Category Archives: Phages and viruses

September 1, 2018

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Have a nice weekend! Today, several reviews about different aspects of human genome (from Vitamin D to the Impact of Colonialism in the changes of health in Indigenous people). Today, we have also several studies about poultry microbiome and changes in food microbiota, in addition with interesting studies about microbiota drug metabolism.

 

General and Human Microbiome

Review: The hygiene hypothesis at a glance: early exposures, immune mechanism and novel therapies – Gabriel M.Alexandre-Silva – Acta Tropica

Review: Dietary vitamin D, vitamin D receptor, and microbiome – Jun Sun – Current Opinion in Clinical Nutrition and Metabolic Care

Theory and Synthesis: Consequences of colonialism: A microbial perspective to contemporary Indigenous health – Emily Skelly – American Journal of Physical Anthropology

Review: Early-Life Exposures and Risk of Diabetes Mellitus and Obesity – Véronique Gingras – Current Diabetes Reports

Review: Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer – Veronica Lazar – Frontiers in Immunology

Review: Early Disruption of the Microbiome Leading to Decreased Antioxidant Capacity and Epigenetic Changes: Implications for the Rise in Autism – Rebecca S. Eshraghi – Frontiers in Cellular Neuroscience

Review: Energy balance and gastrointestinal cancer: risk, interventions, outcomes and mechanisms – Cornelia M. Ulrich – Nature Reviews Gastroenterology & Hepatology

Review: Microbial Production of Conjugated Linoleic Acid and Conjugated Linolenic Acid Relies on a Multienzymatic System – Ana S. Salsinha – Microbiology and Molecular Biology Reviews

News & Views: Gut microbiome, microbial metabolites and the development of NAFLD – Cyrielle Caussy – Nature Reviews Gastroenterology & Hepatology

Does Severity of Alzheimer’s Disease Contribute to Its Responsiveness to Modifying Gut Microbiota? A Double Blind Clinical Trial – Azadeh Agahi – Frontiers in Neurology

Evaluation of relationship between dental caries, diabetes mellitus and oral microbiota in diabetics – Bhagyashri Ramachandra Latti – Journal of Oral and Maxillofacial Pathology

Effects of Japanese diet in combination with exercise on visceral fat accumulation – Masaki Asano – Nutrition

Enteric Virome and Bacterial Microbiota in Children with Ulcerative Colitis and Crohn’s Disease – Melissa A. Fernandes – Journal of Pediatric Gastroenterology and Nutrition

Temporal instability of the post-surgical maxillary sinus microbiota – Ioannis Koutsourelakis – BMC Infectious Diseases

Influence of cigarette smoking on the human duodenal mucosa-associated microbiota – Erin R. Shanahan – Microbiome

 

Animal Microbiome

Review: A Review of Prebiotics Against Salmonella in Poultry: Current and Future Potential for Microbiome Research Applications – Andrew C. Micciche – Frontiers in Veterinary Science

Gut Microbiota and Relevant Metabolites Analysis in Alcohol Dependent Mice – Guanhao Wang – Frontiers in Microbiology

Gut microbiota mediates the anti-obesity effect of calorie restriction in mice – Shuo Wang – Scientific Reports

Effect of humic substances on rumen fermentation, nutrient digestibility, methane emissions, and rumen microbiota in beef heifers – Stephanie A Terry – Journal of Animal Science

Effects of glucose oxidase on growth performance, gut function, and cecal microbiota of broiler chickens – Shengru Wu – Poultry Science

16S ribosomal RNA sequencing reveals a modulation of intestinal microbiome and immune response by dietary L-theanine supplementation in broiler chickens – Muhammad Saeed – Poultry Science

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) – Jeremiah J. Minich – Microbiology Open

Effect of oat hulls as a free choice feeding on broiler performance, short chain fatty acids and microflora under a mild necrotic enteritis challenge – Sarbast K.Kheravii – Animal Nutrition

Application of Illumina-MiSeq high throughput sequencing and culture-dependent techniques for the identification of microbiota of silver carp (Hypophthalmichthys molitrix) treated by tea polyphenols – Shiliang Jia – Food Microbiology

 

Beneficial Microbes and Compounds

Rhubarb Peony Decoction Ameliorates Ulcerative Colitis in Mice by Regulating Gut Microbiota to Restoring Th17/Treg Balance – Shuang Luo – Journal of Ethnopharmacology

Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury – Sabrina Duranti – PLoS One

Beneficial Effect of Virgin Coconut Oil on Alloxan-Induced Diabetes and Microbiota Composition in Rats – Sinisa Djurasevic – Plant Foods for Human Nutrition

 

Food Microbiome

Microbiota dynamics and volatilome profile during stink bean fermentation (Sataw-Dong) with Lactobacillus plantarum KJ03 as a starter culture – Krittanon Jampaphaeng – Food Microbiology

Microbial spoilage investigation of thawed common cuttlefish (Sepia officinalis) stored at 2 °C using next generation sequencing and volatilome analysis – F. F. Parlapani – Food Microbiology

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 – Food Microbiology

Revealing the influence of microbiota on the quality of Pu-erh tea during fermentation process by shotgun metagenomic and metabolomic analysis – Zhongyuan Li – Food Microbiology

Influence of lactate and acetate removal on the microbiota of French fresh pork sausages – Agnès Bouju-Albert – Food Microbiology

 

Plant Microbiome

The future has roots in the past: the ideas and scientists that shaped mycorrhizal research – Paola Bonfante – New Phytology Trust

 

Experiments

Chemoselective Probe Harboring a Unique Bioorthogonal Cleavage Site for Investigation of Gut Microbiota Metabolism – Neeraj Garg – Angewandte Chemie  

An ex vivo fermentation screening platform to study drug metabolism by human gut microbiota – Evita van de Steeg – Drug Metabolism and Disposition

 

August 28, 2018

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A brief Digest today featuring a review on how the microbiota affects drug disposition, a study adopting fungal growth measurement in the soil to that in the medium and in the plants, and a genetic approach to specifically depleting microbiome-derived metabolites in the host tissue.

General microbiology

* Minireview: How to determine the role of the microbiome in drug disposition – Jordan E Bisanz et al. – Drug Metabolism and Disposition

Loss of genomic diversity in a Neisseria meningitidis clone through a colonization bottleneck – Araceli Lamelas et al. – Genome Biology and Evolution

Human gut microbiome

Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol – Lara R. Dugas et al. – BMC Public Health

Multi-omics analyses to deliver the most effective treatment to every patient with inflammatory bowel disease – Rinse K. Weersma et al. – Gastroenterology

Plant, root and soil microbiome

Preprint: Antimicrobial, Antioxidant and Anti-Inflammatory Activities of Proteins of Phaseoulus lunatus (Fabaceae) Baby Lima Beans Produced in Ecuador – Javier Tamayo et al. – bioRxiv

* Preprint: Fungal growth is affected by and affects pH and redox potential (Eh) of the growth medium – Lydia Bousset et al. – bioRxiv

Water and extremophile microbiome

Preprint: The role of land use types and water chemical properties in structuring the microbiome of a connected lakes system – Sophi Marmen et al. – bioRxiv

Phages and viruses

Preprint: Repurposing of drugs as novel influenza inhibitors from clinical gene expression infection signatures – Mario Andres Pizzorno et al. – bioRxiv

Technology

Preprint: Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples – Fabien Cholet et al. – bioRxiv

** Preprint: Depletion of microbiome-derived molecules in the host using Clostridium genetics – Chun-Jun Guo et al. – bioRxiv

Bioinformatics

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data – Benjamin Sobkowiak et al. – BMC Genomics

August 27, 2018

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Highlights: how microbes influence the system they inhabit, maternal microbial metabolism, gut microbiota in pancreatic disease and other metabolic disorders, core and staphylococcal microbiota in skin & nose of pigs, wheat head microbiome bacteria,  abundant & rare biospheres of hot springs, antibiotic degradation by microbes, virome.

General microbiome

Review: Understanding how microbiomes influence the systems they inhabit – Ed K. Hall – Nature Microbiology

Male Bladder Microbiome Relates to Lower Urinary Tract Symptoms – Petar Bajic – European Urology Focus

Pregnancy and early life

Is maternal microbial metabolism an early-life determinant of health? – Kymberleigh A. Romano – LabAnimal

Human oral microbiome

The oral microbiome in oral lichen planus during a one‐year randomized clinical trial – Camilla Kragelund – Oral Diseases

Human respiratory microbiome

Interaction between the microbiome and TP53 in human lung cancer – K. Leigh Greathouse – Genome Biology

Human gut microbiome

The Gut Microbiome in Pancreatic Disease – Venkata S. Akshintala – Clinical Gastroenterology and Hepatology

FXR-Dependent Modulation of the Human Small Intestinal Microbiome by the Bile Acid Derivative Obeticholic Acid – Elliot S. Friedman – Gastroenterology

Review: Role of gut microbiota in chronic low‐grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies – I. C. L. van den Munckhof – Obesity Reviews

Bile acid homeostasis and intestinal dysbiosis in alcoholic hepatitis – Dragos Ciocan – Alimentary Pharmacology & Therapeutics

Characterization and induction of prophages in human gut-associated Bifidobacterium hosts – Travis N. Mavrich – Scientific Reports

In Vitro Ecological Response of the Human Gut Microbiome to Bioactive Extracts from Edible Wild Mushrooms – Emanuel Vamanu – Molecules

Review: The journey of gut microbiome – An introduction and its influence on metabolic disorders – Ankita Chattopadhyay -Frontiers in Biology

Animal experiments 

Sulfated polysaccharide from sea cucumber modulates the gut microbiota and its metabolites in normal mice – Zhenjun Zhu – International Journal of Biological Macromolecules

Chitin-based barrier immunity and its loss predated mucus-colonization by indigenous gut microbiota – Keisuke Nakashima – Nature Communications

Reduced particle size wheat bran is efficiently colonized by lactic acid producing community and reduces Enterobacteriaceae levels in the cecal microbiota of broilers – Karen Vermeulen – Applied and Environmental Microbiology

A High Salt Diet Modulates the Gut Microbiota and Short Chain Fatty Acids Production in a Salt-Sensitive Hypertension Rat Model – Ariel Bier – Nutrients

Animal microbiome 

A detailed investigation of the porcine skin and nose microbiome using universal and Staphylococcus specific primers – Mikael Lenz Strube – Scientific Reports

Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions – Daniel Crespo-Piazuelo – Scientific Reports

Cnidarian Interaction with Microbial Communities: From Aid to Animal’s Health to Rejection Responses – Loredana Stabili – Marine Drugs

Plant, root, and soil microbiome

Wheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation – Yun Chen – Nature Communications

Biodegradation of oxytetracycline and enrofloxacin by autochthonous microbial communities from estuarine sediments – Malek Harrabi – Science of The Total Environment

Soil micro-food web interactions and rhizosphere priming effectSoil micro-food web interactions and rhizosphere priming effect – Xinchang Kou – Plant and Soil

Burkholderia pseudomallei-absent soil bacterial community results in secondary metabolites that kill this pathogen – Chotima Potisap – AMB Express

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit – Jessica Wallace – PeerJ

Contrasting responses of the bacterial communities in ectomycorrhizal roots and rhizosphere soils to defoliation or winter hardening – Hironari Izumi – Rhizosphere

Water and extremophile microbiome 

Abundant and rare microbial biospheres respond differently to environmental and spatial factors in Tibetan hot springs – Yanmin Zhang – Frontiers in Microbiology

Built environment 

Review: Microbiology of the built environment – Jack A Gilbert – Nature Reviews

Application of hybrid anaerobic reactor: Treatment of increasing cyanide containing effluents and microbial composition identification – Pragya Gupta – Journal of Environmental Management

A little breath of fresh air into an anaerobic system: How microaeration facilitates anaerobic digestion process – Duc Nguyen – Biotechnology Advances

Managing microbial communities in membrane biofilm reactors – A. Ontiveros-Valencia – Applied Microbiology and Biotechnology

Phages and viruses

Preprint: May the phage be with you? Prophage-like elements in the genomes of Soft Rot Pectobacteriaceae (Pectobacterium spp. and Dickeya spp.) – Robert Czajkowski – bioRxiv

Occurrence, integrity and functionality of AcaML1–like viruses infecting extreme acidophiles of the Acidithiobacillus species complex – Paulo C. Covarrubias – Research in Microbiology

Chapter: Robust Analysis of Time Series in Virome Metagenomics – Jose Manuel Martí – The Human Virome

Chapter: A Method for Isolation of the Virome from Plasma Samples – Pilar Domingo-Calap – The Human Virome

Chapter: Virome Sequencing of Stool Samples – Lenka Kramná – The Human Virome

Chapter: Protocol for Generating Infectious RNA Viromes from Complex Biological Samples – Sonia Monteil-Bouchard – The Human Virome

Techniques

Review: Transcriptome Sequencing Approaches to Elucidate Host–Microbe Interactions in Opportunistic Human Fungal Pathogens – Hrant Hovhannisyan – Current Topics in Microbiology and Immunology 

Chapter: Flow Cytometry and Direct Sequencing of Viruses – Mária Džunková – The Human Virome

 

 

August 24, 2018

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Intra-individual microbiome biogeography, a review on IgA responses to the microbiota, seasonal fluctuations in the gut microbiota of white-faced capuchin monkeys, and the microbial composition of fog.

Pregnancy and early life

Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population – Anne G Hoen – Scientific Reports

Multi-site human microbiome

Assessing and Interpreting the Within-Body Biogeography of Human Microbiome Diversity – Zhanshan Ma – Frontiers in Microbiology

Human vaginal microbiome

Review: Investigating the effect of an abnormal cervico‐vaginal and endometrial microbiome on assisted reproductive technologies: A systematic review – Timothy Bracewell-Milnes – American Journal of Reproductive Immunology

Human gut microbiome

Review: IgA Responses to Microbiota – Jeffrey J Bunker – Immunity

Review: Comparing fecal microbiota transplantation to standard-of-care treatment for recurrent Clostridium difficile infection: a systematic review and meta-analysis – Muhammad Y Khan – European Journal of Gastroenterology & Hepatology

Animal experiments

Dietary L-Tryptophan Modulates the Structural and Functional Composition of the Intestinal Microbiome in Weaned Piglets – Haiwei Liang – Frontiers in Microbiology

Animal microbiome

Seasonality of the gut microbiota of free-ranging white-faced capuchins in a tropical dry forest – Joseph D Orkin – The ISME Journal

The microbiota in the intestinal and respiratory tracts of naked mole-rats revealed by high-throughput sequencing – Wei Cong – BMC Microbiology

Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses – Canaan M Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems – Shuo Jiao – Microbiome

Fungal Communities Along a Small-Scale Elevational Gradient in an Alpine Tundra Are Determined by Soil Carbon Nitrogen Ratios – Yingying Ni – Frontiers in Microbiology

Water and extremophile microbiome

The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition – Sarah E Evans – Science of the Total Environment

Growth promotion and inhibition induced by interactions of groundwater bacteria – Patricia Geesink – FEMS Microbiology Ecology

Microbial diversity along a gradient in peatlands treating mining-affected waters – Katharina Kujala – FEMS Microbiology Ecology

Food microbiology

Volatile Flavor Components, Microbiota and Their Correlations in Different Sufu, a Chinese Fermented Soybean Food – Chunzhi Xiv – Journal of Applied Microbiology

Biogenic amines analysis and microbial contribution in traditional fermented food of Douchi – Lu Li – Scientific Reports

Changes in the microbial communities in vacuum-packaged smoked bacon during storage – Xinfu Li – Food Microbiology

Phages and viruses

MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins – Deyvid Amgarten – Frontiers in Genetics

Techniques

Comparative evaluation of a new magnetic bead-based DNA extraction method from fecal samples for downstream next-generation 16S rRNA gene sequencing – Kara D McGaughey – PLOS ONE

August 19, 2018

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Featured today: culturing novel bacteria, microbiota of cystic fibrosis, marker in urine for determining gut microbial diversity, stress determinant of soil microbial communities, fescue enhances the PAH degradation by rhizospheric microbes, phages from healthy skin metavirome.

General microbiome

Dietary specialization in mutualistic acacia‐ants affects relative abundance but not identity of host‐associated bacteria – BER Rubin – Journal Molecular Ecology

Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria – T Ito – Gut Microbes

Multi-site human microbiome

The urinary microbiome associated with bladder cancer – V Bučević Popović – Scientific Reports

Human respiratory microbiome

Review: Cystic fibrosis respiratory microbiota: unraveling complexity to inform clinical practice – LJ Caverly – Expert Review of Respiratory Medicine

Human vaginal microbiome

Vulvovestibular Syndrome and Vaginal Microbiome: A Simple Evaluation – M Vadala – Journal of Clinical Medicine Research

Human gut microbiome

Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry – SJ Guzman-Castaneda – bioRxiv

Assessment of urinary 3-indoxyl sulfate as a marker for gut microbiota diversity and abundance of Clostridiales – F Farowski – Gut Microbes

Periodontal Therapy Favorably Modulates the Oral-Gut-Hepatic Axis in Cirrhosis – JS Bajaj – American Journal of Physiology-Gastrointestinal and Liver Physiology

Animal experiments

Neonatal gut and immune maturation is determined more by postnatal age than by post-conceptional age in moderately preterm pigs – S Rens – American Journal of Physiology-Gastrointestinal and Liver Physiology

Effects of Astragalus membranaceus fiber on growth performance, nutrient digestibility, microbial composition, VFA production, gut pH, and immunity of weaned pigs – D Che – Microbiology Open

Plant, root, and soil microbiome

Soil microbial communities alter conspecific and congeneric competition consistent with patterns of field coexistence in three Trifolium congeners – A Siefert – Journal of Ecology

Initial state of soil microbial communities determines their stress response – W Riah-Anglet – Journal of Environmental Chemical Engineering

Natural grassland as the optimal pattern of vegetation restoration in arid and semi-arid regions: Evidence from nutrient limitation of soil microbes – Y Cui – Science of The Total Environment

Characteristics of microbial community indicate anthropogenic impact on the sediments along the Yangtze Estuary and its coastal area, China – X-p Guo – Science of The Total Environment

Soil bacterial communities exhibit systematic spatial variation with landform across a commercial potato field – S Neupane – Geoderma

Plant host habitat and root exudates shape fungal diversity – M Hugoni – Mycorrhiza

Enhanced polycyclic aromatic hydrocarbons degradation in rhizosphere soil planted with tall fescue: Bacterial community and functional gene expression mechanisms – M Guo – Chemosphere

Microbial community of nitrogen cycle‐related genes in aquatic plant rhizospheres of Lake Liangzi in winter – X Yin – Journal of Basic Microbiology

Water and extremophile microbiome 

Surviving in hot and cold: psychrophiles and thermophiles from Deception Island volcano, Antarctica – AG. Bendia – Extremophiles

Probiotics / prebiotics

Probiotics and Evidence-based Medicine: To All Involved – M Koch – Journal of Clinical Gastroenterology

Co‐Administration of Probiotics with Prescribed Antibiotics for Preventing Clostridium difficile Diarrhea – SI Ahmed – Academic Emergency Medicine

Phages and viruses

Novel phages of healthy skin metaviromes from South Africa – LJ van Zyl – Scientific Reports

 

August 18, 2018

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The virome of California mosquitoes, effects of climate warming on grassland microbial communities, and a few “bacteria and art” entries including a 92-foot inflatable E. coli sculpture.

General microbiome

Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction – Stephan Noack – Trends in Biotechnology

Growth tradeoffs produce complex microbial communities on a single limiting resource – Michael Manhart – Nature Communications

Human oral microbiome

Oral microbiome development during childhood: an ecological succession influenced by postnatal factors and associated with tooth decay – Majda Dzidic – The ISME Journal

Animal experiments

Loss of HDAC6 alters gut microbiota and worsens obesity – Arnon D Lieber – The FASEB Journal

Animal microbiome

Pre-print: CRISPR/Cas9-mediated gene deletion of the ompA gene in an Enterobacter gut symbiont impairs biofilm formation and reduces gut colonization of Aedes aegypti mosquitoes – Shivanand Hegde – bioRxiv

Plant, root, and soil microbiome

Climate warming leads to divergent succession of grassland microbial communities – Xue Guo – Nature Climate Change

Water and extremophile microbiome

Bacterial Diversity in Replicated Hydrogen Sulfide-Rich Streams – Scott Hotaling – Microbial Ecology

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration – Sylvain Monteux – The ISME Journal

Phages and viruses

Virome of > 12 thousand Culex mosquitoes from throughout California – Mohammadreza Sadeghi – Virology

Comprehensive comparative analysis of methods and software for identifying viral integrations – Xun Chen – Briefings in Bioinformatics

Phage-inducible chromosomal islands are ubiquitous within the bacterial universe – Alfred Fillol-Salom – The ISME Journal

Metabolomics

Metabotypes Related to Meat and Vegetable Intake Reflect Microbial, Lipid and Amino Acid Metabolism in Healthy People – Runmin Wei – Molecular Nutrition & Food Research

More microbes

Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea – Michaeline B N Albright – Microbial Ecology

Bacteria art

Linen and Bacteria: The Hidden History of Microbiology – Clara Rodríguez Fernández – Labiotech.eu

Pomona Arts: Sara Parent Ramos: Jumble, Bunch, Grow – Inland Empire

Oxford Natural History exhibition explores benefits of bacteria – BBC News

August 13, 2018

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Today’s Digest is full of amazing research from focusing on causation in microbiome studies to increased efficacy of BLAST searches in the age of high throughput sequencing.

General Microbiome

Microbiome: Focus on Causation and Mechanism.Fischbach MA. Cell.

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial.Harris VC. Cell Host and Microbe

Enhancing Rotavirus Vaccination: A Microbial Fix? Parker EPK. Cell Host and Microbe

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia. Barlow EV. Geobiology.

Background levels of microorganisms in the busy urban environment of transport hubs.Patel KV. Journal of Applied Microbiology.

Immunomodulation as Therapy for Fungal Infection: Are We Closer?Sam QH. Frontiers in Microbiology

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.Grahl N. mSphere.

Oral Microbiome

Comparison of oral microbiota in orthodontic patients and healthy individuals.Sun F. Microbial Pathogenesis

Skin Microbiome

Mud therapy and skin microbiome: a review.Antonelli M. International Journal of Biometeorology

Gut Microbiome

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.Bradley PH. PLoS Computational Biology

Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia.Martin I. PLoS Neglected Tropical Disease.

Faecal Microbiome

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China.Peng Z. Science Total Environment

Fecal Microbiota Alterations Associated With Diarrhea-Predominant Irritable Bowel Syndrome.Zhuang X. Frontiers in Microbiology.

Plant, Soils, and Air Microbiome

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils.Tang Y. Science of Total Environment

Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. Kumar V. PLoS One.

Trichoderma polysporum selectively inhibits white-nose syndrome fungal pathogen Pseudogymnoascus destructans amidst soil microbes.Singh A. Microbiome.

Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.Ren F. Microbial Ecology

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Yu C. Applied Microbiology and Biotechnology.

Traits-Based Integration of Multi-Species Inoculants Facilitates Shifts of Indigenous Soil Bacterial Community.Wang J. Frontier in Microbiology

Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest.Song M. Frontiers in Microbiology

Water Microbiome

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.Berner C. Frontiers in Microbiology

Coral Microbiome Database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes.Huggett MJ. Environmental Microbiology Reports

Animal Experiments and Microbiome

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. Kashinskaya EN. Journal of Applied Microbiology

Yeast-like microorganisms in the scale insect Kermes quercus (Insecta, Hemiptera, Coccomorpha: Kermesidae). Newly acquired symbionts?Podsiadło E. Arthropod Structure and Development

Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.Leis ML. Veterinary Ophthalmology

High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (<i>Moschus berezovskii</i>).Hu X. Frontiers in Microbiology

A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals.Hong B. Frontiers in Microbiology

Identification of spider-mite species and their endosymbionts using multiplex PCR.Zélé F. Experimental and Applied Acarology

Soil microarthropods alter the outcome of plant-soil feedback experiments.Kuťáková E. Scientific Reports

Techniques/Bioinformatics 

Metagenome complexity and template length are the main causes of bias in PCR-based bacteria community analysis.Peng W. Journal of Basic Microbiology

Single-cell RNA sequencing technologies and bioinformatics pipelines.Hwang B. Experimental and Molecular Medicine

Negative Binomial Mixed Models for Analyzing Longitudinal Microbiome Data.Zhang X. Frontiers in Microbiology

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Hu Y. Scientific Reports

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.Tristão Ramos RJ. Bioinformatics

August 9, 2018

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Horizontal gene transfer in microbiomes, metabolic study of the microbiota isolated from the camel rumen, a review on the bacteriophage virome in IBD.

General microbiome

Review: Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives – Rafael Pinilla-Redondo – Plasmid

Review: Learning from bacterial competition in the host to develop antimicrobials – Manuela Raffatellu – Nature Medicine

Pregnancy and early life

Early life colonization of the human gut: microbes matter everywhere – Katri Korpela – Current Opinion in Microbiology

Human respiratory microbiome

Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use – Vijay R Ramakrishnan – Allergy & Rhinology

Human skin microbiome

Sensitive scalp is associated with excessive sebum and perturbed microbiome – Li Ma – Journal of Cosmetic Dermatology

Animal experiments

Effects of host genetics and environmental conditions on fecal microbiota composition of pigs – Tereza Kubasova – PLOS ONE

Animal microbiome

A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation – Javad Gharechahi – Biotechnology for Biofuels

Plant, root, and soil microbiome

Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota – Allen Van Deynze – PLOS Biology

Brazilian Ironstone Plant Communities as Reservoirs of Culturable Bacteria With Diverse Biotechnological Potential – Washington L Caneschi – Frontiers in Microbiology

Water and extremophile microbiome

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change – Trine Markussen – Environmental Microbiology

Pre-print: Resource diversity structures aquatic bacterial communities – Mario E Muscarella – bioRxiv

Pre-print: Modular assembly of polysaccharide-degrading microbial communities in the ocean – Tim N Enke – bioRxiv

Food microbiology

Review: Bakery yeasts, a new model for studies in ecology and evolution – Belen Carbonetto – Yeast

Inferences from inventories of microbes in ecological vineyard settings – Hans-Josef Schroers – International Journal of Environmental Quality

Phages and viruses

Review: Bacteriophage virome in IBD – Clemens Thoma – Nature Reviews Gastroenterology and Hepatology

Bioinformatics

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis – Simon A Hardwick – Nature Communications

August 7, 2018

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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

August 6, 2018

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In today’s digest, look for probiotic trials for renal insufficiency and metabolic syndrome, experimental dysbiosis in SIV-infected primates, bacterial and fungal network analyses in soils, and recombination in the human virome. Plus, bacteria in the popular press, hints for scientists using Twitter, the first stem cell therapies for Parkinson’s Disease, and more!

Human gut microbiome
Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease – Linda Stewart – Clinical and Experimental Immunology

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

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs – Marion Lemaire – Scientific Reports

Animal microbiome
Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs – Sara C. Bell – Frontiers in Microbiology

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

Plant, root, and soil microbiome
Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes – Andrew T. Nottingham – Ecology

Soil bacterial networks are less stable under drought than fungal networks – Franciska T. de Vries – Nature Communications

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits – Miguel A. Redondo – The ISME Journal

Variations in microbial community and di-(2-ethylhexyl) phthalate (DEHP) dissipation in different rhizospheric compartments between low- and high-DEHP accumulating cultivars of rice (Oryza sativa L.) – Xue-Xue Chen – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Evaluation of performance and microbial community successional patterns in an integrated OCO reactor under ZnO nanoparticle stress – Zhenghui Liu – RSC Advances

Screening of quorum quenching activity of the bacteria isolated from dairy industry waste activated sludge – J. Kaur – International Journal of Environmental Science and Technology

Food Microbiology
Identification of Mesophilic Spore-formers in Whey Powder using Shotgun Metagenomic Sequencing – Aoife J. McHugh – Applied and Environmental Microbiology

Probiotics/Prebiotics
An open-label, randomized, placebo-controlled study on the effectiveness of a novel probiotics administration protocol (ProbiotiCKD) in patients with mild renal insufficiency (stage 3a of CKD) – Mariadelina Simeoni – European Journal of Nutrition

Probiotic and synbiotic supplementation could improve metabolic syndrome in prediabetic adults: A randomized controlled trial – Nazila Kassaian – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

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

Microbes in the news
Hong Kong Subway Study Shows How Quickly Bacteria Travel Across a City – Gizmodo

Bacteria hysteria
Please Don’t Give Up Your Pet Over The Fear Of Dog-Lick Bacteria – Huffington Post

Science, publishing, and career
Scientists on Twitter: Preaching to the choir or singing from the rooftops? – Isabelle Côté – Facets

Alyson’s non-microbiology picks
‘Reprogrammed’ stem cells to be tested in people with Parkinson’s

These tiny, stretchy speakers and microphones let your skin play music