August 7, 2018

Today’s Digest features a lot of soil and plant microbiome articles. Highlights include an opinion piece on hypothesis-driven microbiome research, a study on the spread of MCR-3 colistin resistance in China, and a consortium of bacteria to protect plants from pathogents.

General microbiology

** Are microbiome studies ready for hypothesis-driven research? – Anupriya Tripathi et al. – Current Opinion in Microbiology

Mitracarpus frigidus: A promising antifungal in the treatment of vulvovaginal candidiasis – Lara M. Campos et al. – Industrial Crops and Products

Isolation, growth, enzyme assay and identification via 16S rRNA full sequencing of cellulolytic microbes from Nepal for biofuel production – Binayak Raj Pandey et al. – Renewable Energy

Review (Uncorrected Proof): From hairballs to hypotheses – biological insights from microbial networks – Lisa Röttjers & Karoline Faust – FEMS Microbiology Reviews

Review: Barriers and opportunities in bio-based production of hydrocarbons – Yongjin J. Zhou, Eduard J. Kerkhoven & Jens Nielsen – Nature Energy

Antibiotic resistance

** Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study – Yongchang Xu et al. – EBioMedicine

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize – Qing-Lin Chen et al. – Science of The Total Environment

Carbapenem resistance in bacteria isolated from soil and water environments in Algeria – Katia DJENADI et al. – Journal of Global Antimicrobial Resistance

Human respiratory microbiome

Prospective study of timing and pattern of bacteria and viruses in the nasopharyngeal microbiome in a birth cohort – J.L.Mathew et al. – International Journal of Infectious Diseases

Human gut microbiome

Population changes of colon lumen microbiota in patients with chronic hepatitis C – A. Sydorchuk et al. – International Journal of Infectious Diseases

Multi-site human microbiome

Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria – S. H. Kose et al. – Scientific Reports

Food microbiology

Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process – Louise Vermote et al. – International Dairy Journal

Exploring core functional microbiota responsible for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Microbiology

Review: Spoilage yeasts: What are the sources of contamination of foods and beverages? – A. Hernández et al. – International Journal of Food Microbiology

Animal experiments

Consumption of virgin coconut oil in Wistar rats increases saturated fatty acids in the liver and adipose tissue, as well as adipose tissue inflammation – Marianade Moura e Dias et al. – Journal of Functional Foods

Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz et al. – Nature Medicine

Animal microbiome

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract – Nicole A. Lloyd, Sylvie Nazaret & TamarBarkay – Marine Pollution Bulletin

Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray – Benthobatis moresbyi – Tina Kollannoor Johny et al. – Ecological Genetics and Genomics

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart et al. – American Journal of Veterinary Research

Plant, root and soil microbiome

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems – Madangchanok Imchen et al. – Scientific Reports

Structural development and assembly patterns of the root-associated microbiomes during phytoremediation – Yanmei Chen et al. – Science of The Total Environment

A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities – Allison M Spring et al. – Air, Soil and Water Research

Plant-microbe interactions drive denitrification rates, dissolved nitrogen removal, and the abundance of denitrification genes in stormwater control measures – Natalie R Morse et al. – Environmental Science & Technology

Short- and long-term warming alters soil microbial community and relates to soil traits – Hongying Yu et al. – Applied Soil Ecology

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils – Yuqian Tang et al. – Science of The Total Environment

Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil – Kunkun Fan et al. – Soil Biology and Biochemistry

Influence of biochars on the accessibility of organochlorine pesticides and microbial community in contaminated soils – Neelum Ali et al. – Science of The Total Environment

Structure and activity of soil microbial communities in three Mediterranean forests – Felicia Grosso et al. – Applied Soil Ecology

Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria – Srinivasa R. Chaluvadi & Jeff Bennetzen – Frontiers in Plant Science

Review: Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture – D. Maurer et al. – Plant Biology

** Nutrient-and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen – Maureen Berg & Britt Koskella – Current Biology

Network Analyses Can Advance Above-Belowground Ecology – Kelly S.Ramirez et al. – Trends in Plant Science

Minireview: Microbial anaerobic Fe(II) oxidation – ecology, mechanisms and environmental implications – C Bryce et al. – Environmental Microbiology

Phages and viruses

No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster – Mang Shi et al. – Proceedings B

Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms – Shaun T. Cross et al. – Viruses

Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff et al. – Scientific Reports

Microbes in the news

Endophytes: Study Shows GMO Corn Has No Impact On Good Bacteria – Science 2.0


July 31, 2018

Today’s Digest features a report that different types of tobacco products can cause oral microbial dysbiosis, an update on fecal microbiome transplant, and exploration into Westernization and evolution of gut microbiota. Enjoy reading!

General microbiology

Alterations of Salmonella Typhimurium Antibiotic Resistance under Environmental Pressure – Mengfei Peng et al. – Applied and Environmental Microbiology

Preprint: Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome – Tabitha Innocent et al. – bioRxiv

Human oral microbiome

Chicken or the Egg: Microbial Alterations in Biopsy Samples of Patients with Oral Potentially Malignant Disorders – Gabor Decsi et al. – Pathology & Oncology Research

** Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study – Yvonne Vallès et al. – Scientific Reports

Human respiratory microbiome

Decreased microbiome diversity in the HIV small airway epithelium – Stella Xu et al. – Respiratory Research

Human gut microbiome

Antibiotic Exposure and Reduced Short Chain Fatty Acid Production after Hematopoietic Stem Cell Transplant – Lindsey ERomick-Rosendale et al. – Biology of Blood and Marrow Transplantation

** Review: Fecal Microbiota Transplantation: Current Status in Treatment of GI and Liver Disease – Byron P.Vaughn et al. – Clinical Gastroenterology and Hepatology

The association between the incidence of intestinal graft-versus-host disease and antibiotic use after allogeneic hematopoietic stem cell transplantation – Daisuke Hidaka et al. – Clinical Transplantation

Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients – Carola Venturini et al. – Intensive Care Medicine Experimental

** Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization – Jacobo de la Cuesta-Zuluaga et al. – Scientific Reports

A diverse range of human gut bacteria have the potential to metabolise the dietary component gallic acid – María Esteban-Torres et al. – Applied and Environmental Microbiology

Metagenomic analysis of gut microbial communities from a Central Asian population – Almagul Kushugulova et al. – BMJ Open

Animal experiments

Early cellular responses of germ-free and specific-pathogen-free mice to Francisella tularensis infection – ZuzanaKrocova et al. – Microbial Pathogenesis

Rat: Gut microbiota modulation accounts for the neuroprotective properties of anthocyanins – Cláudia Marques et al. – Scientific Reports

Mouse: Complementary intestinal mucosa and microbiota responses to caloric restriction – Kalina Duszka et al. – Scientific Reports

Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys – Quentin N. Wilson et al. – Scientific Reports

Medicinal Mushrooms Supplements Alter Chicken Intestinal Microbiome – Janelle Robinson et al. – International Journal of Medicinal Mushrooms

Review: Standardization in host-microbiota interaction studies: challenges, gnotobiology as a tool, and perspective – Catherine Mooser et al. – Current Opinion in Microbiology

Animal microbiome

Review: Where in the serotonergic system does it go wrong? Unravelling the route by which the serotonergic system affects feather pecking in chickens – Elske Haas & Jerine A.J.van der Eijk – Neuroscience & Biobehavioral Reviews

Exploring the pathology of an epidermal disease affecting a circum-Antarctic sea star – Laura Núñez-Pons et al. – Scientific Reports

Assessment of rumen microbiota from a large cattle cohort reveals the pan and core bacteriome contributing to varied phenotypes – Mingyuan Xue et al. – Applied and Environmental Microbiology

Preprint: Whole genome screen reveals a novel relationship between Wolbachia and Drosophila host translation – Yolande Grobler et al. – bioRxiv

Food microbiology

Dynamics and biodiversity of bacterial and yeast communities during the fermentation of cocoa beans – Jatziri Mota-Gutierrez et al. – Applied and Environmental Microbiology

Plant, root and soil microbiome

Alternate life history phases of a common seaweed have distinct microbial surface communities – Matthew A Lemay et al. – Molecular Ecology

Diversity of bacterial microbiota of coastal halophyte Limonium sinense and amelioration of salinity stress damage by symbiotic plant growth-promoting actinobacterium Glutamicibacter halophytocola KLBMP 5180 – Sheng Qin et al. – Applied and Environmental Microbiology

Bacterial microbiota protect an invasive bark beetle from a pine defensive compound – Chihang Cheng et al. – Microbiome

Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO2 – Panqing Yin et al. – Marine Environmental Research

Mutualistic fungus Phomopsis liquidambari increases root aerenchyma formation through auxin-mediated ethylene accumulation in rice (Oryza sativa L.) – Li-Yan Hu et al. – Plant Physiology and Biochemistry

Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient – Ming Ma et al. – Science of The Total Environment

Isolation and diversity of culturable rhizobacteria associated with economically important crops and uncultivated plants in Québec, Canada – Di Fan et al. – Systematic and Applied Microbiology

Phages and viruses

Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron – Yvan Bettarel et al. – Scientific Reports


Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity – Anton Bankevich & Pavel A.Pevzner – Cell Systems

Microbes in the news

Gut bacteria can protect against Salmonella infections – Press Trust of India – Business Standard

July 19, 2018

An all-around Digest today features newly discovered Wolbachia in Anopheles mosquitoes that can lead to probiotic therapy for malaria, a novel mechanism for the plants to control rhizosphere microbiota, growth and defense, and fascinating art produced entirely by microbes. Enjoy!

General microbiology

Review: Large noncoding RNAs in bacteria – Kimberly A. Harris & Ronald R. Breaker – Microbiology spectrum

Bioremediation and microbial metabolism of benzo(a)pyrene – E M Ostrem Loss & J H Yu – Molecular Microbiology

Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses – Fábio Campioni et al. – Scientific Reports

Preprint: Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen – Alicia Fajardo-Lubian et al. – bioRxiv

Pregnancy and early life

Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester – María Florencia Zacarías et al. – PLoS One

Mini-Review: Antibiotics and lactation: An overview of relative infant doses and a systematic assessment of clinical studies – J.J. van Wattum et al. – Basic & Clinical Pharmacology & Toxicology

Human respiratory microbiome

Characterisation of the nasal microbiota in granulomatosis with polyangiitis – Rennie L Rhee et al. – Annals of the Rheumatic Diseases

Human skin microbiome

Human skin commensals augment Staphylococcus aureus pathogenesis – Emma Boldock et al. – Nature Microbiology

Human oral microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen et al. – Scientific Reports

Human gut microbiome

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages – Chris M Rands et al. – Environmental Microbiology

Review: Recent advances in probiotics as live biotherapeutics against gastrointestinal diseases – Kota RK et al. – Current Pharmaceutical Design

Review: Microbiota–Host Crosstalk: A Bridge Between Cardiovascular Risk Factors, Diet, and Cardiovascular Disease – Jacques Amar – American Journal of Hypertension

Human built environment microbiome

β-Lactam and Fluoroquinolone-Resistant Enterobacteriaceae Recovered from the Environment of Human and Veterinary Tertiary Care Hospitals – Dimitria A. Mathys et al. – Vector-Borne and Zoonotic Diseases


Quantitative metabolomics comparison of traditional blood draws and TAP capillary blood collection – Alexis Catala et al. – Metabolomics

Functional genetic discovery of enzymes using full-scan mass spectrometry metabolomics – Amy A. Caudy et al. – Biochemistry and Cell Biology

Animal experiments

Dietary L-Arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut microbiota in Broiler Chickens Challenged by Clostridium perfringens – Beibei Zhang et al. – Frontiers in Microbiology

Dissertation: Recent Evolution of Host Genetic Control of Microbiota in Cichlid Fishes and Humans – Kaitlin Patricia Coyle – North Carolina State University

Mouse: Gut Microbiota-Stimulated Innate Lymphoid Cells Support b-Defensin 14 Expression in Pancreatic Endocrine Cells, Preventing Autoimmune Diabetes – Michela Miani et al. – Cell Metabolism

Mouse: In vitro probiotic properties of vaginal Lactobacillus fermentum MG901 and Lactobacillus plantarum MG989 against Candida albicans – Chang-Ho Kang et al. – European Journal of Obstetrics & Gynecology and Reproductive Biology

Betaine Improves Intestinal Functions by Enhancing Digestive Enzymes, Ameliorating Intestinal Morphology, and Enriching Intestinal Microbiota in High-salt stressed Rats – Haichao Wang et al. – Nutrients

The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract – Xiaoxi B. Lin et al. – The ISME Journal

Differences Between the Intestinal Lumen Microbiota of Aberrant Crypt Foci (ACF)-Bearing and Non-bearing Rats – Xiuli Xiao et al. – Digestive Diseases and Sciences

Mouse: A selective gut bacterial bile salt hydrolase alters host metabolism – Lina Yao et al. – eLife

Diabetes-Associated Alterations in the Cecal Microbiome and Metabolome are Independent of Diet or Environment in the UC Davis Type 2-Diabetes Mellitus Rat Model – Brian D. Piccolo et al. – American Journal of Physiology-Endocrinology and Metabolism

Animal microbiome

Effects of dietary energy levels on rumen bacterial community composition in Holstein heifers under the same forage to concentrate ratio condition – Yanliang Bi et al. – BMC Microbiology

The cecal microbiome of commercial broiler chickens varies significantly by season – Brian B Oakley et al. – Poultry Science

American beaver: Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome – Zachary Armstrong et al. – The ISME Journal

High Gut Microbiota Diversity Provides Lower Resistance against Infection by an Intestinal Parasite in Bumblebees – Kathrin Näpflin & Paul Schmid-Hempel – The American Naturalist

Effect of Dietary Fructooligosaccharide (FOS) Supplementation on Ileal Microbiota in Broiler Chickens – Yue Shang et al. – Poultry Science

Arrival date and microorganisms in barn swallows – Z. Al Rubaiee et al. – Journal of Avian Biology

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

Plant, root and soil microbiome

Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds – Sabarni Biswas, Asok K. Biswas & Bratati De – Plant Signaling & Behavior

* Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota – Lingfei Hu et al. – Nature Communications

Water and extremophile microbiome

Abstract: Exploring the relative importance of surficial cyanobacteria communities versus physical, chemical and bioloigical processes at depth on sulfur cycling in two microbial mat environments – Maya Gomes et al. – Caltech Authors

Temperature driven changes in benthic microbial diversity influences biogeochemical cycling in coastal sediments – Natalie Hicks et al. – Frontiers in Microbiology

Resistance and Recovery of Methane-Oxidizing Communities depends on Stress Regime and History; a Microcosm Study – Henri van Kruistum et al. – Frontiers in Microbiology

Enterococci Concentrations in a Coastal Ecosystem are a Function of Fecal Source Input, Environmental Conditions, and Environmental Sources – Derek Rothenheber & Stephen Jones – Applied and Environmental Microbiology

Agulhas Current properties shape microbial community diversity and potential functionality – Sandra Phoma et al. – Scientific Reports

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities – Tim N. Enke et al. – Nature Communications

Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays – Manel Ben Abdallah et al. – Extremophiles

Microplastic bacterial communities in the Bay of Brest: Influence of polymer type and size – Laura Frère et al. – Environmental Pollution

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative – Mark V. Brown et al. – Scientific Data

Microbes in space

The influence of bioregenerative life‐support system (BLSS) dietary structure and lifestyle on the gut microbiota: A 105‐day ground‐based space simulation in Lunar Palace 1 – Zikai Hao et al. – Environmental Microbiology

Probiotics, Prebiotics and Synbiotics

Harms Reporting in Randomized Controlled Trials of Interventions Aimed at Modifying Microbiota: A Systematic Review – Aïda Bafeta et al. – Annals of Internal Medicine

Lactobacillus acidophilus and Clostridium butyricum ameliorate colitis in murine by strengthening the gut barrier function and decreasing inflammatory factors – Y. Wang et al. – Beneficial Microbes


Review: Interkingdom microbial consortia mechanisms to guide biotechnological applications – Shu Zhang et al. – Microbial Biotechnology

Establishing a mucosal gut microbial community in vitro using an artificial simulator – LinShu Liu et al. – PLoS One


Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome – Jun Miyoshi et al. – PeerJ

Preprint: Macroecological relationships in the dynamics of gut microbiota – Brian W. Ji et al. – bioRxiv

Microbes in the news

Designer microbiomes – Alfie Gleeson & Abigail Sawyer – BioTechniques

* You need to see this award-winning artwork made entirely from microbes – Irish News

Disgusting Things You Never Knew Your Pets Are Bringing Into Your Home – Amanda Harding – Cheat Sheet

Scientific education

Preprint: Long term impact of intensive post graduate laboratory training at the Cold Spring Harbor Neurobiology of Drosophila summer course – Sarah Ly et al. – bioRxiv

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