February 12, 2019

Today’s Digest features a major effect to tackle the dark matter in the human gut microbiome, comparison of 8 methods to extract DNA from the oral cavity that yielded an unexpected result, and the investigation on whether we can predict sex/age by our gut microbiota. Enjoy!

General microbiology

Perspective: Bridging the Holistic-Reductionist Divide in Microbial Ecology – Robin Tecon et al. – mSystems

Microbioime sister journal: Welcome to Animal Microbiome – Sharon A. Huws

Engineering microbial consortia by division of labor – Garrett W. Roell et al. – Microbial Cell Factories

Preprint: Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update – Pablo Cruz-Morales et al. – bioRxiv

Human skin microbiome

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene – Dilyara S. Martykanova et al. – BioMed Research International

Human oral microbiome

Qualitative and quantitative differences in the subgingival microbiome of the restored and unrestored teeth – Steven W. H. Rademacher et al. – Journal of Periodontal Research

Human respiratory microbiome

Comparison of Subtyping Approaches and the Underlying Drivers of Microbial Signatures for Chronic Rhinosinusitis – Kristi Biswas et al. – mSphere

Human gut microbiome

** 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses – Yuanqiang Zou et al. – Nature Biotechnology

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon – Caroline C. Kim et al. – The ISME Journal

Pinning down the role of common luminal intestinal parasitic protists in human health and disease – status and challenges – Christen Rune Stensvold – Parasitology

Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment During Hematopoietic Stem Cell Transplantation – Vincent Bekker & Romy D. Zwittink et al. – Biology of Blood and Marrow Transplantation

Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial – Jessica Allegretti et al. – The American Journal of Gastroenterology

** Preprint: Age and sex-dependent patterns of gut microbial diversity in human adults – Jacobo de la Cuesta-Zuluaga et al. – bioRxiv

Human reproductive tract microbiome

Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study – Johanna Wiik – BMC Women’s Health

Built environment microbiome

Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China – Hu Li et al. – Science of the Total Environment

Animal experiments

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice – Xinxin Ke et al. – Molecular Metabolism

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens – Chaoliang Wen et al. – The ISME Journal

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome – Nielsen T. Baxter et al. – mSphere

Animal microbiome

Effects of polyethylene microplastics on the gut microbial community, reproduction and avoidance behaviors of the soil springtail, Folsomia candida – Hui Ju et al. – Environmental Pollution

Effects of host blood meal source on reproductive output, nutrient reserves and gut microbiome of West Nile virus vector Culex quinquefasciatus – Aparna Telang & Jessica Skinner – Journal of Insect Physiology

Plant, root and soil microbiome

Soil microbes alter plant fitness under competition and drought – Connor R. Fitzpatrick et al. – Journal of Evolutionary Biology

Multi-resistant plant growth-promoting actinobacteria and plant root exudates influence Cr(VI) and lindane dissipation – María ZoleicaSimón Solá et al. – Chemosphere

Interactions between Pseudomonas spp. and their role in improving the red pepper plant growth under salinity stress – Sandipan Samaddar et al. – Microbiological Research

Plant Defense by VOC-Induced Microbial Priming – Hongwei Liu & Laura E. Brettell – Trends in Plant Science

Water and extremophile microbiome

Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge – Rosa Margesin & Tony Collins – Applied Microbiology and Biotechnology

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria – Noelle A. Held et al. – mSystems

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices – C. S. Neethu et al. – Scientific Reports

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community – Ke Yu et al. – Microbiome

Effects of biomass pyrolysis derived wood vinegar on microbial activity and communities of activated sludge – Fang Zhang et al. – Bioresource Technology

Anti-seasonal submergence dominates the structure and composition of prokaryotic communities in the riparian zone of the Three Gorges Reservoir, China – Yan Fang et al. – Science of The Total Environment

Phages and viruses

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems – Vera Bischoff et al. – The ISME Journal

In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids – Guy Schleyer et al. – Nature Microbiology


The mucosal–luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography – Walid Mottawea et al. – Pediatric Research

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling – Nina Sillner et al. – Journal of Chromatography B

** Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota – Jennifer Rosenbaum et al. – Scientific Reports

Xin’s Non-microbiology pick

Preprint: Where do our graduates go? A toolkit for retrospective and ongoing career outcomes data collection for biomedical PhD students and postdoctoral scholars – Elizabeth A. Silva et al. – bioRxiv


January 29, 2019

Today’s Digest features a defined gut consortium providing protection against pathogen and cancer, a primer on parasitic modulation of host behavior, and an international collaboration all about crAssphage. Enjoy reading and stay warm!

General microbiology

Low molecular weight organic acids enhance the high molecular weight polycyclic aromatic hydrocarbons degradation by bacteria – Anithadevi Kenday Sivaram et al. – Chemosphere

Review: Function of Biohydrogen Metabolism and Related Microbial Communities in Environmental Bioremediation – Ying Teng et al. – Frontiers in Microbiology

Rare Taxa Exhibit Disproportionate Cell-Level Metabolic Activity in Enriched Anaerobic Digestion Microbial Communities – Yangyang Jia et al. – mSystems

Antimicrobial resistance

Rationally designing antisense therapy to keep up with evolving bacterial resistance – Seyfullah Kotil & Eric Jakobsson – PLoS One

Preprint: Bacteriophage resistance alters antibiotic mediated intestinal expansion of enterococci – Anushila Chatterjee et al. – bioRxiv

Preprint: Selection for antibiotic resistance is reduced when embedded in a natural microbial community – Uli Klümper et al. – bioRxiv

Higher Temperatures Do Not Always Achieve Better Antibiotic Resistance Genes Removal in Anaerobic Digestion of Swine Manure – Xu Huang et al. – Applied and Environmental Microbiology

Human respiratory microbiome

Metagenome – Inferred bacterial replication rates in cystic fibrosis airways – Katarzyna Pienkowska et al. – Journal of Cystic Fibrosis

Review: The respiratory microbiota: new insights into pulmonary tuberculosis – Setegn Eshetie & Dick van Soolingen – BMC Infectious Diseases

Human gut microbiome

Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome – Ziwei Song et al. – Microbiome

** A defined commensal consortium elicits CD8 T cells and anti-cancer immunity – Takeshi Tanoue et al. – Nature

Press: A gut punch fights cancer and infection – Nathan E. Reticker-Flynn & Edgar G. Engleman – Nature

Faecal microbiota transplant for eradication of multidrug-resistant Enterobacteriaceae: a lesson in applying best practice? – Benjamin H. Mullish et al. – Clinical Microbiology and Infection

Screening-level microbial risk assessment of acute gastrointestinal illness attributable to wastewater treatment systems in Nunavut, Canada – Kiley Daley et al. – Science of The Total Environment

Review: Probiotics: How Effective Are They in the Fight against Obesity? – Kiran Mazloom et al. – Nutrients

The gut microbiota heterogeneity and assembly changes associated with the IBD – Yang Sun et al. – Scientific Reports

Human gut-microbiome-brain axis

Exploration of microbiota targets for major depressive disorder and mood related traits – Yu-Chu Ella Chung et al. – Journal of Psychiatric Research

Food microbiology

Role of Intestinal Microbiota in the Bioavailability and Physiological Functions of Dietary Polyphenols – K Kawabata et al. – Molecules

Review: Dietary Advanced Glycation End Products: Digestion, Metabolism and Modulation of Gut Microbial Ecology – Matthew Snelson & Melinda T. Coughlan

Animal experiments

Intestinal bacteria modulate the foraging behavior of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae) – Mazarin Akami et al. – PLoS One

Effect of ZFN-edited myostatin loss-of-function mutation on gut microbiota in Meishan pigs – Wen-Tao Cui et al. – PLoS One

Oral Candida administration in a Clostridium difficile mouse model worsens disease severity but is attenuated by Bifidobacterium – Wimonrat Panpetch et al. – PLoS One

Gut microbiota affects development and olfactory behavior in Drosophila melanogaster – Huili Qiao et al. – Journal Experimental Biology

Animal microbiome

** Primer: Parasite manipulation of host behavior -David P. Hughes & Frederic Libersat – Current Biology

Effects of the captive and wild environment on diversity of the gut microbiome of deer mice (Peromyscus maniculatus) – Elliott Schmidt et al. – The ISME Journal

A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology – Christopher A. Gaulke et al. – Microbiome

Microbiota comparison of Pacific white shrimp intestine and sediment at freshwater and marine cultured environment – Lanfen Fan et al. – Science of The Total Environment

T6SS contributes to gut microbiome invasion and killing of an herbivorous pest insect by plant-beneficial Pseudomonas protegens – Jordan Vacheron et al. – The ISME Journal

Genomic diversity landscape of the honey bee gut microbiota – Kirsten M. Ellegaard & Philipp Engel

Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight – Jiqiang Fan et al. – Scientific Reports

Plant, root and soil microbiome

Forum: Microbiome Applications from Lab to Field: Facing Complexity – Angela Sessitsch, Nikolaus Pfaffenbichler & Birgit Mitter – Trends in Plant Science

Review: Plant growth promoting rhizobacteria in sustainable agriculture: from theoretical to pragmatic approach – Samar Mustafa et al. – Symbiosis

Plant evenness modulates the effect of plant richness on soil bacterial diversity – Yao-Qin Sun et al. – Science of The Total Environment

Water and extremophile microbiome

Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula – Elisabeth L. Clifford et al. – Microbial Ecology

Organic matter from Arctic sea-ice loss alters bacterial community structure and function – Graham J. C. Underwood et al. – Nature Climate Change

Review: The unexpected habitat in sewer pipes for the propagation of microbial communities and their imprint on urban waters – Sandra L McLellan & Adélaïde Roguet – Current Opinion in Biotechnology

In situ enrichment of microbial communities on polarized electrodes deployed in alkaline hot springs – Abdelrhman Mohamed et al. – Journal of Power Sources

Genomic and metagenomic insights into the microbial community of a thermal spring – Renato Pedron et al. – Microbiome

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence – Alexander Burkert et al. – Applied and Environmental Microbiology

Phages and viruses

Adjunct phage treatment enhances the effectiveness of low antibiotic concentration against Staphylococcus aureus biofilms in vitro – James Dickey & Véronique Perrot – PLoS One

** Preprint: Global phylogeography and ancient evolution of the widespread human gut virus crAssphage – Robert Edwards et al. – bioRxiv


Metabolomics and Microbiomes as Potential Tools to Evaluate the Effects of the Mediterranean Diet – Qi Jin et al. – Nutrients

Effects of sample preservation on marine microbial diversity analysis – Athenia L.Oldham et al. – Journal of Microbiological Methods

January 1, 2019

Happy New Year! 2019 comes with a short Digest featuring a review on metabolic regulation by gut microbiota and a high throughput yeast two-hybrid screening method. May 2019 bring much success and happiness.

General microbiology

Probabilistic modeling of microbial networks for integrating partial quantitative knowledge within the nitrogen cycle – Damien Eveillard et al. – Frontiers in Microbiology

Methods to Watch: Microbial interactions – Lei Tang – Nature Methods

Human gut microbiome

Dietary quality of predominantly traditional diets is associated with blood glucose profiles, but not with total fecal Bifidobacterium in Indonesian women – Shiela Stefani et al. – PLoS One

** Review: Gut microbiota as important modulator of metabolism in health and disease – Xiang-qian Wang et al. – Royal Society of Chemistry Advances

Review: Colonization and probiotic function of Bifidobacterium longum – Chengcheng Zhang et al. – Journal of Functional Foods

Food microbiome

Microbial communities and volatile metabolites in different traditional fermentation starters used for Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Research International

Plant, root and soil microbiome

Soil parameters drive the diversity of Citrus sinensis rhizosphere microbiota which exhibits a potential in plant drought stress alleviation – Marwa Cherni et al. – Applied Soil Ecology

Revealing microbial processes and nutrient limitation in soil through ecoenzymatic stoichiometry and glomalin-related soil proteins in a retreating glacier forefield – Yonglei Jiang et al. – Geoderma

Water and extremophile microbiome

Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments – Zaisheng Yan et al. – Journal of Hazardous Materials

Addition of algicidal bacterium CZBC1 and molasses to inhibit cyanobacteria and improve microbial communities, water quality and shrimp performance in culture systems – Wujie Xu et al. – Aquaculture

Sludge anaerobic digestion with high concentrations of tetracyclines and sulfonamides: dynamics of microbial communities and change of antibiotic resistance genes – Yang Bai et al. – Bioresource Technology

Temperature dependence of denitrification microbial communities and functional genes in an expanded granular sludge bed reactor treating nitrate-rich wastewater – Runhua Liao et al. – Royal Society of Chemistry Advances

Built environment microbiome

Bacillus species at the Canberra Airport: A comparison of real-time polymerase chain reaction and massively parallel sequencing for identification – M.E. Gahan et al. – Forensic Science International


** A user-friendly platform for yeast two-hybrid library screening using next generation sequencing – Marie-Laure Erffelinck & Bianca Ribeiro et al. – PLoS One

December 25, 2018

Merry Christmas to those of you who celebrate, and Happy Holidays to those of you taking a break! Today’s Digest is dense, so get prepared. This Digest includes many articles in Animal Experiments and Plant, Root and Soil Microbiome. It also features finding antimicrobial resistance in indoor dust, how commensals help maintain epithelial homeostasis, and a carnivorous plant farming microbes for digesting preys. Enjoy!

Antimicrobial resistance

Bioaccumulation of antibiotics in crops under long-term manure application: Occurrence, biomass response and human exposure – Fangkai Zhao et al. – Chemosphere

Preprint: From genotype to antibiotic susceptibility phenotype in Enterobacteriaceae: a clinical perspective – Etienne Ruppé et al. – bioRxiv

Review: Action of Antimicrobial Peptides against Bacterial Biofilms – Muhammad Yasir et al. – Materials

** Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors – Ashkaan K. Fahimipour et al. – mSystems

Pregnancy and early life

Maternal antibiotic prophylaxis affects Bifidobacterium spp. counts in the human milk, during the first week after delivery – M. Padilha et al. – Beneficial Microbes

Human oral microbiome

Preprint: Microbiome composition comparison in oral and atherosclerotic plaque from patients with and without periodontitis – Daichi Isoshima et al. – bioRxiv

Meta-review: Barrett’s esophagus and esophageal cancer: Links to microbes and the microbiome – Teminioluwa A. Ajayi et al. – PLoS Pathogens

Human respiratory microbiome

Lower airway microbiota associates with inflammatory phenotype in severe preschool wheeze – Polly F.M. Robinson et al. – Journal of Allergy and Clinical Immunology

Human gut microbiome

Population-Based Gut Microbiome Associations With Hypertension – Hamdi Jama et al. – Circulation Research

Response to: Population-Based Gut Microbiome Associations With Hypertension – Claire J. Steves & Matthew A. Jackson – Circulation Research

Gut Microbiota and Endothelial Dysfunction Markers in Obese Mexican Children and Adolescents – Khemlal Nirmalkar et al. – Nutrients

Gut mucosal-associated microbiota better discloses Inflammatory Bowel Disease differential patterns than faecal microbiota – Annamaria Altomare et al. – Digestive and Liver Disease

Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT – R. Murphy et al. – Beneficial Microbes

Review: Synthetic consortia of nanobody-coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis-associated diseases and co-morbidities – Kenneth Timmis et al. – Microbial Biotechnology

Human gut-microbiome-brain axis

Review: A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis – S. Du Preez et al. – Systematic Reviews

Built environment microbiome

Carbapenem-resistant Enterobacteriaceae dispersal from sinks is linked to drain position and drainage rates in a laboratory model system – P.Aranega Bou et al. – Journal of Hospital Infection

Enriching Beneficial Microbial Diversity of Indoor Plants and Their Surrounding Built Environment With Biostimulants – Alexander Mahnert et al. – Frontiers in Microbiology

Food microbiome

Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China – Yan Zhu & Yingying Cao et al. – PeerJ

Animal experiments

Gut microbiota profiling in Norwegian weaner pigs reveals potentially beneficial effects of a high-fiber rapeseed diet – Özgün Candan Onarman Umu et al. – PLoS One

** Mouse: Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis – Mayara Grizotte-Lake et al. – Immunity

Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota – Jialin Liu & Ruirui Chang et al. – Frontiers in Microbiology

Genetic Effects on the Gut Microbiota Assemblages of Hybrid Fish From Parents With Different Feeding Habits – Wuhui Li, Junmei Liu & Hui Tan et al. – Frontiers in Microbiology

Mouse: Aspirin eugenol ester regulates cecal contents metabolomic profile and microbiota in an animal model of hyperlipidemia – Ning Ma et al. – BMC Veterinary Research

Effects of Early Intervention with Maternal Fecal Microbiota and Antibiotics on the Gut Microbiota and Metabolite Profiles of Piglets – Chunhui Lin et al. – Metabolites

Mouse: Impact of Cyanocobalamin and Methylcobalamin on Inflammatory Bowel Disease and the Intestinal Microbiota Composition – Xuan Zhu et al. – Journal of Agricultural and Food Chemistry

Impact of probiotics on development and behaviour in Drosophila melanogaster – a potential in vivo model to assess probiotics – E. Gómez et al. – Beneficial Microbes

Effects of chronic caffeine exposure during adolescence and subsequent acute caffeine challenge during adulthood on rat brain serotonergic systems – M.R. Arnold et al. – Neuropharmacology

Mouse: A Microtube Array Membrane (MTAM) Encapsulated Live Fermenting Staphylococcus epidermidis as a Skin Probiotic Patch against Cutibacterium acnes – Albert-Jackson Yang et al. – International Journal of Molecular Sciences

Animal microbiome

Wild bees and their nests host Paenibacillus bacteria with functional potential of avail – Alexander Keller et al. – Microbiome

Field-level clothianidin exposure affects bumblebees but generally not their pathogens – Dimitry Wintermantel et al. – Nature Communications

Plant, root and soil microbiome

** Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant – Dagmara Sirová & Jiří Bárta et al. – Microbiome

The influence of Bt maize cultivation on communities of arbuscular mycorrhizal fungi revealed by MiSeq sequencing – Huilan Zeng et al. – Frontiers in Microbiology

Evaluation of the possible persistence of potential human pathogenic bacteria in olive orchards irrigated with treated urban wastewater – Adriano Sofo et al. – Science of The Total Environment

Relationships between the properties of Spitsbergen soil, number and biodiversity of rhizosphere microorganisms, and heavy metal concentration in selected plant species – Agnieszka Hanaka et al. – Plant and Soil

Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils – Tianzhu Meng et al. – Applied Microbiology and Biotechnology

Shift of millet rhizosphere bacterial community during the maturation of parent soil revealed by 16S rDNA high-throughput sequencing – Lixia Xu et al. – Applied Soil Ecology

Molecular characterization of eukaryotic algal communities in the tropical phyllosphere based on real-time sequencing of the 18S rDNA gene – Huang Zhu et al. – BMC Plant Biology

The impact of carbon addition on the organisation of rhizosheath of chickpea – Sheikh M. F. Rabbi et al. – Scientific Reports

Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long-term biodiversity experiment – Marc W. Schmid et al. – Molecular Ecology

Review: The role of water in plant-microbe interactions – Kyaw Aung et al. – The Plant Journal

Toxicity of phthalate esters to lettuce (Lactuca sativa) and the soil microbial community under different soil conditions – Tingting Ma et al. – PLoS One

Water and extremophile microbiome

Review: Acidithiobacillus ferrooxidans – Raquel Quatrini & D. Barrie Johnson – Trends in Microbiology

Phages and viruses

Perspective: Minimum Information about an Uncultivated Virus Genome (MIUViG) – Simon Roux et al. – Nature Biotechnology

Data: Whole-genome of Mexican-crAssphage isolated from the human gut microbiome – Melany Cervantes-Echeverría et al. – BMC Research Notes

Virome analysis of tick-borne viruses in Heilongjiang Province, China – Fei Meng et al. – Ticks and Tick-borne Diseases

Preprint: Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and mutation – Nicolas M Suarez et al. – bioRxiv

Simultaneous Detection of Beta and Gamma Human Herpesviruses by Multiplex qPCR Reveals Simple Infection and Coinfection Episodes Increasing Risk for Graft Rejection in Solid Organ Transplantation – Yessica Sánchez-Ponce et al. – Viruses

Finer-Scale Phylosymbiosis: Insights from Insect Viromes – Brittany A. Leigh – mSystems


Design and application of a novel two-amplicon approach for defining eukaryotic microbiota – Ana Popovic et al. – Microbiome

Preprint: Optimization of DNA extraction from human urinary samples for mycobiome community profiling – A. Lenore Ackerman et al. – bioRxiv


Combining multiple functional annotation tools increases coverage of metabolic annotation – Marc Griesemer & Jeffrey A. Kimbrel et al. – BMC Genomics

Scientific Communication and Education

Preprint: The economy and environmental attitudes: Does a good economy make citizens care more about the environment? – Stephanie Marie Rizio & Yoshihisa Kashima – bioRxiv

Preprint: Professional medical writing support and the quality, ethics and timeliness of clinical trial reporting: a systematic review – Obaro Evuarherhe et al. – bioRxiv

Preprint: A data-driven approach to reduce gender disparity in invited speaker programs at scientific meetings – Ann-Maree Vallence – bioRxiv

December 4, 2018

A short and sweet Digest today. Many preprints, so take them with a grain of salt. Interesting highlights include skin odor and microbiome, plant derived alternative to antibiotics for growth promotion, and host specialization for bee gut symbionts.

General microbiology

Preprint: The genome of the fungal pathogen Verticillium dahliae reveals extensive bacterial to fungal gene transfer – Xiaoqian Shi et al. – bioRxiv

Antibiotic resistance

Preprint: Antimicrobial Resistance Surveillance Among Gram Negative Bacterial Isolates from Patients in Khartoum State Hospitals – Hana Salaheldin Elbadawi et al. – bioRxiv

Preprint: Linking the Resistome and Plasmidome to the Microbiome – Thibault Stalder et al. – bioRxiv

Human skin microbiome

** Understanding the microbial basis of body odor in pre-pubescent children and teenagers – Tze Hau Lam et al. – Microbiome

Animal experiments

** The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids – Peng Huang, Yan Zhang, Kangpeng Xiao & Fan Jiang et al. – Microbiome

Animal microbiome

** Preprint: Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5 – Kirsten M Ellegaard et al. – bioRxiv

Preprint: Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades – Nicholas D Youngblut et al. – bioRxiv

Water and extremophile microbiome

Preprint: Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia – Vitalii Timofeev et al. – bioRxiv

Phages and viruses

Preprint: Dengue and Chikungunya among Febrile Outpatients in Kinshasa, Democratic Republic of Congo: a cross-sectional study – Sam Proesmans et al. – bioRxiv

Preprint: Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression – Lauren M. Oko et al. – bioRxiv

Scientific communication

Preprint: Cross-Lagged Panel Model in Medical Research: A Cautionary Note – Satoshi Usami et al. – bioRxiv

Preprint: Which author is which? Gender Authorship Position in Aquaculture Literature – Morgan Chow et al. – bioRxiv

November 20, 2018

Here’s your Digest before the US Thanksgiving holiday with a burst of human gut microbiome/animal experiment papers. Science publishes a special edition on diet and health, how do human gut microbes fare against mouse gut commensals, and watch out for the water used in your microbiome studies!


Open Rank Tenure Track Faculty Position – Baylor College of Medicine

General microbiology

Preprint: Natural strain diversity reveals novel biofilm regulation in squid-colonizing Vibrio fischeri – Ella R. Rotman et al. – bioRxiv

Preprint: Genotyping of Salmonella spp. on the basis of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) – Calvin Jiksing et al. – bioRxiv

Pregnancy and early life

Iron-containing micronutrient powders modify the effect of oral antibiotics on the infant gut microbiome and increase post-antibiotic diarrhoea risk: a controlled study in Kenya – Daniela Paganini et al. – Gut

Human skin microbiome

Review: The epithelial immune microenvironment (EIME) in atopic dermatitis and psoriasis – Teruki Dainichi et al. – Nature Immunology

Human oral microbiome

The Effect of Influenza Virus on the Human Oropharyngeal Microbiome – Elisa Ramos-Sevillano et al. – Clinical Infectious Diseases

Human vaginal microbiome

Review: Ecological dynamics of the vaginal microbiome in relation to health and disease – Shirley Greenbaum et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Preprint: Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome – Benjamin D. Ross et al. – bioRxiv

Review: Calorie restriction and its impact on gut microbial composition and global metabolism – Xiaojiao Zheng et al. – Frontiers of Medicine

Fecal microbiota transplantation with frozen capsules for a patient with refractory acute gut graft-versus-host disease – Satoshi Kaito et al. – Blood Advances

Review: Salts and energy balance: A special role for dietary salts in metabolic syndrome
Christopher W.Brey et al. – Clinical Nutrition

IL23R-protective coding variant promotes beneficial bacteria and diversity in the ileal microbiome in healthy individuals without inflammatory bowel disease – Martha Zakrzewski et al. – Journal of Crohn’s and Colitis

In vitro: A four-strain probiotic exerts positive immunomodulatory effects by enhancing colonic butyrate production in vitro – Frédéric Moens et al. – International Journal of Pharmaceutics

Review: Obesity and Cancer Risk: Emerging biological mechanisms and perspectives – Konstantinos I. Avgerinos et al. – Metabolism

Review: Endocrine regulation of gut function – a role for glucagon-like peptide-1 in the pathophysiology of irritable bowel syndrome – Dervla O’Malley – Experimental Physiology

The Human Metabolism of Nuts Proanthocyanidins Does not Reveal Urinary Metabolites Consistent with Distinctive Gut Microbiota Metabotypes – Adrián Cortés‐Martín et al. – Molecular Nutrition & Food Research

Review: The role of dietary factors in inflammatory bowel diseases: new perspectives – Yi Quan Zhou et al. – Journal of Digestive Diseases

Review: Interaction of gut microbiota with dysregulation of bile acids in the pathogenesis of nonalcoholic fatty liver disease and potential therapeutic implications of probiotics – Jiezhong Chen et al. – Journal of Cellular Biochemistry

Review: Cross-Talk Between Gluten, Intestinal Microbiota and Intestinal Mucosa in Celiac Disease: Recent Advances and Basis of Autoimmunity – Atul Munish Chander et al. – Frontiers in Microbiology

Review: Control and dysregulation of redox signalling in the gastrointestinal tract – Eric L. Campbell & Sean P. Colgan – Nature Reviews Gastroenterology & Hepatology

** Review: The gut microbiota at the intersection of diet and human health – Christopher L. Gentile & Tiffany L. Weir – Science

Review: Gut Microbiota and Their Neuroinflammatory Implications in Alzheimer’s Disease – Vo Van Giau et al. – Nutrients

Review: Gut microbiota in diabetes and HIV: Inflammation is the link – Vicente Estrada & Noemi Gonzalez – EBioMedicine

Human gut-microbiome-brain axis

Can the gut be the missing piece in uncovering PD pathogenesis? – Guillaume Chapelet et al. – Parkinsonism & Related Disorders

Human multi-site microbiome

Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions – Lara Costantini et al. – Scientific Reports

Review: Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption – Jessica L.Metcalf – Forensic Science International: Genetics

Boston Type I Keratoprosthesis: Antibacterial Resistance and Microbiota Evaluation of Soft Contact Lenses – Emilio A.Torres-Netto et al. – American Journal of Ophthalmology

Food microbiome

Combined effects of thymol, carvacrol and packaging on the shelf-life of marinated chicken – Layal Karam et al. – International Journal of Food Microbiology

Effect of post-harvest interventions on surficial carrot bacterial community dynamics, pathogen survival, and antibiotic resistance – Vaishali Dharmarha et al. – International Journal of Food Microbiology

The potential use of probiotic and beneficial bacteria in the Brazilian dairy industry – Monique Colombo et al. – Journal of Dairy Research

Animal experiments

In vitro: Environmental pollutant-mediated disruption of gut microbial metabolism of the prebiotic inulin – Jessie Hoffman et al. – Anaerobe

Assessment of the adverse impacts of aflatoxin B1 on gut-microbiota dependent metabolism in F344 rats – Jun Zhou et al. – Chemosphere

Dietary Tomato Powder Inhibits High-Fat Diet-Promoted Hepatocellular Carcinoma with Alteration of Gut Microbiota in Mice Lacking Carotenoid Cleavage Enzymes – Hui Xia et al. – Cancer Prevention Research

Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs – Eric F.Lucking et al. – EBioMedicine

Microbiota-Derived Lactate Activates Production of Reactive Oxygen Species by the Intestinal NADPH Oxidase Nox and Shortens Drosophila Lifespan – Igor Iatsenko et al. – Immunity

A polysaccharide extracted from Astragalus membranaceus residue improves cognitive dysfunction by altering gut microbiota in diabetic mice – Yameng Liu et al. – Carbohydrate Polymers

Mouse: Role of Bile Acids and GLP-1 in Mediating the Metabolic Improvements of Bariatric Surgery – Vance L. Albaugh et al. – Gastroenterology

Evaluation of Sialyllactose Supplementation of a Prebiotic-Containing Formula on Growth, Intestinal Development, and Bacterial Colonization in the Neonatal Piglet – Marcia H Monaco et al. – Current Developments in Nutrition

Mouse: The Probiotic Effectiveness in Preventing Experimental Colitis Is Correlated With Host Gut Microbiota – Sharmila Suwal et al. – Frontiers in Microbiology

Soy-Induced Fecal Metabolome Changes in Ovariectomized and Intact Female Rats: Relationship with Cardiometabolic Health – Victoria J. Vieira-Potter et al. – Scientific Reports

** Selective colonization ability of human fecal microbes in different mouse gut environments – Wei Zhou et al. – The ISME Journal

Rat: Potential Involvement of Peripheral Leptin/STAT3 Signaling in the Effects of Resveratrol and Its Metabolites on Reducing Body Fat Accumulation – Andrea Ardid-Ruiz et al. – Nutrients

Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice – Tim Hendrikx et al. – Gut

Effects of polystyrene microplastics on the composition of the microbiome and metabolism in larval zebrafish – Zhiqin Wan et al. – Chemosphere

Animal microbiome

The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production – A.K. Vasquez et al. – Journal of Dairy Science

Plant, root and soil microbiome

Community diversity and potential functions of rhizosphere-associated bacteria of nickel hyperaccumulators found in Albania – Séverine Lopez et al. – Science of The Total Environment

Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum – Ye Sun et al. – International Journal of Systematic and Evolutionary Microbiology

Linking bacterial community composition to soil salinity along environmental gradients – Kristin M. Rath et al. – The ISME Journal

Soil microbial community composition closely associates with specific enzyme activities and soil carbon chemistry in a long-term nitrogen fertilized grassland – Yue Li et al. – Science of The Total Environment

Water and extremophile microbiome

Periodic and spatial spreading of alkanes and Alcanivorax bacteria in deep waters of the Mariana Trench – Wen-Li Li et al. – Applied and Environmental Microbiology

Distinct bacterial and archaeal diversities and spatial distributions in surface sediments of the Arctic Ocean – Yuguang Wang et al. – FEMS Microbiology Letters

Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands – Dean J Horton et al. – FEMS Microbiology Letters

Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river – Yuzhan Yang et al. – FEMS Microbiology Letters

Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments – Luis J. Perez Calderon et al. – MicrobiologyOpen

Phages and viruses

Preprint: Complete genome of a Measles virus from Roraima state, Brazil – Catia Meneses et al. – bioRxiv

Safety Studies of Pneumococcal Endolysins Cpl-1 and Pal – Marek Harhala et al. – Viruses


Preprint: Controlling complex microbial communities: a network-based approach – Marco Tulio Angulo et al. – bioRxiv

** H2Oh No! The importance of reporting your water source in your in vivo microbiome studies – Jacqueline A. Barnett & Deanna L. Gibson – Gut Microbes


Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut – Yoshihisa Wakita et al. – BMC Microbiology

Non-microbiology picks

Preprint: Benchmarking university medical centres for responsible metrics. A cross sectional study on timely results dissemination across 36 German centres – Susanne Wieschowski et al. – bioRxiv

November 15, 2018

Here’s your Thursday Digest. Highlights include a photo competition to showcase your research, Titanium ion enhancing fresh flower longevity, and an update on the UNITE database for fungal classification.


** BMC ‘Research in progress’ photo competition – deadline tomorrow, November 16.

General microbiology

Review: The birth, evolution and death of metabolic gene clusters in fungi – Antonis Rokas et al. – Nature Reviews Microbiology

Considerations When Designing a Microbiome Study: Implications for Nursing Science – Katherine A. Maki et al. – Biological Research For Nursing

Review: Probiotics in human health and disease: from nutribiotics to pharmabiotics – Eun-Sook Lee et al. – Journal of Microbiology

Antimicrobial resistance

Review: Genome-based prediction of bacterial antibiotic resistance – Michelle Su et al. – Journal of Clinical Microbiology

Pregnancy and early life

Colonization of Cutibacterium avidum during infant gut microbiota establishment – Vanesa Natalin Rocha Martin et al. – FEMS Microbiology Ecology

Human skin microbiome

The proteomic and metabolomic characterization of exercise-induced sweat for human performance monitoring: A pilot investigation – Sean W. Harshman et al. – PLoS One

Human oral microbiome

In vitro: The effect of the stress hormone cortisol on the metatranscriptome of the oral microbiome – Ana E. Duran-Pinedo et al. – npj Biofilms and Microbiomes

Human gut microbiome

Alterations of fecal bacterial communities in patients with lung cancer – Wei-Quan Zhang et al. – American Journal of Translational Research

Temporal Variability of Escherichia coli Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics – Taylor K. S. Richter et al. – mSphere

Review: An insight into the intestinal web of mucosal immunity, microbiota, ​and diet and their role in inflammation and infection – Eliana Marino & Yu Anne Yap – Frontiers in Immunology

Human multisite microbiome

Determinants of the urinary and serum metabolome in children from six European populations – Chung-Ho E. Lau et al. – BMC Medicine

Human gut-microbiome-brain axis

Alteration of gut microbiota-associated epitopes in children with autism spectrum disorders – Mingbang Wang et al. – Brain, Behavior, and Immunity


Metabolomic biomarkers and novel dietary factors associated with gestational diabetes in China – Xuyang Chen et al. – Metabolomics

Animal experiments

An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis – Aliia R. Fatkhullina et al. – Immunity

Gut microbiota dysbiosis correlates with a low-dose PCB126-induced dyslipidemia and non-alcoholic fatty liver disease – Yulang Chi et al. – Science of The Total Environment

Animal microbiome

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status – Sarah M. Hird et al. – mSphere

Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation – Wei Xu et al. – Scientific Reports

Food microbiome

An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China – Mengxi Xie et al. – Food Research International

Plant, root and soil microbiome

The ability of plants to produce strigolactones affects rhizosphere community composition of fungi but not bacteria – Lilia Costa Carvalhais et al. – Rhizosphere

Root exudates induce soil macroaggregation facilitated by fungi in subsoil – Vera L. Baumert et al. – Frontiers in Environmental Science

Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China – Xinwei Cui et al. – Scientific Reports

** Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity – Cai-Xia Li et al. – Microbial Ecology

Ectomycorrhizal fungi inoculation alleviates simulated acid rain effects on soil ammonia oxidizers and denitrifiers in Masson pine forest – Yan Li et al. – Environmental Microbiology

Compounded disturbance chronology modulates the resilience of soil microbial communities and N-cycle related functions – Kadiya Calderón et al. – Frontiers in Microbiology

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials – Sihang Yang et al. – Science of The Total Environment

Silver Toxicity Thresholds for Multiple Soil Microbial Biomarkers – Sotirios Vasileiadis et al. – Environmental Science & Technology

Ectomycorrhizal fungal communities and their functional traits mediate plant-soil interactions in trace element contaminated soils – Marta Gil-Martínez et al. – Frontiers in Plant Science

Modulation of litter decomposition by the soil microbial food web under influence of land use change – Amber Heijboer et al. – Frontiers in Microbiology

Water and extremophile microbiome

Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants – Yu Miao et al. – Water Research

In situ real-time quantification of microbial communities: Applications to cold and dry volcanic habitats – Linda S.Powers et al. – Global Ecology and Conservation

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis – Martin Alexander Fischer et al. – Microbial Biotechnology

Importance of soil texture to the fate of pathogens introduced by irrigation with treated wastewater – Olabiyi Obayomi et al. – Science of The Total Environment

Active pathways of anaerobic methane oxidation across contrasting riverbeds – Li-dong Shen et al. – The ISME Journal

Drying and rainfall shape the structure and functioning of nitrifying microbial communities in riverbed sediments – Maria Isabel Arce et al. – Frontiers in Microbiology

Microbes in space

Inner Workings: Hunting for microbial life throughout the solar system – Adam Mann – PNAS

Confirmation of Microbial Ingress from Space – N. C. Wickramasinghe et al. – Advances in Astrophysics

Phages and viruses

Review: Targeting mechanisms of tailed bacteriophages – Franklin L. Nobrega et al. – Nature Reviews Microbiology

Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil – William Marciel de Souza et al. – Scientific Reports

Review: Respiratory Viral Infection-induced Microbiome Alterations and Secondary Bacterial Pneumonia – Shigeo Hanada et al. – Frontiers in Immunology


Review: Model Microbial Consortia as Tools for Understanding Complex Microbial Communities – Haruta, Shin & Yamamoto, Kyosuke – Current Genomics

Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer – Manasi S. Shah et al. – PLoS One


** The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications – Rolf Henrik Nilsson et al. – Nucleic Acids Research

Bioinformatics tools to assess metagenomic data for applied microbiology – Otávio G. G. Almeida & Elaine C. P. De Martinis – Applied Microbiology and Biotechnology

Pan-genomic analysis provides novel insights into the association of E. coli with human host and its minimal genome – Zhi-Kai Yang et al. – Bioinformatics

Microbes in the news

You Are What Your Bacteria Eat – Patricia Conway & Jorgen Schlundt – Innovation Magazine