June 8, 2018

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.


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


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



June 1, 2018

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


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


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 8, 2018

Today’s Digest is again short and sweet. Human RNA interacts with oral commensals, viral communities diverge between different delivery modes, and Wash U researchers reveal how soil bacteria can digest antibiotics.Today’s Digest is again short and sweet. Human RNA interacts with oral commensals, viral communities diverge between different delivery modes, and Wash U researchers reveal how soil bacteria can digest antibiotics.

Jobs and Events

Microbial Sequencing and Analytics Core Director – Cleveland Clinic – Cleveland, OH, United States

Microbial Culturing and Engineering Core Director – Cleveland Clinic – Cleveland, OH, United States

Personalization and the microbiome in precision medicine: Probiota Americas 2018 program revealed – Stephen Daniells – NutraIngredients-USA

Pregnancy and early life

Preprint: The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks et al. – bioRxiv

Human oral microbiome

** Human tRNA-Derived Small RNAs Modulate Host–Oral Microbial Interactions – X He & F Li et al. – Journal of Dental Research

Press: UCLA researchers discover cellular messengers communicate with bacteria in the mouth – Brianna Aldrich – UCLA Newsroom

Animal experiments

Mouse: Frontline Science: Microbiota reconstitution restores intestinal integrity after cisplatin therapy – Alfredo Perales‐Puchalt & Jairo Perez‐Sanz et al. – Journal of Leukocyte Biology

Preprint: Antibiotic-induced dysbiosis predicts mortality in an animal model of Clostridium difficile infection – Charles Burdet et al. – bioRxiv

Water and extremophile microbiome

Screening of polyhydroxyalkanoate- producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico – Carolina A. Martı ́nez-Gutie ́rrez et al. – PeerJ

Phages and viruses
** Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann, Feargal J. Ryan, & Stephen R. Stockdale et al. – PeerJ

Microbes in the news

Are the gut microbiota determined by genes or the environment? – C.I. Villamil – Medical News Bulletin

The Skin microbiota: a target for Next Generation active ingredients – M. Bey, E. Filaire and JY. Berthon – Premium Beauty News

AI Detects Patterns Of Gut Microbes for Cholera Risk – Marla Vacek Broadfoot – Duke Today

Catheter-associated Infections: Prevention using Polymers – Christine Kelly

Faecal bacteria found in coffee shop ice after random checks – BBC

** Wash U researchers reveal how some bacteria are able to eat antibiotics –  Shahla Farzan – St. Louis Public Radio

Superbugs: are we returning to an era where bacteria are a major killer without a cure? – Anthony McDonnell – LSE blogs

What does ape dung tell us about human health? Gut bacteria in primates’ faeces suggests we are deficient in fibre – Alexandra Thompson – Daily Mail

Vegan Kimchi Is Microbially Pretty Close to the Original – Marissa Fessenden – Smithsonian Mag

Calf gut health starts at birth – Jennifer Carrico – High Plains Journal

Microbes on the market

Amway signs R&D partnership – Rachel Watson – GRBJ

May 1, 2018

A light Digest today with many bioRxiv articles and news pieces. The European Food Safety Authority warns about an emerging fungal pathogen for salamanders, heavy drinking doesn’t bode well for your oral microbiota, and a company is lifting the scientific bar for probiotics.


Program Manager, Microbiology – Rutgers, The State University of New Jersey – Ewing, NJ

General microbiology

** Risk of survival, establishment and spread of Batrachochytrium salamandrivorans (Bsal) in the EU – EFSA Panel on Animal Health and Welfare et al. – EFSA Journal

Preprint: Identification of small regulatory RNAs involved in persister formation – Shanshan Zhang et al. – bioRxiv

Preprint: Identification of novel genes including rpmF and yjjQ critical for Type II persister formation in Escherichia coli – Shuang Liu et al. – bioRxiv

Pregnancy and early life

Preprint: Neonatal gut-microbiome-derived 12,13 DiHOME impedes tolerance and promotes childhood atopy and asthma – Sophia R Levan et al. – bioRxiv

Animal experiments

Preprint: Changes in the gut microbiota and fermentation products associated with enhanced longevity in acarbose-treated mice – Byron J. Smith et al. – bioRxiv

Animal microbiome

Preprint: To B or not to B: Arsenophonus as a source of B-vitamins in whiteflies – Diego Santos-Garcia et al. – bioRxiv

Plant, root and soil microbiome

Preprint: Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed potential Plant Growth Promoting activities – Madhusmita Borah et al. – bioRxiv

Water and extremophile microbiome

Exogenous acyl-homoserine lactones adjust community structures of bacteria and methanogens to ameliorate the performance of anaerobic granular sludge – Longyi Lv et al. – Journal of Hazardous Materials

Preprint: Parallel Evolution of Key Genomic Features and Cellular Bioenergetics Across the Marine Radiation of a Bacterial Phylum – Eric W Getz et al. – bioRxiv


Preprint: Genome Wide Identification Of Bacterial Genes Required For Plant Infection By Tn-Seq – Kevin Royet et al. – bioRxiv

Preprint: Longitudinal tracking of Plasmodium falciparum clones in complex infections by amplicon deep sequencing – Anita Lerch et al. – bioRxiv

Preprint: Diagnosis of Human Leptospirosis: High Resolution Melting Analysis for Direct Detection of Leptospira in the Early Stage of the Disease in a Clinical Setting – Lisa Marques Esteves et al. – bioRxiv

Microbes in the news

Does Gut Microbiota Manipulate Our Minds? – Sci-News

Pancreatic Cancer and the Microbiome — In the Clinic – C. Andrew Kistler – Cancer Therapy Advisor

University of Hohenheim to start microbiome research center – Feedstuffs

** Heavy drinking may increase ‘bad’ bacteria in your mouth, study finds – Jason Lemon – Atlanta Journal Constitution

Vapers and non-smokers have the same flourishing gut flora – Science Daily

Drink kills good bacteria, leaving you at the mercy of disease-causing ‘baddies’ – ELIZABETH MERAB – Healthy Nation

Clinical trial offers natural eczema treatment, using good bacteria to fight the bad – EurekAlert

Why some bacteria eat antibiotics and what we can do about it – Maggie Fox – NBC News

Mediterranean diet increases ‘good’ gut bacteria – Honor Whiteman – Medical News Today

Probiotics For Babies And Kids? New Research Explores Good Bacteria – Allison Aubrey – NPR

Microbes on the market

Evogene unit Biomica designs molecules to analyze bacteria – Gali Weinreb – Globes

** Seed could change the $50 billion probiotic market by relying on real science – Erin Brodwin – The Australian Financial Review

Scientific Communication

Preprint: High impact journals in ecology cover proportionally more statistically significant findings – Silvia Ceausu et al. – bioRxiv

April 17, 2018

Today’s Digest is brief, but not without highlights. Brazilian and MIT scientists created artificial antimicrobial peptides using computer algorithms, ecologists model intransitive competition, and we urgently need to tackle flesh-eating bacteria. In addition, do check out several new issues’ table of contents now, if you have access.

General microbiology

** In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design – William F. Porto et al. – Nature Communications

Press: Artificial antimicrobial peptides could help overcome drug-resistant bacteria – Anne Trafton – MIT News

Memories Are Made of This: Bacteria Remember Who Their Enemies Are with CRISPRs – Marcia Stone – BioScience

Human gut microbiome

Review: Drug‐induced enterocolitis: Prevention and management in primary care – Ignazio Grattagliano et al. – Journal of Digestive Diseases

Journal of Gastroenterology and Hepatology – Issue Information – TOC

Animal experiments

Gnotobiotic and Conventional Mouse Systems to Support Microbiota Based Studies – Richard Lavin et al. – Current Protocols in Immunology

Food Microbiology

Journal of Food Science – Issue Information – TOC

Plant, root and soil microbiome

Commentary: Taking the step: from Evo‐Devo to plant–microbe interaction evolution with the liverwort Marchantia – Mélanie Rich and Pierre‐Marc Delaux – New Phytologist

** Intransitive competition is common across five major taxonomic groups and is driven by productivity, competitive rank and functional traits – Santiago Soliveres et al. – Journal of Ecology

Preprint: Phylogenomics reveals dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism – Steven A Higgins et al. – bioRxiv

Phages and viruses

Preprint: Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut – Emma Guerin et al. – bioRxiv

Preprint: Modelling phage-bacteria interactions driving predation and horizontal gene transfer – Jorge Moura de Sousa et al. – bioRxiv

Microbes in the news

Could Microbiota Predict Response to Anti-TNF Agents in Spondyloarthritis? – Kelly Davio – The Center for Biosimilars

You cannot escape poop bacteria – Sara Chodosh – Popular Science

Scientists Want to Replace Pesticides With Bacteria – Elizabeth G Dunn – Bloomberg Businessweek

Spikes of graphene can kill bacteria on implants – Science Daily

** Flesh-eating bacteria cases on the rise and we need an urgent response – Daniel O’Brien – The Conversation

Bacteria and feces found in fake cosmetics similar to popular makeup brands – Miriam Hernandez – ABC13

BESSY II sheds light on how the internal compass is constructed in magnetotactic bacteria – Science Daily

Connection Between Gut Bacteria And Autoimmunity Strengthens – Julianna LeMieux – American Council on Science and Health

In pictures: The bacteria living on your hands right now – Gaya Chandramohan – Channel NewsAsia

April 10, 2018

After a brief hiatus, your Digest is back! After screening several hundred papers, progress seems to concentrate on a selected fields, including human gut microbiome and plant/soil microbiome. The WHO advocates for a global atlas of zoonotic viruses, a PDF link to a book volume full of application of microbiome engineering in agriculture, environmental protection and industry, and 16s rDNA primers can cross-react with mitochondrial sequences in eukaryotic cells. Last but not least, what can we all do to help young scientists, including ourselves, cope with immense pressure and distress?

General microbiology

Role of Partially Saturated Canthaxanthin and Ergosterol in the Survival of Aspergillus carbonarius Mutant at Extreme Acidic Condition – A. Kumar et al. – Microbiology

Coupled iron-microbial catalysis for CO2 hydrogenation with multispecies microbial communities – Elise Blanchet et al. – Chemical Engineering Journal

An integrated membrane bioreactor system with iron-dosing and side-stream co-fermentation for enhanced nutrient removal and recovery: System performance and microbial community analysis – Ruo-hong Li et al. – Bioresource Technology

The Microbiome and Population Health: Considerations to Enhance Study Design and Data Analysis in Observational and Interventional Epidemiology – Ryan T Demmer – American Journal of Epidemiology

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates – Anna J. Lee et al. – PNAS USA

Human oral microbiome

Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing – Federico Mussano and Ilario Ferrocino et al. – BMC Oral Health

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt and Hazel Poyntz et al. – Clinical & Translational Immunology

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction – Xin Zhou, Jing Li and Junli Guo et al. – Microbiome

Book chapter: Influence of the Gut Microbiome on Immune Development During Early Life – Shankar S. Iyer and Richard S. Blumberg – Physiology of the Gastrointestinal Tract (Sixth Edition)

Book chapter: Gut Barrier: Innate Immunity – Gerco den Hartog et al. – Physiology of the Gastrointestinal Tract (Sixth Edition)

Review: Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases – Jessica Y. Lee et al. – Proteomes

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo – Alba C. Mayta-Apaza et al. – The Journal of Nutritional Biochemistry

Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls – Qi-Xiang Mei et al. – Pancreatology

Human multi-site microbiome

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz et al. – Medical Hypotheses

Animal experiments

Nile tilapia: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles – Gioacchini Giorgia et al. – Microbial Ecology

Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang et al. – Biomedicine & Pharmacotherapy

Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response – Vrishketan Sethi et al. – Gastroenterology

The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot – E.A. Melchior et al. – Livestock Science

Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle – Natalia C. Maldonado et al. – Livestock Science

Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice – Yassine Aitbali et al. – Neurotoxicology and Teratology

Animal microbiome

Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus Japonicus) and its variation during gut regeneration – Luo Wang et al. – Aquaculture Research

Review: The adherence and colonization of microorganisms in fish gastrointestinal tract – Xuemei Li et al. – Reviews in Aquaculture

Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broiler – Chubin Qin and Li Gong et al. – Animal Nutrition

Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. – Thao V. Nguyen et al. – Marine Biotechnology

Review: Use of antibiotics in broiler production: Global impacts and alternatives – Youcef Mehdi et al. – Animal Nutrition

Food Microbiome

PDF: High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation – Dão Pedro de Carvalho Neto et al. – Food Technology and Biotechnology

The impact of vegan production on the kimchi microbiome – Michelle Zabat et al. – Food Microbiology

Plant, root and soil microbiome

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure – Sonya Erlandson et al. – Molecular Ecology

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi – Ko‐Hsuan Chen et al. – New Phytologist

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils – Muhammad Atikul Islam Khan et al. – Ecotoxicology and Environmental Safety

Effects of redox potential on soil Cadmium solubility: Insight into microbial community – Delong Meng et al. – Journal of Environmental Sciences

Long-term phosphorus application to a maize monoculture influences the soil microbial community and its feedback effects on maize seedling biomass – Ming Lang et al. – Applied Soil Ecology

Book chapter: Differential Responses of Plants to Biotic Stress and the Role of Metabolites – Maham Saddique et al. – Plant Metabolites and Regulation Under Environmental Stress

Role of Phenolic Acids from the Rhizosphere Soils of Panax notoginseng as a Double-Edge Sword in the Occurrence of Root-Rot Disease – Ya-Meng Zhao et al. – Molecules

Forum: From Petri Dishes to Model Ecosystems – Oskar Siemianowski et al. – Trends in Plant Science

An Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis – Wenzhao Wang et al. – Journal of Agricultural and Food Chemistry

Seasonal characterization of sugarcane vinasse: Assessing environmental impacts from fertirrigation and the bioenergy recovery potential through biodigestion – Lucas Tadeu Fuess et al. – Science of The Total Environment

Soil microbial biomass: A key soil driver in management of ecosystem functioning – Jay Shankar Singh and Vijay Kumar Gupta – Science of The Total Environment

Phosphorus fertilising potential of fly ash and effects on soil microbiota and crop – Deborah Schönegger et al. – Resources, Conservation and Recycling

Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil – Shuikuan Bei et al. – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone – E. V. Lavrentyeva et al. – Microbiology

Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea – A. S. Savvichev et al. – Microbiology

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats – Taruna Schuelke et al. – Molecular Ecology

Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing – Ryan De Sotto et al. – Journal of Environmental Management

PDF: 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 et al. – Bioresource Technology

Antibiotic resistance in wastewater treatment plants: Tackling the black box – Célia M. Manaia et al. – Environment International

Phages and viruses

** Building a global atlas of zoonotic viruses – Dennis Carroll et al. – Bulletin of WHO

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes – Jeffrey K. Cornuault et al. – Microbiome

Dual Insect specific virus infection limits Arbovirus replication in Aedes mosquito cells – Michaela J. Schultz et al. – Virology


** Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run – Yi-Chun Yeh et al. – mSystems

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method – Xinxu Zhang et al. – Applied and Environmental Microbiology

Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections – A. Mizrahi et al. – Infectious Diseases

Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids – Sean P. Leonard et al. – ACS Synthetic Biology

** Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples – Shailendra Yadav et al. – Current Microbiology

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods – Dongxue Zhang et al. – Analytical Chemistry

** Book chapter PDF: Microbial, Plant, Environmental and Industrial Technologies – Debmalya Barh and Vasco Azevedo – Microbial Omics: Applications in Biotechnology

Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses – Jun Feng and Jing Yang et al. – Biotechnology for Biofuels

eDNA-based bioassessment of coastal sediments impacted by an oil spill – Yuwei Xie et al. – Environmental Pollution

Using natural biomass microorganisms for drinking water denitrification – Darleila Damasceno Costa et al. – Journal of Environmental Management


Cluster and Multiple Correspondence Analyses in Rheumatology: Paths to Uncovering Relationships in a Sea of Data – Lu Han et al. – Rheumatic Disease Clinics of North America

Microbes in the news

Faecal transplantation: do not try this at home – Talha Khan Burki – The Lancet Gastroenterology & Hepatology

Non-microbiology picks

** Editorial: Time to talk about why so many postgrads have poor mental health – Nature

Editorial: Using Preprints for Journal Clubs – Arturo Casadevall and Neil Gow – mBio


March 20, 2018

Still short and sweet. Highlights include combining bacterial and archaeal membranes, a reference catalog for the rumen microbiome and your gut microbiome keeping you awake at night, but really?


Research Associate, Microbiology – Kintai Therapeutics – Cambridge, MA

Partners with relevant publications are needed – Faculty of Agriculture, Ain Shams University – Egypt

Biomedical Scientist or Trainee Biomedical Scientist (Microbiology) – York Teaching Hospital, UK

General microbiology

Identification of Biofilm Inhibitors by Screening Combinatorial Libraries of Metal Oxide Thin Films – Michal M. Dykas et al. – Applied Materials and Interfaces

** Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane – Antonella Caforio et al. – PNAS, USA

Press: Scientists engineer new life form with mixed Bacteria and Archaea membrane – Tibi Puiu – ZME Science

Preprint: Antibiotic-induced cell chaining triggers pneumococcal competence by reshaping quorum sensing to autocrine signaling – Arnau Domenech et al. – bioRxiv

Animal microbiome

** Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection – Rekha Seshadri et al. – Nature Biotechnology

Press: A reference catalog for the rumen microbiome – Joint Genome Institute, DOE

Water and extremophile microbiome

Preprint: Growth arrest in the active rare biosphere – Bela Hausmann et al. – bioRxiv

Phages and viruses

Preprint: Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection – Maxine Zylberberg et al. -bioRxiv


Essay: Which experimental systems should we use for human microbiome science? – Angela E. Douglas – PLoS Biology

Preprint: Efficient genome editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 system for analyzing magnetotactic behavior – Haitao Chen et al. – bioRxiv

Microbes in the news

Could the Microbiome Treat Side Effects of Stem Cell Transplants? – Alexander Burik – Labiotech

Rapid Starch Increases, Decreases in Horse Diets Upset Gut Microbiome – Kristen M. Janicki – the Horse

** Could it be your gut keeping you awake at night? – Kate Leaver – the Guardian

Molecular cuisine for gut bacteria – ScienceDaily

Bacteria churn out a million potential protein drugs – KATRINA KRÄMER – ChemistryWorld

Bacteria that can kill wild sheep and goats has never turned up in Alaska — until now – Zaz Hollander – Anchorage Daily News

News Bites: New molecule able to kill drug-resistant bacteria, FDA approves at-home breast cancer risk test – Chu Meiyi – MIMS Today

Non-antibiotic drugs promote antibiotic resistance – The Economist

Microbes on the market

Microbiome Therapeutics Market Overview with Qualitative analysis, Competitive landscape & Forecast 2023 – Healthcare Journal