on the larvae of a lepidopteran pest, microbiota of berries, building a local scientific community in data science and lots of articles for today’s digest.

General microbiome

Pharmacology in the age of the Holobiont – P Norvaisas – Current Opinion in Systems Biology

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production – D Gallagher – Bioresource Technology

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium – N Vardanyan – Environmental Technology

Variation in Electrode Redox Potential Selects for Different Microorganisms Under Cathodic Current Flow From Electrodes in Marine Sediments – BR Lam – Environmental Microbiology

Diurnal patterns of airborne algae in the Hawaiian Islands: a preliminary study – HW Singh – Aerobiologia

Novel human microbe-disease associations inference based on network consistency projection – S Zou – Scientific Reports

Multi-site human microbiome

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans – A Vanhatalo – Free Radical Biology and Medicine

Review: Biodiversity of the Human Oral Mycobiome in Health and Disease – HMHN Bandara – Oral Diseases

 

Human nearly-sterile sites 

Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation – D-L Vu – Clinical Microbiology and Infection

Human gut microbiome

Review: Liver–Microbiome Axis in Health and Disease – TE Adolph – Trends in Immunology

Preprint: Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis. – MM David – bioRxiv

Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome – N Maharshak – Digestive Diseases and Sciences

Prevention and treatment of Clostridium difficile associated diarrhea by reconstitution of the microbiota – N Eliakim-Raz – Human Vaccines & Immunotherapeutics

Animal experiments 

Bifidobacterium spp. reshaping in the gut microbiota by low dose of juçara supplementation and hypothalamic insulin resistance in Wistar rats – G Jamar – Journal of Functional Foods

Salvianolic acid B alters the gut microbiota and mitigates colitis severity and associated inflammation – X Wu – Journal of Functional Foods

Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model – X Zhang – Journal of Functional Foods

Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities – W-F Dai – Fish & Shellfish Immunology

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Z Ge – Scientific Reports

Animal microbiome 

Preprint: The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – MT Schwarz – bioRxiv

Plant, root, and soil microbiome

Review: High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota – A pilot study – J Lukša – Food Research International

Microbial functional responses to long-term anthropogenic impact in mangrove soils – L Cabral – Ecotoxicology and Environmental Safety

Foliage application of nitrogen has less influence on soil microbial biomass and community composition than soil application of nitrogen – X Huang – Journal of Soils and Sediments

Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments – Y Chen – Science of The Total Environment

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5 – J Gao – Ecotoxicology and Environmental Safety

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+‐pumping pyrophosphatase in pepper plants – G Vigani – Environmental Microbiology

Defining plant growth promoting rhizobacteria molecular and biochemical networks in beneficial plant-microbe interactions – A Rosier – Plant and Soil

Roles of Plant-Associated Microbiota in Traditional Herbal Medicine – W Huang – Trends in Plant Science

Spatial structuring of soil microbial communities in commercial apple orchards – G Deakin – Applied Soil Ecology

Effects of root colonization by zinc-solubilizing bacteria on rice plant (Oryza sativa MR219) growth – NMI Othman – Agriculture and Natural Resources

Promising filamentous native fungi isolated from paddy soils for arsenic mitigation in rice grains cultivated under flooded conditions – FR Segura – Journal of Environmental Chemical Engineering

Soil respiration in Chinese tea gardens: autotrophic and heterotrophic respiration – LC Fan – European Journal of Soil Science

Water and extremophile microbiome 

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and ‘Candidatus Methanohalarchaeum thermophilum’, extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. – DY Sorokin – International Journal of Systematic and Evolutionary Microbiology

 

Food microbiology

The Genus Wallemia—From Contamination of Food to Health Threat – J Zajc- Microorganisms

Phages and viruses

Biological species in the viral world – L-M Bobay – PNAS

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium – K Moon – Scientific Reports

 

Non-microbiology picks

Preprint: Building a local community of practice in scientific programming for Life Scientists – SLR Stevens – bioRxiv

 

May 24, 2018

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Pest gut microbiota indirectly effects plant defenses in corn, evolution of microbial social behavior from shearing in flow environments, a model to predict cytokine responses based on multi-comics data integration.

General microbiome

Shearing in flow environment promotes evolution of social behavior in microbial populations – Gurdip Uppal – eLIFE

Pregnancy and early life

Review: The Neonatal Microbiome and Its Partial Role in Mediating the Association between Birth by Cesarean Section and Adverse Pediatric Outcomes – D Montoya-Williams – Neonatology

Human respiratory microbiome

Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota – Thanit Chalermwatanachai – Scientific Reports

Human oral microbiome

Metagenomic study of bacterial microbiota in persistent endodontic infections using Next‐generation sequencing – G Sánchez-Sanhueza – International Endodontic Journal

Human gut microbiome

Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease – Jean-Paul Motta – Inflammatory Bowel Diseases

Temporal and long‐term gut microbiota variation in allergic disease: A prospective study from infancy to school age – Kotryna Simonyté Sjödin – European Journal of Allergy and Clinical Immunology

Bangladeshi children with acute diarrhea show fecal microbiomes with increased Streptococcus abundance, irrespective of diarrhea etiology – Silas Kieser – Environmental Microbiology

Animal experiments

Effects of a protease and essential oils on growth performance, blood cell profiles, nutrient retention, ileal microbiota, excreta gas emission, and breast meat quality in broiler chicks – J H Park – Poultry Science

Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice – Jonathon Mitchell – Inflammatory Bowel Diseases

Review: Microbial Signatures as a Predictive Tool in IBD—Pearls and Pitfalls – Nadine Waldschmitt – Inflammatory Bowel Diseases

Oral hydroxysafflor yellow A reduces obesity in mice by modulating the gut microbiota and serum metabolism – Juan Liu – Pharmacological Research

Impact of commensal flora on periodontal immune response to lipopolysaccharide – Daiki Fukuhara – Journal of Periodontology

Animal microbiome

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes – Rocky D Patil – Journal of Animal Science

Plant, root, and soil microbiome

Cadmium phytoextraction potential of king grass (Pennisetum sinese Roxb.) and responses of rhizosphere bacterial communities to a cadmium pollution gradient – Li Hu – Environmental Science and Pollution Research

Gut-Associated Bacteria of Helicoverpa zea Indirectly Trigger Plant Defenses in Maize – Jie Wang – Journal of Chemical Ecology

Water and extremophile microbiome

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer – María E Alcamán-Arias – FEMS Microbiology Letters

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands – Catiane Pelissari – Water Research

Pre-print: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines – Andrian P Gajigan – PeerJ

Food microbiology

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry – Naama Massad-Ivanir – Scientific Reports

Probiotics/prebiotics

Survival of Planktonic and Sessile Cells of Lactobacillus rhamnosus and Lactobacillus reuteri upon Exposure to Simulated Fasting-State Gastrointestinal Conditions – Kyle B Klopper – Probiotics and Antimicrobial Proteins

Phages and viruses

Pre-print: A novel oceanic uncultured temperate cyanophage lineage – José Flores-Uribe – bioRxiv

Bioinformatics

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses – Olivier B Bakker – Nature Immunology

More microbes

Pre-print: New sequential touch method for determining bacterial contact transfer rate from finger to surface – Pengcheng Zhao – bioRxiv

Amy’s non-microbiology picks

Restoration of paper artworks with microemulsions confined in hydrogels for safe and efficient removal of adhesive tapes – Nicole Bonelli – PNAS

May 17, 2018

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Genome engineering tools for non-model prokaryotes, microgravity and space radiation’s effects on microbes, an analysis of science podcasts.

General microbiome

Taking the technical microbiome into the next decade – Jo De Vrieze – Environmental Microbiology

Pre-print: Links between environment, diet, and the hunter-gatherer microbiome – Gabriela K Fragiadakis – bioRxiv

Human vaginal microbiome

The effect of vaginal microbial communities on colonization by Staphylococcus aureus with the gene for toxic shock syndrome toxin 1 (TSST-1): a case–control study – Jacob D Pierson – FEMS Pathogens and Disease

Human urinary microbiome

Lactobacillus and Urine Microbiome in Association with Urinary Tract Infections and Bacterial Vaginosis – Jun-Mo Kim – Urogenital Tract Infection

Human gut microbiome

Combination Antibiotics Improves Disease Activity and Alters Microbial Communities In Children with Ulcerative Colitis – Kattayoun Kordy – Journal of Pediatric Gastroenterology and Nutrition

Animal experiments

Postnatal colonization with human “infant-type” Bifidobacterium species alters behavior of adult gnotobiotic mice – Berkley Luk – PLOS ONE

A gene catalogue of the Sprague-Dawley rat gut metagenome – Hudan Pan – Gigascience

Animal microbiome

Changes in intestinal microbiota of Bufo gargarizans and its association with body weight during metamorphosis – Lihong Chai – Archives of Microbiology

Metagenomic analysis of Varroa-free Australian honey bees (Apis mellifera) shows a diverse Picornavirales virome – John M K Roberts – Journal of General Virology

Plant, root, and soil microbiome

Strong associations between plant genotypes and bacterial communities in a natural salt marsh – Gregory P Zogg – Ecology and Evolution

What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs – Julian Taffner – mSphere

Rhizosphere hydrophobicity limits root water uptake after drying and subsequent rewetting – Mohsen Zarebanadkouki – Plant and Soil

Crop rotational diversity increases disease suppressive capacity of soil microbiomes – Ariane L Peralta – Ecosphere

Water and extremophile microbiome

A thiotrophic microbial community in an acidic brine lake in Northern Chile – Lorena Escudero – Antonie van Leeuwenhoek

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium – Andrew Hart – PLOS ONE

Microbes in space

Review: Effect of microgravity & space radiation on microbes – Giuliana Senatore – Future Microbiology

Food microbiology

Bacterial community analysis in three types of the fermented seafood, jeotgal, produced in South Korea – Eun-Ji Song – Bioscience, Biotechnology, and Biochemistry

Metabolomics

Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean – Wenshu Kang – BMC Plant Biology

Techniques

Review: Building a genome engineering toolbox in non‐model prokaryotic microbes – Emily Freed – Biotechnology and Bioengineering

Pre-print: Effective soil extraction method for cultivating previously uncultured soil bacteria – Tuan Manh Nguyen – bioRxiv

More microbes

Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another – Jessica L Abbate – PLOS Neglected Tropical Diseases

Pre-print: Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells – Shraddha Shitut – bioRxiv

Science, career, and publishing

Pre-print: Science podcasts: analysis of global production and output from 2004 to 2018 – Lewis E MacKenzie – bioRxiv

May 16, 2018

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Today we have a interesting set of reviews. In addtion: research about virome in infants, microbiome changes in Alzheimer’s disease and changes in neonate and maternal microbiome under gestational diabetes. We have also the report of the Oral Microbiome Bank of China and some papers about invertebrate microbiome.  

 

Human/General Microbiome

Review: Microbiome-Immune Interactions and Liver Disease – James H. Tabibian –  Clinical Liver Disease

Review: Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications – Anne Hall – Journal of Pediatric Gastroenterology and Nutrition

Review: Starch Tolerance and the Short Bowel – Jan de Laffolie – Journal of Pediatric Gastroenterology and Nutrition

Review: Microbial Fermentation of Starch: Its Impact on the Range of Acceptable Carbohydrate Intake – Satish C. Kalhan – Journal of Pediatric Gastroenterology and Nutrition

Review: Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories – K. L. Stanhope – Obesity Reviews

Review: On the potential role of intestinal microbial community in hepatocarcinogenesis in chronic hepatitis B – Ashraf Mohamadkhani – Cancer Medicine

Review: The gut microbiota and the brain-gut-kidney axis in hypertension and chronic kidney disease – Tao Yang – Nature Reviews Nephrology

Review: Epithelial Barrier Dysfunctions in Atopic Dermatitis: A Skin-Gut-Lung Model Linking Microbiome Alteration and Immune Dysregulation – T.H. Zhu – British Journal of Dermatology

Review: Association between Fusobacterium nucleatum and colorectal cancer: Progress and future directions – Sheng Zhang – Journal of Cancer

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann​ – PeerJ

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus – Jinfeng Wang – Gut

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease – Sumathi Sankaran Walters – SOJ Microbiology & Infectious Diseases

Gut Microbiome is Altered in Patients with Alzheimer’s Disease – Zhuang, Zhen-Qian – Journal of Alzheimer’s Disease

The Oral Microbiome Bank of China – Peng Xian – International Journal of Oral Science

 

Animal Microbiome

Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice – Maria Carolina S Mendes – World Journal of Gastroenterology

A cytokine network involving IL-36γ, IL-23, and IL-22 promotes antimicrobial defense and recovery from intestinal barrier damage – Vu L. Ngo – PNAS

Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiome – Anja Malawi Brandon – Environmental Science and Technology

Supplementation with organic acids showing different effects on growth performance, gut morphology and microbiota of weaned pigs fed with highly or less digestible diets – S. Li – Journal of Animal Science

Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3”Me) – Xin Zhang – Molecular Nutrition and Food Research

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – Francisca Zepeda-Paulo​ – PeerJ

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts – Anne Duplouy – PeerJ

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution

 

Food Microbiome

The changes of dominant lactic acid bacteria and their metabolites during corn stover ensiling – Zhenshang Xu – Journal of Applied Microbiology

Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing – Ziqiang Pan – Journal of Food Protection

Succession of bacterial microbiota in tilapia fillets at 4 °C and in situ investigation of spoilers – Shan Duan – World Journal of Microbiology and Biotechnology

 

Bioinformatics/Genomics

Preprint: Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis – Patricia Vera-Wolf (and featuring our Microbiome Digest founder, Elisabeth Bik) – BioRxiv

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments – Alexandre Almeida – GigaScience

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – Molecular Ecology

 

Beneficial Microbes and Compounds

Review: Vitamin D in inflammatory bowel disease: more than just a supplement – John Gubatan – Current Opinion in Gastroenterology

Review: Bleach for Atopic Dermatitis – Melody Maarouf – Dermatitis

Simultaneous Amelioratation of Colitis and Liver Injury in Mice by Bifidobacterium longum LC67 and Lactobacillus plantarum LC27 – Se-Eun Jang – Scientific Reports

 

Pathogens

Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen – Tim Rollenske – Nature Immunology

 

Environmental Microbiome (including Built environments)

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K.Nuy – Science of The Total Environment

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing – Lauren O’Connell​​ – PeerJ

 

Antimicrobial Resistance

Emerging Infectious Diseases, Antimicrobial Resistance and Millennium Development Goals: Resolving the Challenges through One Health – G. V. Asokan – Central Asian Journal of Global Health

 

Other

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins – Nitzan Koppel – eLife

The Interaction of Anti-diabetic α-Glucosidase Inhibitors and Gut Bacteria α-Glucosidase – Kemin Tan – Protein Science

 

May 15, 2018

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Comparison of the cottage cheese and artisanal cheese microbiota, no microbes found in amniotic fluid from healthy term pregnancies, impacts of ocean warming on the oyster microbiome.

General microbiome

Molecular (Me)micry? – Orly Avni – Cell Host & Microbe

Pregnancy and early life

Amniotic fluid from healthy term pregnancies does not harbor a detectable microbial community – Efrem S Lim – Microbiome

Multi-site human microbiome

Data on the gut and saliva microbiota from a cohort of atherosclerosis patients determined by 16S rRNA gene sequencing – Gregory B Gloor – Data in Brief

Human skin microbiome

Antiseptic Agents Elicit Short-Term, Personalized and Body Site-Specific Shifts in Resident Skin Bacterial Communities – Adam J SanMiguel – The Journal of Investigative Dermatology

Human gut microbiome

Review: Systematic review assessing the effectiveness of dietary intervention on gut microbiota in adults with type 2 diabetes – David Houghton – Diabetologia

Animal experiments

Increased butyrate priming in the gut stalls microbiome associated-gastrointestinal inflammation and hepatic metabolic reprogramming in a mouse model of Gulf War Illness – Ratanesh Kumar Seth – Toxicology and Applied Pharmacology

Light exposure influences the diurnal oscillation of gut microbiota in mice – Guangyan Wu – Biochemical and Biophysical Research Communications

Early-Life Antibiotic-Driven Dysbiosis Leads to Dysregulated Vaccine Immune Responses in Mice – Miriam Anne Lynn – Cell Host & Microbe

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens – Phillippa L Connerton – Microbiome

Animal microbiome

Potential impacts of hypoxia and a warming ocean on oyster microbiomes – Bushra Khan – Marine Environmental Research

Mixed-Mode Transmission Shapes Termite Gut Community Assemblies – Rafael R da Costa – Trends in Microbiology

Plant, root, and soil microbiome

Effect of compost application on the dynamics of carbon in a nectarine orchard ecosystem – E Baldi – Science of the Total Environment

Review: Current research trends on plastic pollution and ecological impacts on the soil ecosystem: A review – Yooeun Chae – Environmental Pollution

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine Vanissa Tchuisseu Tchakounté – Microbiological Research

Characterisation of antagonistic yeasts for biocontrol applications on apples or in soil by quantitative analyses of synthetic yeast communities – Simon Gross – Yeast

Water and extremophile microbiome

Microbial ecology of two hot springs of Sikkim: Predominate population and geochemistry – Ishfaq Nabi Najar – Science of the Total Environment

Exploring abundance, diversity and variation of a widespread antibiotic resistance gene in wastewater treatment plants – Ziyan Wei – Environment International

Antimicrobial resistance and potential virulence of Vibrio parahaemolyticus isolated from water and bivalve mollusks from Bahia, Brazil – Irana Paim Silva – Marine Pollution Bulletin

Diversity and distribution of Archaea in global estuarine ecosystems – Xiaobo Liu – Science of the Total Environment

Microbes in space

Acute exposure to space flight results in evidence of reduced lymph Transport, tissue fluid Shifts, and immune alterations in the rat gastrointestinal system – W E Cromer – Life Sciences in Space Research

Food microbiology

Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses – Hao Jin – Journal of Dairy Science

Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods – Steven C Ricke – Advances in Applied Microbiology

Probiotics/prebiotics

Strategies to improve the functionality of probiotics in supplements and foods – Claude P Champagne – Current Opinion in Food Science

Phages and viruses

Pre-print: Diversity of active viral infections within the Sphagnum microbiome – Joshua M A Stough – bioRxiv

Review: Composition of gut microbiota and its influence on the immunogenicity of oral rotavirus vaccines – Cliff A Magwira – Vaccines

Metabolomics

Review: A Review on Human Fecal Metabolomics: Methods, Applications and the Human Fecal Metabolome Database – Naama Karu – Analytica Chimica Acta

More microbes

Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance – D G Joakim Larsson – Environment International

May 12, 2018

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Today’s highlights in our Microbiology picks: Antibacterial activity of nested concentric patterns, relationship between the microbiota epitopes and antigenic epitopes, a book chapter on N-Acetyl transferase microbes, core microbiota for de novo IBD, soil microbes and disease suppression, fungi of office dust, microbes of potable  water from the Himalayan region, articles from ‘Techniques’ section.

Today’s highlights in our non-microbes picks: Epidemiology is important, recent on-goings on harassment, mental health awareness in academia, mimicking the prebiotic chemistry using flow chemistry, step taken by Wellcome Trust against misconduct in academia including harassment, Horizon 2020 budget for 2021-27.

 

Events and jobs

Laboratory Manager : New York, NY, United States – Albert Einstein College of Medicine – Deadline: 18 May 2018

General microbiome

Supramolecular Kandinsky circles with high antibacterial activity – H Wang – Nature Communications

Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes – SC Pro – PLoS One

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia – JB Benoit – PLoS One

Book chapter: N-Acetyltransferases Microorganisms – S Boukouvala – Arylamine N-acetyltransferases in Health and Disease:From Pharmacogenetics to Drug Discovery and Diagnostics

 

Human vaginal microbiome

Preprint: Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Z-L Deng – bioRxiv

Human gut microbiome

Preprint: Variability of core microbiota in newly diagnosed treatment-naïve paediatric Inflammatory Bowel Disease patients – TGJ de Meij – bioRxiv

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Y Zhang – mBio

Animal experiments 

Preprint: Bottlenecks in the transmission of Porcine reproductive and respiratory syndrome virus (PRRSV1) to naïve pigs and quasi-species variation during infection in partially immune pigs – M Cortey – bioRxiv

Lactobacillus gasseri PA-3 utilizes the purines GMP and guanosine and decreases their absorption in rats – N Yamada – Nucleosides, Nucleotides & Nucleic Acids

An exclusive metabolic niche enables strain engraftment in the gut microbiota – ES Sheperd – Nature

Interleukin 1α-Deficient Mice Have an Altered Gut Microbiota Leading to Protection from Dextran Sodium Sulfate-Induced Colitis – M Nunberg – mSystems

Animal microbiome 

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – F Zepeda-Paulo – PeerJ

Plant, root, and soil microbiome

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression – BEA Dignam – PLoS One

Relations between bacterial communities and enzyme functions of two paddy soils – X Luo – European Journal of Soil Science

Nematophagus fungi increasing phosphorus uptake and promoting plant growth – TSA Monteiro – Biological Control

Water and extremophile microbiome 

Effect of elevated pressure on ferric iron reduction coupled to sulfur oxidation by biomining microorganisms – R Zhang – Hydrometallurgy

Halophilic & halotolerant prokaryotes in humans – EH Seck – Future Medicine

Preprint: Structural variability and functional association in the epiphytic bacteria assemblies of freshwater macrophytes (Myriophyllum spicatum) – L Xian – bioRxiv

Investigation of nutrients and faecal coliforms removal in wastewater using a hydroponic system – SF Ndulini – Physics and Chemistry of the Earth, Parts A/B/C

Built environment 

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – J-H Park – Indoor Air

 

Phages and viruses

Preprint: First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region – AK Singh – bioRxiv

Preprint: “In plaque-mass spectrometry imaging” reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions – G Schleyer – bioRxiv

Preprint: Adventitious viruses persistently infect three commonly used mosquito cell lines – J Weger-Lucarelli – bioRxiv

Techniques

Preprint: High-resolution ISR amplicon sequencing reveals personalized oral microbiome – C Mukherjee – bioRxiv

Preprint: Transcriptome Analysis of Neisseria gonorrhoeae During Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants Between Men and Women – K Nudel – bioRxiv

Designer cells programming quorum-sensing interference with microbes – F Sedlmeyer – Nature Communications

A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum – A Roth – Nature Communications

Preprint: Detection and quantification of the heterogeneity of S. aureus bacterial populations to identify antibiotic-induced persistence – MH Hasan – bioRxiv

Rapid isolation of fast-growing methanotrophs from environmental samples using continuous cultivation with gradually increased dilution rates – J Kim – Applied Microbiology and Biotechnology

Microbes in the news

Stanley Falkow, Who Saw How Bacteria Cause Disease, Dies at 84 – NY Times

How the Bugs In Your Gut Could Affect Your Blood Vessels – Live Science

Faeces transplant: The best cure for severe diarrhoea may be more faeces – Times Live

Cancer-killing viruses show promise — and draw billion-dollar investment – Nature

Does where we live affect our skin microbiome? – Medical News Bulletin

Non-Microbiology Picks

Editorial: Epidemiology is a science of high importance – Nature Communications

Mimicking the surface and prebiotic chemistry of early Earth using flow chemistry – DJ Ritson – Nature Communications

I’d whisper to my student self: you are not alone – D Reay – Nature

Harassment should count as scientific misconduct – E Marín-Spiotta – Nature

€100-billion budget proposed for Europe’s next big research programme – I Vesper – Nature

Editorial: The #MeToo campaign is gaining ground in China – Nature

Editorial: What to do to improve postgraduate mental health – Nature

Report harassment or risk losing funding, says top UK science funder – H Else – Nature

78,000-year-old record of Middle and Later stone age innovation in an East African tropical forest – C Shipton – Nature Communications

KACST Impact – Nature Communications