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 3, 2018

Today’s digest full of great and fun studies including a fungal survey of the atmosphere and links between gut microbiome and MS.

General Microbiome

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Egert M. Methods

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.Cardona C. mSystems

Biohydrogen production from space crew’s waste simulants using thermophilic consolidated bioprocessing.Wang J. Bioresource Technology

Prevalence of <i>Trichomonas vaginalis</i> infection and protozoan load in South African women: a cross-sectional study.de Waaij DJ.BMJ Open

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.Seridi L. PLoS One

Gut Microbiome

A gut feeling about multiple sclerosis.Quintana FJ. Proceedings of the National Academy of Sciences

Dietary fat and gut microbiota: mechanisms involved in obesity control.Coelho OGL. Critical Reviews in Food Science and Nutrition

Probiotic Species in the Modulation of Gut Microbiota: An Overview.Azad MAK J. Biomedical Research International.

The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.Lv Y. Journal of Diabetes Research

The Gut Microbiome Profile in Obesity: A Systematic Review.Castaner O. International Journal of Endocrinology.

The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation.O’Flaherty S. mSphere

Skin Microbiome

Early-life skin microbiota in hospitalized preterm and full-term infants.Younge NE. Microbiome.

Oral Microbiome

Stimulated and unstimulated saliva samples have significantly different bacterial profiles.Gomar-Vercher S. PLoS

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.Presti RM. AIDS

Oral microbiota in youth with perinatally acquired HIV infection. Starr JR. Microbiome

Air and Water Microbiome

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland.Cousins CR. Geobiology

Taxonomic diversity of fungi deposited from the atmosphere.Woo C. ISME Journal.

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.Garcia SL. mSphere.

Animal Experiments and Microbiome

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.Zhang Z. Microbiome

Longevity extension in Drosophila through gut-brain communication.Westfall S. Scientific Reports

Exploring the diversity-stability paradigm using sponge microbial communities.Glasl B. Scientific Reports

Exploring the Microbiome of Callinectes sapidus (Maryland Blue Crab).Ramachandran P. Genome Announcements

Effect of different types of olive oil pomace dietary supplementation on the rumen microbial community profile in Comisana ewes.Mannelli F. Scientific Reports

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period.Salem SE. Scientific Reports

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus).Mekuchi M. PLoS One

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.Herstad KMV.PLoS One

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera). Ziganshina EE. Biomedical Research International.

Plant and Soil Microbiomes

Antibiotic Resistance in Plant-Pathogenic Bacteria. Sundin GW. Annual Review of Phytopathology

Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with <i>Salicornia</i> for Treatment of Marine Aquaculture Effluents.Ma X. Archaea.

Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses.Acevedo FE. Molecular Plant-Microbe Interactions

Multifunctional potential of endophytic and rhizospheric microbial isolates associated with Butia purpurascens roots for promoting plant growth.da Silva CF. Antonie Van Leeuwenhoek

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.Gołębiewski M. Microbial Ecology

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.Bartoli C. ISME Journal.


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 23, 2018

Today’s digest is packed full of awesome gut microbiome studies, a bunch of plant/soil studies, new features to QIIME and other bioinformatics, as well as a good serving of interesting pre-prints, editorials, and doctoral theses. Enjoy!

General microbiome

Microbial micropatches within microbial hotspots – Lisa M. Dann – PLOS ONE

Pregnancy and early life

The matter of the reproductive microbiome – Sam Schoenmakers – Obstetric Medicine

Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum – Mie Korslund Wiinblad Crusell – Microbiome

The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health – W Allan Walker – Pediatric Research

Human oral microbiome

Oral health status in historic population: Macroscopic and metagenomic evidence – Claire Willmann – PLOS ONE

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study – Meng Shi – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

[Pre-print] Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns – Federica Del Chierico – Frontiers in Microbiology

Clinical applications of gut microbiota in cancer biology – Sunny H. Wong – Seminars in Cancer Biology

* Microbiome-Mediated Effects of the Mediterranean Diet on Inflammation – Melisa A Bailey – Advances in Nutrition

** Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury – Benjamin M Howard – Trauma Surgery & Acute Care Open

Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota – Junyue Xing – Nature Communications

Animal experiments

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets – Wei Jin – Antonie van Leeuwenhoek

Effects of whole-grain rice and wheat on composition of gut microbiota and short-chain fatty acids in rats – Fei Han – Journal of Agriculture and Food Chemistry

Animal microbiome

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles – Chelsea L. Blankenchip – PeerJ

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – World Journal of Microbiology and Biotechnology

The gut microbiome is associated with behavioural task in honey bees – J. C. Jones – Insectes Sociaux

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Plant, root, and soil microbiome

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems – Anil Somenahally – Soil Biology and Biochemistry

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands – Liang Zhang – Environmental Pollution

[Doctoral thesis] Imprint of management on microbial communities in arable soil – Putz, Martina

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination – Dhote, Monika – International Journal of Phytoremediation

Effect of different potassium levels on nitrogen metabolism, nitrogen bacteria and nitrogen archaea bacteria communities in rhizosphere of tobacco plant – WENG Zebin – Acta Tabacaria Sinica

Canola Root–Associated Microbiomes in the Canadian Prairies – Chih-Ying Lay – Frontiers in Microbiology

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves – Leandro Pio de Sousa – Genetics and Molecular Biology

[Review] Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression – Giuliano Bonanomi – Annual Review of Phytopathology

[Pre-print] Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore – Kevin D. Kohl – bioRxiv

[Pre-print] Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California – Sabah Ul-Hasan – bioRxiv

Water and extremophile microbiome 

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community – M.Peces – Water Research

Built environment

[Editorial] Microbiome Yarns: microbiome of the built environment, paranormal microbiology, and the power of single cell genomics – Kenneth Timmis – microbial biotechnology

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces – Ariel L. Furst – Biochemistry

* [Pre-print] Strain­level overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes – Matthew R. Olm – bioRxiv

Probiotics / prebiotics

The effects of probiotics supplementation on metabolic health in pregnant women: An evidence based meta-analysis – Jia Zheng – PLOS ONE


[Pre-print / doctoral thesis] Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning – Alneberg, Johannes – DiVA

** Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin – Nicholas A. Bokulich – Microbiome


Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia – Martina Lardi – High-Throughput

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens – Yi Zhang – Europe PMC

Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol – Ankur Naqib – Gene Expression Analysis

Ed’s non-microbiology picks 

The Environmental Protection Agency in the Early Trump Administration: Prelude to Regulatory Capture

Perspectives on the Great Amazon Reef: Extension, Biodiversity, and Threats

Fasting boosts stem cells’ regenerative capacity

Eggs not linked to cardiovascular risk, despite conflicting advice

Noninvasive spinal stimulation method enables paralyzed people to regain use of hands, study finds

Cannabidiol significantly reduces seizures in patients with severe form of epilepsy

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

Lab photo stock fun: Pipetting Sideways

The Verge had a fun article by Rachel Becker on Thursday about funny science stock photos called “Stock photos of scientists reveal that science is mostly about staring – 
Sometimes at chickens“.

In case you did not know, I made a whole collection of these on this blog – brought together on this page: Lab Stock Photo Fails.

And it made me realize that it was time for a new installment of this series. Today, let’s focus on some great ways to pipet sideways. Because gravity is so over-rated.




89630079-hands-of-scientist-in-the-biochemical-lab-with-pipette-and-multiwells-plate-technician-pipetting-pla (2).jpg














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