Category Archives: Human reproductive or urinary

December 5, 2017

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Today we have interesting reviews, one about proteomics and human microbiome by C.A. Kolmedar, the other about oral microbiome by L.P.Shaw and the third about human gut virome by L.A. Ogilvie. In Water section you can read the study by V.J. Koles who developed a model that simulates metagenomes and metatranscriptomes for comparison with observations. In section Bioinformatics you can read about new tools MetaLab and ASAR while in non-microbiology pics you can check podcast “Dances with rocks” with A. Denton, geologist and planetary scientist who wants to dance on Mars. Enjoy!

Jobs

Microbiology Supervisor, Rockville, Maryland

Associate Bioengineer II, Analytical R&D, Warren, NJ

Events

9th Congress of Microbiology and Parasitology Kicks Off in Cuba

General microbiome

Microbially Mediated Electrosynthesis Processes – Mohita Sharma – Microbial Fuell Cell

Development of Suitable Anode Materials for Microbial Fuel Cells – Thi Hiep Han – Microbial Fuel Cell

Progress and Future Direction of Chromosome-Centric Human Proteome Project – Young-Ki Paik – Journal of Proteome Research

Review: Proteomics and the human microbiome: where we are today and where we would like to be – Carolin Adriane Kolmeder – Emerging Topics in Life Sciences

March of the Microbes: Harnessing the Power of the Human Microbiome to Improve Health and Target Disease – Helen Albert – Clinical OMICs

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Pregnancy and early life

Development of the Microbiota in Infants and its Role in Maturation of the Gut Mucosa and the Immune System – Cecilia Ximenez – Archives of Medical Research

Human nearly-sterile sites

The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults -Xiaofeng Wen – Immunology and Microbiology

Human respiratory microbiome

Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae – David W Cleary – bioRxiv

The nasopharyngeal microbiome – David W. Cleary- Emerging Topics in Life Sciences

The lung microbiome in health and disease – Miriam F Moffatt – Clinical Medicine

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report – Russell P. Bowler – Annals of the American Thoracic Society

Fungal microbiota in chronic airway inflammatory disease and emerging relationships with the host immune response – Irene Zhang – Frontiers in Microbiology

Oral microbiome

Nonleachable Imidazolium-Incorporated Composite for Disruption of Bacterial Clustering, Exopolysaccharide-Matrix Assembly, and Enhanced Biofilm Removal – Geelsu Hwang – ACS Applied Materials & Interfaces

Review: The oral microbiome – Liam P. Shaw – Emerging Topics in Life Sciences

Use of Probiotics and Oral Health – Robert P. Allaker – Current Oral Health Reports

Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing – Jeffrey B. Payne – mSphere

Human vaginal microbiome

The human female urogenital microbiome: complexity in normality – David A. MacIntyre – Emerging Topics in Life Sciences

Human gut microbiome

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

The gut microbiome and hypertension – Pevsner-Fischer – Current Opinion in Nephrology and Hypertension

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota – Ibrahim Hamad – Scientific Reports

Lymphatic system and gut microbiota affect immunopathology of neuroinflammatory diseases, including multiple sclerosis, neuromyelitis optica and Alzheimer’s disease – Ikuo Tsunoda – Clinical & Experimental Neuroimmunology

Effect of different treatments and alcohol addiction on gut microbiota in minimal hepatic encephalopathy patients – Zan Zuo – Experimental and Therapeutic Medicine

Microbes Tickling Your Tummy: the Importance of the Gut-Brain Axis in Parkinson’s Disease – Paula Perez-Pardo – Current Behavioral Neuroscience Reports

Gancao-Gansui combination impacts gut microbiota diversity and related metabolic functions – Jingao Yu – Journal of Ethnopharmacology

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Gut microbiota in human SLE and a mouse model of lupus – Xin M. Luo – Applied and Environmental Microbiology

The interaction between smoking, alcohol and the gut microbiome – Gabriele Capurso – Best Practice & Research Clinical Gastroenterology

Animal experiments

Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids’ metabolomics relationships in dairy cows – Hui-Zeng Sun – BMC Genomics

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform – Junhyung Kim – Gut Pathogens

Chronic glucocorticoid treatment induced circadian clock disorder leads to lipid metabolism and gut microbiota alterations in rats – Tao Wu – Life Sciences

Animal microbiome

Gut microbiota composition is associated with environmental landscape in honey bees – Julia C Jones –  Ecology and Evolution

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams – M. Milan – Aquatic Toxicology

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management – Jin-JaeLee  – Food Research International

Plant, root, and soil microbiome

Studies on mycorrhizal biodiversity in medicinal plant species of Pookode lake area, Wayanad, Kerala, India – Saranya Babu Jayaprakash C.M. – Annals of Plant Sciences

Effects of Iron Amendments on the Speciation of Arsenic in the Rice Rhizosphere after Drainage – Noriko Yamaguchi – Soils

Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora – Hongjun Liu – Plant and Soil

Seasonal changes in a maize-based polyculture of central Mexico reshape the co-occurrence networks of soil bacterial communities – Eria A. Rebollar – Frontiers in Microbiology

Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil – Hongna Li – Ecotoxicology and Environmental Safety

Roles of different active metal-reducing bacteria in arsenic release from arsenic-contaminated paddy soil amended with biochar – Jiang-taoQiao – Journal of Hazardous Materials

Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil – Chanyarat Paungfoo-Lonhienne – Scientific Reports

Responses of soil nutrients and microbial communities to three restoration strategies in a karst area, southwest China – Dejun Li – Journal of Environmental Management

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils – Robert Wagner – Environmental Microbiology

Water and extremophile microbiome

Ocean biogeochemistry modeled with emergent trait-based genomics – V. J. Coles – Science

Bacterial Community Profiling of Waters from Aquaculture and Non-aquaculture Sites within Taal Lake Ecosystem through 16S rDNA Analysis – Leslie Michelle M. Dalmacio – The Philippine Journal of Health Research and Development

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments as Revealed by 454 Pyrosequencing – Yin-Xin Zeng –  Frontiers in Microbiology

Microbial communities shaped by treatment processes in a drinking water treatment plant and their contribution and threat to drinking water safety – Qi Li – Frontiers in Microbiology

Diversity of microbial communities and quantitative chemodiversity in layers of marine sediment cores from an causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers in Microbiology

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids – Caroline S. Fortunato –  Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment and water bacterial communities – Arthur Escalas – Environmental Microbiology

Built environment

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm – Pampillón-González L – Journal of Molecular Microbiology and Biotechnology

Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim – Dong Wu – Applied Microbiology and Biotechnology

Effect of ammonia on the active microbiome and metagenome and from stable full-scale digesters – J.Ruiz-Sánchez – Bioresource Technology

Droplet distribution and airborne bacteria in an experimental shower unit – C.E.Estrada-Perez – Water Research

Food Microbiology

Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation – Xueshan Wang – Applied and Environmental Microbiology

Shotgun metagenomics and volatilome profile of the microbiota of fermented sausages -Ilario Ferrocino –  Applied and Environmental Microbiology

Probiotics / prebiotics

Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers – A P Allen  – Translational Psychiatry

Phage and viruses

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study – Hideo Shigeishi – Biomedical Reports

Kullback Leibler divergence in complete bacterial and phage genomes – Sajia Akhter – PeerJ

Review: The human gut virome: form and function – Lesley A. Ogilvie – Emerging Topics in Life Sciences

Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu – Mao-KeLiu – Food Research International

Bioinformatics

Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads – Fanny Perraudeau – bioRxiv

MetaLab: an automated pipeline for metaproteomic data analysis – Kai Cheng – Microbiome

ASAR: visual analysis of metagenomes in R – Askarbek Orakov – Bioinformatics

Bacteria & Biofuels

Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol – Liang Tian – Biotechnology for Biofuels

Biophotovoltaics: Conversion of Light Energy to Bioelectricity Through Photosynthetic Microbial Fuel Cell Technology – Rashmi Chandra – Microbial Fuel Cell

Techniques

Electron microscopy reveals unique nano forms of bacterial spores – Sumanta Ghosh – bioRxiv

Continuous and High-throughput Electromechanical Lysis of Bacterial Pathogens using Ion Concentration Polarization – Minseok Kim – Analytical Chemistry

Microbes in the news

A New Antibiotic Weakness—Drugs Themselves Help Bacteria Survive

Exercise Changes Gut Microbial Composition Independent of Diet, Study Shows

Bacteria and obesity: Reviewing the connection between gut bacteria, obesity, and diet

Bacteria & Art

Bacteria Collection of Icons Vector Illustration

Tina’s non microbiology picks

PODCAST: This Scientist Wants To Dance On Mars (And She Just Might Make That Happen)

How to Review a Manuscript

December 1, 2017

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Happy December! Today’s digest features research articles on prion like domains in phages, effect of high salt challenge on gut microbiota and immune system. Enjoy!

Events and jobs

Assistant Professor, Statistics and Microbiology – The University of Manitoba

Program Manager, Microbiology – RWJ-Pathology-PISC

General microbiome

Review: Experimental design and quantitative analysis of microbial community multiomics – Himel Mallick – Genome Biology

Pregnancy and early life

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants – Priscila T. Dobbler – Frontiers in Microbiology

Human respiratory microbiome

Colonic Bacteroides are positively associated with trabecular bone structure and programmed by maternal vitamin D in male but not female offspring in an obesogenic environment – C R Villa – International Journal of Obesity

Human skin microbiome

Diversity of bacterial communities on the facial skin of different age-group Thai males – Alisa Wilantho – PeerJ

Human oral microbiome

Oral Health and the Oral Microbiome in Pancreatic Cancer: An Overview of Epidemiological Studies – Paige M Bracci – The Cancer Journal

Bacterial alterations in salivary microbiota and their association in oral cancer – Wei-Hsiang Lee – Scientific Reports

Human vaginal microbiome

Review : Is bacterial vaginosis a disease? – Gregor Reid – Applied Microbiology and Biotechnology

Human gut microbiome

The gut mycobiome of the Human Microbiome Project healthy cohort – Andrea K. Nash – Microbiome

Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment – Yanyun Gu – Nature Communications

*Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature

Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice – Sean R.Llewellyn – Gastroenterology

Psychobiotics: A new approach for treating mental illness? – Snigdha Misra – Critical Reviews in Food Science and Nutrition

Small Intestinal Bacterial Overgrowth: Should Screening Be Included in the Pre-fecal Microbiota Transplantation Evaluation? – Jessica R. Allegretti – Digestive Diseases and Sciences

Gut microbiota-mediated generation of saturated fatty acids elicits inflammation in the liver in murine high-fat diet-induced steatohepatitis – Shoji Yamada – BMC Gastroenterology

Animal experiments

Vertical vs. horizontal transmission of the microbiome in akey disease vector, Ixodes pacificus – Jessica Y. Kwan – Molecular Ecology

Gut Microbiome-induced Shift of Acetate to Butyrate Positively Manages Dysbiosis in High Fat Diet – Xu Si – Molecular Nutrition and Food Research

Increased cortical neuronal responses to NMDA and improved attentional set-shifting performance in rats following prebiotic (B-GOS®) ingestion – Benjamin Gronier – European Neuropsychopharmacology

Effects of Lactobacillus acidophilus on gut microbiota composition in broilers challenged with Clostridium perfringens – Zhui Li – Plos One

Doxycycline induces dysbiosis in female C57BL/6NCrl mice – Felicia D. Duke Boynton – BMC Research Notes

Animal microbiome

The effect of dietary energy and protein levels on body weight, size, and microflora of ostrich chicks – Tahereh Nikravesh-Masouleh – Tropical Animal Health and Production

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion – Miriam E. Shiffman – PeerJ

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs – Ana Carolina M. Junqueira – Scientific Reports

Plant, root, and soil microbiome

The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China – Jianming Wang – Frontiers in Microbiology

Water and extremophile microbiome

Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model – Wei Li – Molecular Ecology

Microbial Reduction of Fe(III) and SO42− and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments – Ji-Hoon Lee – Microbial Ecology

The influence of complex fermentation broth on denitrification of saline sewage in constructed wetlands by heterotrophic nitrifying/aerobic denitrifying bacterial communities – Guiping Fu – Bioresource Technology

Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats – Marcelo Baeza – Frontiers in Microbiology

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh – Edwin T. Gnanaprakasam – mBio

Probiotics / prebiotics

Short communication: Does early-life administration of a Megasphaera elsdenii probiotic affect long-term establishment of the organism in the rumen and alter rumen metabolism in the dairy calf? – T.T.Yohe – Journal of Dairy Science

Review: Effect of Probiotic Supplementation on CD4 Cell Count in HIV-Infected Patients: A Systematic Review and Meta-analysis – Asma Kazemi – Journal of Dietary Supplements

Phages and viruses

*Prion-Like Domains in Phagobiota – George Tetz – Frontiers in Microbiology

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior – Elaine Luo – mBio

Anitha’s non-microbiology picks

Hubble in a bubble: Scallop eyes act just like tiny telescopes

Jackpot of fossilized pterosaur eggs unearthed in China

Sorry, Grumpy Cat: Study finds dogs are brainier than cats

November 17, 2017

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Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour, Microbiome

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology

Bioinformatics

HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ

Techniques

Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

November 15, 2017

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Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv

Probiotics/prebiotics

A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology

Bioinformatics

Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv

Metabolomics

Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv

Techniques

Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

November 5, 2017

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A shorter digest today, but includes a lot of human gut microbiome studies and a cool study on microbes used to treat snake bites!

General microbiome

Comparison of two Jatropha species (Euphorbiaceae) used popularly to treat snakebites in Northeastern Brazil: Chemical profile, inhibitory activity against Bothrops erythromelas venom and antibacterial activity – Juliana Félix-Silva, Journal of Ethnopharmacology

Multi-site human microbiome

A slippery slope: On the origin, role and physiology of mucus – Farhan Taherali, Advanced Drug Delivery Reviews

Human gut microbiome

Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial –  Peter Holger Johnsen, The Lancet Gastroenterology & Hepatology

Estrogens and Female Liver Health – Karen L. Chen, Steroids

Safety and Efficacy of Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection in Patients With Cancer Treated With Cytotoxic Chemotherapy: A Single-Institution Retrospective Case Series – Mehrdad Hefazi, Mayo Clinic Proceedings

Gut Microbiota and Cancer Patients: A Broad-Ranging Relationship – Giovanni Cammarota, Mayo Clinic Proceedings

Gut microbiota and hypertension: From pathogenesis to new therapeutic strategies – Yongbo Kang, Clinics and Research in Hepatology and Gastroenterology

Preface to “Gut microbiome in health and disease” – Maikel P. Peppelenbosch, Best Practice & Research Clinical Gastroenterology

Results of the implementation of a multidisciplinary programme of faecal microbiota transplantation by colonoscopy for the treatment of recurrent Clostridium difficile infection – Antonio López-Sanromán, Gastroenterología y Hepatología (English Edition)

Animal experiments

Alterations in ruminal bacterial populations at induction and recovery from diet-induced milk fat depression in dairy cows – D.W. Pitta, Journal of Dairy Science

Chronic chlorpyrifos exposure elicits diet-specific effects on metabolism and the gut microbiome in rats – Bing Fang, Food and Chemical Toxicology

Housing influences tissue cytokine levels and the fecal bacterial community structure in rats – Padmaja Shastri, Journal of Functional Foods

An intact gut microbiota may be required for lactoferrin-driven immunomodulation in rats – Yongping Wen, Journal of Functional Foods

Untargeted metabolomic profiling of urine in Wistar rats reveals enhanced bioavailability of soy isoflavones post short-term consumption of noni (Morinda citrifolia) juice – José-Manuel Fallas-Ramirez, Journal of Functional Foods

Plant, root, and soil microbiome

Long and short term effects of solarization on soil microbiome and agricultural production – Housam Kanaan, Applied Soil Ecology

Water and extremophile microbiome

Microbial communities involved in biogas production exhibit high resilience to heat shocks – Abendroth Christian, Bioresource Technology

Food microbiome

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins, Food Research International

Microbial ecology along the processing of Spanish olives darkened by oxidation – Eduardo Medina, Food Control

Co-fermentation of onion and whey: A promising synbiotic combination – Federica Tinello, Journal of Functional Foods

Diverse yeasts for diverse fermented beverages and foods – Chris Todd Hittinger, Current Opinion in Biotechnology

Techniques

Microbiome measurement: Possibilities and pitfalls – Djawad Radjabzadeh, Best Practice & Research Clinical Gastroenterology

High-throughput eDNA monitoring of fungi to track functional recovery in ecological restoration – DongFeng Yan, Biological Conservation

Commensal Koch’s postulates: establishing causation in human microbiota research – B Anne Neville, Current Opinion in Microbiology

Microbes in the news

Disease outbreak at Marine Corps boot camp abates in San Diego – Carl Prine, The San Diego Union-Tribune

November 3, 2017

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Events and jobs

Assistant Professor in Food Microbiology/Safety – The University of Texas Rio Grande Valley – Close Date: 12/3/2017

Assistant Professor Microbiology – University of New Haven, Connecticut

Microbiology Technician On-Call – Battle Creek, MI – Michigan

 

General microbiome

Closely related methicillin-resistant Staphylococcus aureus isolates from retail meat, cows with mastitis, and humans in Japan – T Sato – PLoS One

Letter:A global resource allocation strategy governs growth transition kinetics of Escherichia coli – DW Erickson – Nature

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – RM Cooper – eLife

 

Pregnancy and early life

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – C Dahl – PLoS One

 

 

Human vaginal microbiome

Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus. – JM Wessels – PLoS One

Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – N Noyes – bioRxiv

Opinion: Committee Opinion No. 725: Vaginal Seeding – KR Wharton – Obstetrics and Gynecology

 

Human gut microbiome

“Omic” investigations of protozoa and worms for a deeper understanding of the human gut “parasitome”. – V Marzano – PLoS Neglected Tropical Diseases

Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use – BN Parsons – PLoS Pathogens

Modeling the temporal dynamics of the gut microbial community in adults and infants – L Shenhav – bioRxiv

The ethnic distribution of sessile serrated polyps in the United States is inversely associated with Helicobacter pylori prevalence – A Sonnenberg – Colorectal Disease

Gut microbiome in gestational diabetes: A Cross-sectional study of mothers and offspring 5 years post-partum. – S Hasan – Acta obstetricia et gynecologica Scandinavica

Protective Roles of Intestinal Microbiota derived Short Chain Fatty Acids in Alzheimer’s Disease-type Beta-Amyloid Neuropathological Mechanisms. – L Ho – Expert Review of Neurotherapeutics

 

Animal experiments 

Microbiota control immune regulation in humanized mice – E Gülden – Journal of Clinical Investigation Insight

Effects of essential oils from Liquidambar orientalis Mill. leaves on growth performance, carcass and some organ traits, some blood metabolites and intestinal microbiota in broilers. –  A Altop – British Poultry Science

PD-1 deficiency protects experimental colitis via alteration of gut microbiota. – SJ Park – Journal of biochemistry and molecular biology.

The Mouse Model of Infection with Citrobacter rodentium – N Bouladoux – Current Protocols in Immunology

Glyphosate has limited short-term effects on commensal bacterial community composition in the gut environment due to sufficient aromatic amino acid levels. – LN Nielsen – Environmental Pollution

 

Animal microbiome 

Strong responses of Drosophila melanogaster microbiota to developmental temperature – NN Moghadam – Fly (Austin)

Amphibian skin defences show variation in ability to inhibit growth of Batrachochytrium dendrobatidis isolates from the Global Panzootic Lineage. – RE Antwis – Microbiology (Reading, England)

Midgut Bacterial Diversity of Wild Populations of Phlebotomus (P.) papatasi, the Vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in Turkey. – M Karakuş – Scientific Reports

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – KF Beckers – PLoS One

 

Plant, root and soil microbiome

Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower). – G Moya – International Journal of Systematic and Evolutionary Microbiology

Priority effects can persist across floral generations in nectar microbial meta-communities – T Hirokazu – Oikos

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Y Zhao – PLoS One

Microbial community-level regulation explains soil carbon responses to long-term litter manipulations – K Georgiou – Nature Communications

 

Water microbiome and extremophiles

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – MW Hinson – bioRxiv

Lessons from simple marine models on the bacterial regulation of eukaryotic development – A Woznica – bioRxiv

Chapter: Sponge Disease and Climate Change – HM Luter – Climate Change, Ocean Acidification and Sponges

 

Probiotics / prebiotics

Lactobacillus plantarum HNU082-derived improvements in the intestinal microbiome prevent the development of hyperlipidaemia – Y Shao – Food & Function

Can Probiotic Supplements Improve Outcomes in Rheumatoid Arthritis? – A Schorpion – Current Rheumatology Reports

 

 

Techniques

A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil – B Ghodsalavi – PLoS One

Bacterium-triggered remodeling of chromatin identifies BasR, a novel regulator of fungal natural product biosynthesis – J Fischer – bioRxiv

Transcriptome analysis of sheep oral mucosa response to Orf virus infection – H Jia – PLoS One

A mechanism for prime-realignment during influenza A virus replication – J Oymans – bioRxiv

 

Microbes in the news

How caries-causing bacteria can survive in dental plaque – EurekAlert

Nicotine’s hold: What the gut and gender have to do with it – Phys.org

‘Big Chicken’ Connects Poultry Farming To Antibiotic-Resistant Bacteria – npr

Microbiology: Crowdsourcing Earth’s microbes – Nature

Fresh off the petri dish: Spend your Thursdays creating art with bacteria – FSU Torch

 

Non-microbiology picks

Nigritoxin is a bacterial toxin for crustaceans and insects – Y Labreuche – Nature Communications

The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity – A Santanach – Nature Communications

 

October 26, 2017

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In today’s digest we have some interesting discussion about lab/bioinformatics techniques, a few editorials on the microbiome job market, and even a little bit of philosophy learned from our tiny microbial friends.

Events and jobs

BioData World West 2018 – 13-14 March 2018 – San Francisco, CA

General microbiome

Cooperation and cheating as innovation: insights from cellular societies – Athena Aktipis – Philosophical Transactions of The Royal Society B

[Pre-Print] Metabolic Interactions Between Dynamic Bacterial Subpopulations – Adam Z Rosenthal – bioRxiv

Pregnancy and early life

Preterm Birth Affects the Risk of Developing Immune-Mediated Diseases – Sybelle Goedicke-Fritz – Frontiers in Immunology

Human oral microbiome

Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus – E. A. Babaev – Bulletin of Experimental Biology and Medicine

Human urinary tract microbiome

Re: Evaluation of the Urinary Microbiota of Women with Uncomplicated Stress Urinary Incontinence – Alan J. Wein – The Journal of Urology

Human gut microbiome

* The fecal microbiome of ALS patients – David Brenner – Neurobiology of Aging

Plant, root, and soil microbiome

Endosphere microbiome comparison between symptomatic and asymptomatic roots of Brassica napus infected with Plasmodiophora brassicae – Ying Zhao – PLOS ONE

Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a Black soil of Northeastern China – Li Wang – Soil Biology and Biochemistry

Water and extremophile microbiome 

Metatranscriptomic and metagenomic description of the bacterial nitrogen metabolism in waste water wet oxidation effluents – Julien Crovadore – Heliyon

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents – Rika E. Anderson – Nature

Food microbiology

Sequence Analysis of Changes in Microbial Composition in Different Milk Products During Fermentation and Storage – Barbora Zalewska – Current Microbiology

Probiotics / prebiotics

* Pharmabiotics as an Emerging Medication for Metabolic Syndrome and Its Related Diseases – Thi Thanh Binh Nguyen – Molecules

[Review] Recurrent urinary tract infections in women: How promising is the use of probiotics? – Varsha Gupta – Indian Journal of Medical Microbiology

Bioinformatics

Using convolutional neural networks to explore the microbiome – Derek Reiman – Engineering in Medicine and Biology Society (EMBC)

Techniques

‘Gracilibacillus phocaeensis’ sp. nov., ‘Sediminibacillus massiliensis’ sp. nov. and ‘Virgibacillus ndiopensis’ sp. nov., three halophilic species isolated from salty human stools by culturomics – B. Senghor – New Microbes and New Infections

Proteomic and metaproteomic approaches to understand host-microbe interactions – Amanda E. Starr – Analytical Chemistry

Impact of Method Variables on Microbiota Sample Disruption – Jaclyn Zecca and David Burden – OPS Diagnostics LLC

Microbes on the market 

Patenting the microbiome: trends, challenges and insights – Anthony D Sabatelli – Future Science

[Editorial] The aquaculture microbiome at the centre of business creation – Karen K. Dittmann – Microbial Biotechnology

Ed’s non-microbiology picks

I put quite a few on here today – enjoy 🙂

More than 75 percent decline over 27 years in total flying insect biomass in protected areas – Caspar A. Hallman – PLOS ONE

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth – Natan-Haim Kalson – ACS Central Science

Games people play: How video games improve probabilistic learning – Sabrina Schenk – Behavioural Brain Research

A process-oriented model linking adolescents’ sleep hygiene and psychological functioning: the moderating role of school start times -Jack S. Peltz – Sleep Health

Decreases in self-reported sleep duration among U.S. adolescents 2009-2015 and links to new media screen time – Jean M. Twenge – Sleep Medicine

Dogs’ recognition of human selfish and generous attitudes requires little but critical experience with people – Fabricio Carballo – PLOS ONE

October 18, 2017

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Today, several reviews, including a trio of reviews about connections between HIV and microbiome.

Gut microbiome

Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data (NPG)

News and Views: Gastric cancer: The gastric microbiota — bacterial diversity and implications – Manish A. Shah – Nature Reviews Gastroenterology & Hepatology

Review: The hygiene hypothesis in autoimmunity: the role of pathogens and commensals – Jean-François Bach – Nature Reviews Immunology

The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity – Alli Lynch – Scientific Reports

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus – Cristina Llorente – Nature Communications

High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut – Timothy Heisel – mSphere

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanisms and Therapy – Junli Ma – Nutrients (MDPI)

Review article: The gut microbiome in inflammatory bowel disease-avenues for microbial management – J. McIlroy – Alimentary Pharmacology & Therapeutics

Commentary: Regulation of glucagon-like peptide-1 sensitivity by gut microbiota dysbiosis – Shunsuke Yamane – Journal Of Diabetes Investigation

Low-grade small intestinal bacterial overgrowth is common in patients with non-alcoholic steatohepatitis on quantitative jejunal aspirate culture – UC Ghoshal – Indian Journal of Gastroenterology

 

Reproductive tract microbiome

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases – Chen Chen – Nature Communication

 

Microbiome in general

The microbiome beyond the horizon of ecological and evolutionary theory – Britt Koskella – Nature Ecology & Evolution

Trios—promising in silico biomarkers for differentiating the effect of disease on the human microbiome network – Zhanshan (Sam) Ma – Scientific Reports

 

Beneficial microbes and molecules

Prebiotic and Synbiotic Modifications of Beta Oxidation and Lipogenic Gene Expression after Experimental Hypercholesterolemia in Rat Liver – Claudia C. Alves – Frontiers in Microbiology

Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats – Qian Zhang – PLoS ONE

Caprylic and Polygalacturonic Acid Combinations for Eradication of Microbial Organisms Embedded in Biofilm – Joel Rosenblatt – Frontiers in Microbiology

PostScript: Faecal microbiota transplantation donor stools need screening for poliovirus – Peter Gerald Speck – Gut (BMJ)

 

Environmental research

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils – Craig Anderson – PeerJ

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI – Miranda H. Hengy – PeerJ

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing – Yanying Zhang – Frontiers in Microbiology

 

HIV and microbiome

Review: HIV and aging: role of the microbiome – Seema N. Desai – Current Opinion in HIV & AIDS

Review: The functional consequences of the microbiome in HIV: insights from metabolomic studies – Sergio Serrano-Villar – Current Opinion in HIV & AIDS

Review: Cross-reactivity of HIV vaccine responses and the microbiome – Wilton B Williams – Current Opinion in HIV & AIDS

 

Respiratory tract microbiome

Lung Microbiota is Related to Smoking Status and to Development of ARDS in Critically Ill Trauma Patients – Ariane R Panzer – American Journal of Respiratory and Critical Care Medicine

 

More microbes

Adjacent-possible ecological niche: growth of Lactobacillus species co-cultured with Escherichia coli in a synthetic minimal medium – Kouhei Mizuno – Scientific Reports

 

October 15, 2017

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General microbiome

Metagenome Analyses of Multispecies Microbial Biofilms: First Steps Toward Understanding Diverse Microbial Systems on Surfaces – Christel Schmeisser, Functional Metagenomics: Tools and Applications

Prediction analysis for microbiome sequencing data – Tao Wang, arxiv

Metagenomic Cosmid Libraries Suitable for Functional Screening in Proteobacteria – Jiujun Cheng, Functional Metagenomics: Tools and Applications

Moulds associated with contaminated ocular and injectable drugs: FDA recalls, epidemiology considerations, drug shortages, and aseptic processing – Donald G. Ahearn, Medical Mycology

Human skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs – Bo Zeng, Frontiers in Microbiology

Human vaginal microbiome

Role of Molecular Biology in Diagnosis and Characterization of Vulvo-Vaginitis in Clinical Practice – Donders G.G.G., Gynecologic and Obstetric Investigation

Human gut microbiome

A Review of the Oesophageal Microbiome in Health and Disease – Dervla Kelly, Methods in Microbiology

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients – Ryo Inoue, Journal of Clinical Biochemistry and Nutrition

Human oral microbiome

The Effect of Supragingival Biofilm Re-development on the Subgingival Microbiota in Chronic Periodontitis – Fátima Aparecida Rocha Resende Hartenbach, Archives of Oral Biology

Animal experiments

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice – Jessica L. Mark Welch, PNAS

Comparative study of probiotic effects of Lactobacillusand Bifidobacteria strains on cholesterol levels, liver morphology and the gut microbiota in obese mice – Rostyslav V. Bubnov, The EPMA Journal

Study on improving anaerobic co-digestion of cow manure and corn straw by fruit and vegetable waste: methane production and microbial community in CSTR process – Xuemei Wang, Bioresource Technology

Animal microbiome

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites – Lavanya Reddivari, mSystems

Hymenobacter cavernae sp. nov., isolated from a karst cave – Hai-Zhen Zhu, International Journal of Systematic and Evolutionary Microbiology

Plant, root, and soil microbiome

Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment – Tongchu Deng, International Journal of Systematic and Evolutionary Microbiology

Deinococcus taklimakanensis sp. nov., isolated from desert soil –  Zuobing Liu, International Journal of Systematic and Evolutionary Microbiology

Improvement of the catalytic characteristics of a salt-tolerant GH10 xylanase from Streptomyce rochei L10904 – Qin Li, International Journal of Biological Macromolecules

Trees harness the power of microbes to survive climate change – Jennifer A. Lau, PNAS

Exploring the earthworm gut as model for soil microbial ecology – Fatima Hussain, MBL

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

The intimate talk between plants and microorganisms at the leaf surface – Wendy Aragón, Journal of Experimental Botany

Metagenomics of Plant Microbiomes – G. Brader, Functional Metagenomics: Tools and Applications

Effects of different soil remediation methods on inhibition of lead absorption and growth and quality of Dianthus superbus L. – Xiaoyu Yang, Environmental Science and Pollution Research

Interactions of Root-Feeding Insects with Fungal and Oomycete Plant Pathogens – Telsa Willsey, Frontiers in Plant Science

Soil proteomics for exploitation of microbial diversity in Fusarium wilt infected and healthy rhizosphere soils of tomato – R. Manikandan, Physiological and Molecular Plant Pathology

Switchgrass Yield, Nutrient Uptake, And Rhizosphere Microbial Community Composition As Affected By Cultivar And Soil Fertility – Anne Sawyer, University of Minnesota Digital Conservancy

Ecoenzymatic stoichiometry and microbial nutrient limitation in rhizosphere soil in the arid area of the northern Loess Plateau, China – Yongxing Cui, Soil Biology and Biochemistry

Soil microbiota respond to green manure in organic vineyards – Claudia M. O. Longa, Journal of Applied Microbiology

Water and extremophile microbiome

Anoxynatronum buryatiense sp. nov., an anaerobic alkaliphilic bacterium from a low mineralization soda lake in Buryatia, Russia – Yana Ryzhmanova, International Journal of Systematic and Evolutionary Microbiology

100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions – Vladimir S. Cheptsov, Extremophiles

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities – Laura Selbmann, Extremophiles

Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations – Almudena Rivadeneyra, Extremophiles

Biosurfactant production by haloalkaliphilic Bacillusstrains isolated from Red Sea, Egypt – Khouloud M.Barakat, The Egyptian Journal of Aquatic Research

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Responses of microbial community to pH stress in bioleaching of low grade copper sulfide – Yuguang Wang, Bioresource Technology

Mass Spectrometry for the Study of Microbial Communities in Environmental Waters – Inês C. Santos, Advances in Chemical Pollution, Environmental Management and Protection

Waste microbes

Microbial characteristics analysis and kinetic studies on substrate composition to methane after microbial and nutritional regulation of fruit and vegetable wastes anaerobic digestion – Chunhui Zhao, Bioresource Technology

Antibiotic resistance genes and associated microbial community conditions in aging landfill systems – Dong Wu, Environmental Science and Technology

Bioinformatics

Bioinformatics in Microbiome Analysis – Yuhan Hao, Methods in Microbiology

Techniques

Enhancing Metagenomic Approaches Through Synthetic Biology – Luana de Fátima Alves, Functional Metagenomics: Tools and Applications

Enhancing Functional Metagenomics of Complex Microbial Communities Using Stable Isotopes – Marcela Hernández, Functional Metagenomics: Tools and Applications

The P/N (Positive-to-Negative Links) Ratio in Complex Networks—A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome – Zhanshan (Sam) Ma, Microbial Ecology

Challenges and Opportunities in Discovery of Secondary Metabolites Using a Functional Metagenomic Approach – Alinne L. R. Santana-Pereira, Functional Metagenomics: Tools and Applications

Emerging whole-cell modeling principles and methods – Arthur P. Goldberg, arxiv

Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli – Anna Lewin, Functional Metagenomics: Tools and Applications

Microbes in the news

AST: The Linchpin of Antimicrobial Stewardship – James Lewis, ModernMedicine Network

The Black Death Rages In Madagascar –  Julianna LeMieux, American Council on Science and Health

Report: 17 New Species Of Bacteria Found Every Day In World’s Rainforest Cafés – The Onion (Satire)

October 8, 2017

Posted on by

General microbiome

Repurposed kinase inhibitors and β-lactams as a novel therapy for antibiotic resistant bacteria – Nathan Wlodarchak, bioRxiv

Isolation and whole genome analysis of endospore-forming bacteria from heroin – Jörn Kalinowski, Forensic Science International: Genetics

Events and jobs

DOCTORAL STUDENT / POSTDOCTORAL RESEARCHER, EARLY INTERACTIONS OF INTESTINAL MICROBIOTA AND THE IMMUNE SYSTEM – University of Helsinki

Director of the Microbiome Research Laboratory – Microbiome Research Laboratory (MRL) at UT Southwestern

Microbiology Faculty Position – University of Chicago

Human gut microbiome

Microbiome, inflammation and colorectal cancer – Ju Chen, Seminars in Immunology

The fecal microbiome of ALS patients – David Brenner, Neurobiology of Aging

Targeting gut microbiota: Lactobacillus alleviated type 2 diabetes via inhibiting LPS secretion and activating GPR43 pathway – Kai-Kai Li, Journal of Functional Foods

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome – Megan Rossi, Clinical Gastroenterology and Hepatology

Proteomics Dataset: The Colon Mucosa from Inflammatory Bowel Disease Patients, Gastrointestinal Asymptomic Rheumatoid Arthritis Patients, and Controls – Tue Bjerg Bennike, Data in Brief

The mycobiome: Role in health and disease, and as a potential probiotic target in gastrointestinal disease – Christopher L. Hager, Digestive and Liver Disease

Overview of paediatric IBD – David C. Wilson, Seminars in Pediatric Surgery

Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition – Ruud S. Kootte, Cell Metabolism

Fasting the Microbiota to Improve Metabolism? – Joel T. Haas, Cell Metabolism

Fecal Transplant in Inflammatory Bowel Disease – Alexander S. Browne, Gastroenterology Clinics of North America

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease  – Charles N. Bernstein, Gastroenterology Clinics of North America

Human oral microbiome

The oral microbiota in colorectal cancer is distinctive and predictive – Burkhardt Flemer, Gut microbiota

Animal experiments

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model – Adam R. Burns, PNAS

Ganoderma lucidum polysaccharides improve insulin sensitivity by regulating inflammatory cytokines and gut microbiota composition in mice – S. Xua, Journal of Functional Foods

Effect of enzymatically hydrolyzed scallop visceral protein powder used as a replacement of fish meal on the growth performance, immune responses, intestinal microbiota and intestinal morphology of broiler chickens – R.E. Xing, Livestock Science

Intestinal microbiota impact sepsis associated encephalopathy via the vagus nerve – Suyan Li, Neuroscience Letters

Animal microbiome

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem – Amanda C. Northrop, Ecosphere

Plant, root, and soil microbiome

Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai –  Katharina Frindte, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

Ultrastructural observations on prokaryotic associates of benthic foraminifera: Food, mutualistic symbionts, or parasites? – Joan M. Bernhard, Marine Micropaleontology

Food microbiology

Potentially active spoilage bacteria community during the storage of vacuum packaged beefsteaks treated with aqueous ozone and electrolyzed water – Cristian Botta, International Journal of Food Microbiology

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment – Heidy M.W. den Besten, International Journal of Food Microbiology

Characterization of lactic acid bacteria recovered from atole agrio, a traditional Mexican fermented beverage – Kati Väkeväinen, LWT – Food Science and Technology

Probiotics / prebiotics

Prebiotics and Inflammatory Bowel Disease – Heather E. Rasmussen, Gastroenterology Clinics of North America

Probiotics in Inflammatory Bowel Disease – Bincy P. Abraham, Gastroenterology Clinics of North America

Enhancing the viability of Lactobacillus rhamnosus GG after spray drying and during storage – Géraldine Broeckx, International Journal of Pharmaceutics

Microbes in the news

Second grade handwashing experiment leads to big decrease in bacteria, illness – INFECTIOUS DISEASES SOCIETY OF AMERICA, EurekAlert!

UTHealth awarded $3.1 million NIH grant to study how gut bacteria relates to diabetes – UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT HOUSTON, EurekAlert!

Scientists are trying to figure out how to keep bacteria from running rampant on space missions –  Claire Maldarelli, Popular Science

“Good” Gut Bacteria Linked to Melanoma Immunotherapy Response – GEN