Category Archives: Techniques

November 8, 2017

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Photosynthesizing bacteria printed on paper, investigations of microbial communities in water dispensers and mines, a review on the health benefits of natural products from truffles.

Human respiratory microbiome

Review: Airway Microbiota and Allergic Diseases: Clinical Implications – Eman M Fouda – International Journal of Pulmonary and Respiratory Sciences

Human oral microbiome

Proton pump inhibitor alters oral microbiome in gastrointestinal tract of healthy volunteers – Tsuyoshi Mishiro – Journal of Gastroenterology and Hematology

Human gut microbiome

Gut Microbiota Interacts with Markers of Adipose Tissue Browning, Insulin Action and Plasma Acetate in Morbid Obesity – José María Moreno-Navarrete – Molecular Nutrition and Food Research

Is there a relationship between intestinal microbiota, dietary compounds, and obesity? – Joanna Kałużna-Czaplińska – Trends in Food Science and Technology

Animal experiments

Combination of quercetin and resveratrol reduces obesity in high-fat diet-fed rats by modulation of gut microbiota – Le Zhao – Food and Function

Post-weaning social isolation of rats leads to long-term disruption of the gut microbiota-immune-brain axis – Fionn Dunphy Doherty – Brain, Behavior, and Immunity

Host-microbiota interaction induces bi-phasic inflammation and glucose intolerance in mice – Antonio Molinaro – Molecular Metabolism

Obesogenic diet-induced gut barrier dysfunction and pathobiont expansion aggravate experimental colitis – June-Chul Lee – PLOS ONE

Animal microbiome

Gut region influences the diversity and interactions of bacterial communities in pikas (Ochotona curzoniae and Ochotona daurica) – Huan Li – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Nitrate induction and physiological responses of two maize lines differing in nitrogen use efficiency: effects on N availability, microbial diversity and enzyme activity in the rhizosphere – Zeno Varanini – Plant and Soil

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface – J R Halliwell – Scientific Reports

Co-existence of Rhizobia and Diverse Non-Rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii，Rhizobium multihospitium–like and Burkholderia pyrrocinia–like Strains – Junkun Lu – Frontiers in Microbiology

Diversity of endophytic bacteria from Piper spp. with antagonistic property against Phytophthora capsici causing foot rot disease in black pepper (Piper nigrum L.) – Nadiya Kollakkodan – Journal of Tropical Agriculture

Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests – Sten Anslan – Soil Biology and Biochemistry

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Resource availability underlies the plant-fungal diversity relationship in a grassland ecosystem – Lauren C Cline – Ecology

Water and extremophile microbiome

Microflora Thermarum Atlas project: biodiversity in thermal spring waters and natural SPA pools – F Valeriani – Water Science and Technology: Water Supply

Modes of carbon xation in an arsenic and CO2-rich shallow hydrothermal ecosystem – Nolwenn Callac – Scientific Reports

Difference of nitrogen-cycling microbes between shallow bay and deep-sea sediments in the South China Sea – Tiantian Yu – Applied Microbiology and Biotechnology

Seasonal Shifts in Bacterial Community Responses to Phytoplankton-Derived Dissolved Organic Matter in the Western Antarctic Peninsula – Catherine M Luria – Frontiers in Microbiology

Built environment

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine – Yanping Bao – Science of the Total Environment

Investigation of microbial communities in water dispensers – Sangjung Park – Applied Biological Chemistry

Food microbiology

Review: Potential health benefits of natural products derived from truffles: A review – Seema Patel – Trends in Food Science and Technology

Probiotics/prebiotics

Review: The development of seaweed-derived bioactive compounds for use as prebiotics and nutraceuticals using enzyme technologies – Suvimol Charoensiddhi – Trends in Food Science and Technology

Phages and viruses

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes – Judith Villager – The ISME Journal

Biodiversity of bacteriophages infecting Lactococcus lactis starter cultures – Joana Oliveira – Journal of Dairy Science

Bioinformatics

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks – Zhu Chengsheng – Nucleic Acids Research

Metabolomics

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database – Wailing Huang – Nucleic Acids Research

mVOC 2.0: a database of microbial volatiles – Marie C Lemfack – Nucleic Acids Research

Techniques

Comparison of DNA-fingerprinting (T-RFLP) and high-throughput sequencing (HTS) to assess the diversity and composition of microbial communities in groundwater ecosystems – Karsten Karczewski – Limnologica Ecology and Management of Inland Waters

More microbes

Review: Our microbes not only produce antibiotics, they also overproduce amino acids – Sergio Sanchez – The Journal of Antibiotics

Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria – José A Gutiérrez-Barranquero – Microbial Biotechnology

Microbes in the news

Bacteria-Activated Wallpaper that Generates Electricity – Katharine Keane – Architect Magazine

US government approves ‘killer’ mosquitoes to fight disease – Emily Waltz – Nature News

Bacteria may help babies’ digestive tracts more than suspected, scientists find – EurekAlert

Using neutrons to study how resistant bacteria evolve – Phys Org

Researchers identify mechanisms through which H. pylori bacteria cause gastric cancer – News Medical Life Sciences

New model reveals possibility of pumping antibiotics into bacteria – EurekAlert

Microbes on the market

Seres Therapeutics Awarded Grant from CARB-X to Support Development of Microbiome Therapeutic Candidate – Business Wire

Michael J. Fox Foundation, 23andMe to Jointly Advance Parkinson’s Disease Research – Carolina Henriques – Parkinson’s News Today

November 7, 2017

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Here’s your daily Digest. Highlights include an attempt to establish the causal link between gut microbiota and colorectal cancer in mice, an electric bandage to fight biofilm and antimicrobial resistance, and a group B Streptococcus vaccine that could save tens of thousands of babies per year.

General microbiology

Oral epithelial cells orchestrate innate type 17 responses to Candida albicans through the virulence factor candidalysin – Akash H. Verma et al. – Science Immunology

Methicillin Resistant Staphylococcus aureus Sequence Type (ST) 5 Isolates from Health Care and Agricultural Sources Adhere Equivalently to Human Keratinocytes – Samantha J. Hau et al. – Applied and Environmental Microbiology

Human gut microbiome

Human microbiome signatures of differential colorectal cancer drug metabolism – Leah Guthrie et al. – npj Biofilms and Microbiomes

Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: a randomised cross-over trial – Henrik Munch Roager et al. – Gut

Multi-site human microbiome

Review: Human microbiome, infections, and rheumatic disease – Ana Clara Camine et al. – Clinical Rheumatology

Review: The Microbiome and Bone and Joint Disease – Christopher J. Hernandez – Current Rheumatology Reports

Animal experiments

* Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional mice – Sunny H. Wong and Liuyang Zhao – Gastroenterology

Animal microbiome

An integrative study on biologically recovered polyhydroxyalkanoates (PHAs) and simultaneous assessment of gut microbiome in yellow mealworm – Su Yean Ong et al. – Journal of Biotechnology

Plant, root and soil microbiome

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3 – Peng Wang et al. – Scientific Reports

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization – Luis H. Orellana et al. – Applied and Environmental Microbiology

Water and extremophile microbiome

High altitude, hyper-arid soils of the Central-Andes harbor mega-diverse communities of actinobacteria – Alan T. Bull et al. – Extremophiles

Sediment nitrogen cycling rates and microbial abundance along a submerged vegetation gradient in a eutrophic lake – Lu Yao et al. – Science of The Total Environment

Technology

* Electric Field Based Dressing Disrupts Mixed-Species Bacterial Biofilm Infection and Restores Functional Wound Healing – Barki, Kasturi Ganesh et al. – Annals of Surgery

Press: Study shows electric bandages can fight biofilm infection, antimicrobial resistance – MedicalXpress

Bioinformatics

Preprint: A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing – Samuel I. W. Lipworth et al. – bioRxiv

Microbes in the news

Your Eyes Have Their Own Microbiome. Here’s What You Need To Do To Take Care Of It – Sam Berne – MBG Health

Does a Healthy Gut Equal a Long, Healthy Life? – Jim Pietrangelo – Healthline

Unlocking the Secrets of the Microbiome – Jane E. Brody – New York Times

Specific gut bacteria can help or hinder cancer treatments – Rich Haridy – New Atlas

Proprietary Prebiotic Fiber Tested in National Institutes of Health Pilot Study with End-Stage Renal Disease Patients – Kimberly J. Decker – Nutritional Outlook

Briny pool bacteria can clean up and power up – King Abdullah University of Science & Technology – EurekAlert

2 million Chinese mothers carry strep bacteria that can be fatal to newborns, study finds – Laurie Chen – South China Morning Post

* Vaccine for bacteria carried by 20% of pregnant women ‘could prevent 100,000 baby deaths’ – Sarah Boseley – The Irish Times

Research finds link between gut fungi, bacteria and obesity – Camille Bienvenu – Diabetes.co.uk

Microbes on the market

Microbiome Therapeutics prepares to launch ‘microbiome modulator’ – Stephen Daniells – NutraIngredients

 

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 4, 2017

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Events and jobs

Microbiology Lab Technician – Manpower – Evansville

Research Associate in Plant and Arthropod Microbiome – Indiana University

 

General microbiome

Review: New Insights into Graft-Versus-Host Disease and Graft Rejection – E Perkey – Annual Review of Pathology

Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete. – J Zhang – Scientific Reports

Review: A Call to Arms: Quest for a Cryptococcal Vaccine – MC Caballero Van Dyke – Cell

 

 

Human respiratory microbiome

Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection. – M Pichon – Vaccines

 

 

Human gut microbiome

Review: Atherosclerosis: Association between the gut microbiome and atherosclerosis – WT Barrington – Nature Reviews

Improvement in cardiometabolic risk markers following a multifunctional diet is associated with gut microbial taxa in healthy overweight and obese subjects. – N Marungruang – European Journal of Nutrition

Opinion: NOD2 and bacterial recognition as therapeutic targets for Crohn’s disease. – M de Bruyn – Expert Opinion on Therapeutic Targets.

 

Animal experiments 

Microbial diversity and composition in different gut locations of hyperlipidemic mice receiving krill oil. – C Lu – Applied Microbiology and Biotechnology

Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration. – X Huang – Scientific Reports

Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. – B Routy – Science

 

Animal microbiome 

The bacterium Wolbachia exploits host innate immunity to establish a symbiotic relationship with the dengue vector mosquito Aedes aegypti. – X Pan – The ISME Journal

Enzymatic dynamics into the Eisenia fetida (Savigny, 1826) gut during vermicomposting of coffee husk and market waste in a tropical environment. – B Ordoñez-Arévalo – Environmental Science and Pollution Research International

Microbial community and ovine host response varies with early and late stages of Haemonchus contortus infection. – S El-Ashram – Veterinary Research Communications

 

Plant, root and soil microbiome

The spent culture supernatant of Pseudomonas syringae contains azelaic acid – SG Javvadi – bioRxiv

Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Z Zhou – Frontiers in Microbiology

Genome Sequencing of Microbacterium sp. Yaish 1, a Bacterial Strain Isolated from the Rhizosphere of Date Palm Trees Affected by Salinity – GA Jana – Genome Announcements

A New Proposal for the Pathogenic Mechanism of Non-Coeliac/Non-Allergic Gluten/Wheat Sensitivity: Piecing Together the Puzzle of Recent Scientific Evidence. – V Leccioli – Nutrients

Identification of novel small RNAs in Burkholderia cenocepacia KC-01 expressed under iron limitation and oxidative stress conditions. – S Ghosh – Microbiology

Conductive particles enable syntrophic acetate oxidation between Geobacter and Methanosarcina from coastal sediments – AE Rotaru – bioRxiv

 

Water and extremophile microbiome

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. – BJ Tully – The ISME Journal

 

 

Phages and viruses

Co-existence of freshwater and marine T4-like myoviruses in a typical subtropical estuary. – L Liu – FEMS Microbiology Ecology

 

Techniques

Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants. – C Alcon-Giner – BMC Genomics

Metagenomic analysis reveals potential interactions in an artificial coculture. – M Ren – AMB Express

Review: Phage Hunters: computational strategies for finding phages in large-scale ‘omics datasets – BL Hurwitz – Virus Research

Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing – M Shnayder – bioRxiv

 

Microbes in the news

Can microbiology tell us exactly what killed the Aztecs? – OUP Blog

Tuning the Microbiome Improves Melanoma Immunotherapy Response – GEN

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

 

November 2, 2017

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Second day of November we have quite a few job offers, nice set of microbiome news, two reviews in “gut microbiome” sector. Two (personal) highlights today would be the Thomas J. Browning’s  paper about phytoplankon nutrient co-limitation and Luke R. Thompson’s paper about The Earth Microbiome Project. Enjoy…

Events and jobs

Research Technician, University of York, UK

Postdoctoral Researcher – Molecular Microbiologist, University of Oxford, Oxford, UK

Bioinformatics Postdoc, Max Planck Institute for Infection Biology, Berlin, Germany

Microbiology Postdoctoral Scholar,  The University of California, Berkeley, California, US

Bioinformatics Analyst, Ares Genetics GmbH, Vienna, Austria

Assistant Professor of Microbiology, The University of Alabama in Huntsville, Huntsville, Alabama, US

Tenure-track Assistant Professor of Microbiology, Miami University, Miami, Ohio, US

Tenure Track Assistant Professor in Microbiology, The University of British Columbia, Vancouver,  Canada

General microbiome

Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU – Theresa Hoelscher – bioRxiv

Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival – Matthew Z. Tien – bioRxiv

Detection of cytosolic Shigella flexneri via a C-terminal triple-arginine motif of GBP1 inhibits actin-based motility – Anthony Piro – bioRxiv

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance – Robert M Cooper – eLIFE

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Human gut microbiome

Rapid Assessment of Microbiota Changes in Individuals with Autism Spectrum Disorder Using Bacteria-derived Membrane Vesicles in Urine – Yunjin Lee – Experimental Neurobiology

Review: Dietary and microbial metabolites in the regulation of host immunity – Jun Kunisawa – frontiers in Microbiology

Review: Gut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics – Mingqian He – Cell & Bioscience

Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study – Tomomi Minato – PLOS One

Animal experiments

Rapid regrowth and detection of microbial contaminants in equine fecal microbiome samples – Kalie F. Beckers – PLOS One

Cecal Microbiota in Broilers Fed with Prebiotics – Dany Mesa – Frontiers in Genetics

Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice – Nobuhiro Nakamoto – Cell Reports

Food restriction followed by refeeding with a casein- or whey-based diet differentially affects the gut microbiota of pre-pubertal male rats – Majdi Masarwi – The Journal of Nutritional Biochemistry

Animal microbiome 
Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella – Valeria Mereghetti -Insect Science

Plant, root, and soil microbiome

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially processed plant derived carbon – Evan P. Starr – bioRxiv

Water and extremophile microbiome 

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

Highly divergent 16S rRNA sequences in ribosomal operons of Scytonema hyalinum (Cyanobacteria) – Jeffrey R. Johansen – PLOS One

Study of Microbial diversity in Ganga river water sample by the use of Metagenomics technique – Jamilah Ali Ahmed Zaed – Journal of Pharmacognosy and Phytochemistry

Niche specialization of bacteria in permanently ice-covered lakes of the McMurdo Dry Valleys, Antarctica – Miye Kwon – Environmental Microbiology

Influence of bicarbonate on the abundance of microbial communities capable of reducing U(VI) in groundwater – Dianxin Li – RSC Advances

Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone – Steven J. Hallam – Scientific Data

Synechococcus plasticity under environmental changes – Cristiana Callieri – FEMS Microbiology Letters

Nutrient co-limitation at the boundary of an oceanic gyre – Thomas J. Browning -Nature

Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake – Junyi Zhang – Science of The Total Environment

Microbial community structures and functions of wastewater treatment systems in plateau and cold regions – Dexin Fang – Bioresource Technology

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus — Jessika Füssel – Science Advances

Food microbiology

Characterization of Enterococcal Community Isolated from an Artisan Istrian Raw Milk Cheese: Biotechnological and Safety Aspects – Mirna Mrkonjic Fuka – Food Technology and Biotechnology

Probiotics / prebiotics
Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? – Yolande Bertin – PLOS One

Bioinformatics

MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota – Evgenii I Olekhnovich – Bioinformatics

Techniques

Quantification of diverse virus populations in the environment using the polony method – Nava Baran – Nature Microbiology

Microbes in the news 

Microbiome Link with Colorectal Cancer Drug Toxicity Points to Predictive Tests and Prevention – Genetic Engineering and Biotechnology News

Gut bacteria composition could predict toxicity of chemotherapy drugs in cancer patients – News Medical

Versatile marine bacteria could be an influence on global warming, scientists discover – Science Daily

By 2100, climate change could alter key microbial interactions in the ocean  – Phys Org

Microbes on the market 

Symbiotix Biotherapies Receives $5 Million in Institutional Financing to Advance its Development of Molecular Therapeutics that Modulate Regulatory T Cell Activity

Tina’s (non)microbiology picks 

Concept Inventory Development Reveals Common Student Misconceptions about Microbiology – Amy G. Briggs – Journal of Microbiology & Biology Education

Announcing the winner of this year’s ‘Dance Your Ph.D.’ contest – John Bohannon – Science

 

October 31, 2017

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Today’s Digest is short, but not without highlights. The highlights all go to antibiotics. Ed Yong wrote about the history of methicillin resistance, colistin resistance was found to be increasing in Chinese hospitals, and fox poop could save us from vegetable and fruit waste.

General microbiology

A CRISPR–Cas9-based gene drive platform for genetic interaction analysis in Candida albicans – Rebecca S. Shapiro et al. – Nature Microbiology

Reduction of bacterial burden by copper alloys on high-touch athletic center surfaces – Zina Ibrahim et al. – American Journal of Infection Control

Press: New Study Shows Copper Surfaces on Athletic Equipment Reduce Bacteria by 94 Percent – Business Wire

Plant, root and soil microbiome

Assessing and characterising the repertoire of constitutive promoter elements in soil metagenomic libraries in Escherichia coli – Caua Antunes Westmann et al. – bioRxiv

Technology

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan Raju et al. – bioRxiv

Microbes in the news

Flesh-eating bacteria kills man helping repair Harvey-damaged homes – Claire Z. Cardona – Dallas News

Gut bacteria found to have a role in both PTSD and Alzheimer’s disease – Rich Haridy – New Atlas

* Bacteria Can Evolve Resistance to Drugs Before Those Drugs Are Used – Ed Yong – The Atlantic

* New Study Detects Increase in MCR-1 Positive Multidrug-Resistant Bacteria in Humans – Samar Mahmoud – Contagion Live

Vaginal Microbiota Profile Predictive of Chlamydia Susceptibility – Jessica Martin – Infectious Disease Advisor

* War on waste: Antimicrobial borne by feral foxes slows decay saving food and money – Jennifer Nichols – ABC News

Microbes on the market

Video: Bioengineers recreated spider silk by fermenting E. Coli bacteria – Mashable

Kane Biotech Inc. Provides Overview of Biofilm Industry, Clinical Development and Growth Drivers in New SNNLive Video Interview with StockNewsNow.com – Global Newswire

Evivo™ Gains Health Canada Approval, Providing First International Expansion Opportunity – Global Newswire

 

October 30, 2017

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Today’s digest is short and sweet — including some articles on the connection between gut and bone metabolism, the biodegradation of oil in the ocean, and a good number of rhizosphere papers. Enjoy!

General Microbiome

Listeria monocytogenes virulence factors are secreted in biologically active Extracellular Vesicles – Carolina Coelho, bioRxiv

Multi-site human microbiome

Microbiota and cancer: a complex equation with a lot of exciting unknowns – Oxana Dmitrieva, Seminars in Immunology

Osteomicrobiology: A New Cross-Disciplinary Research Field – Claes Ohlsson, Calcified Tissue International

Prebiotics, Bone and Mineral Metabolism – Corrie M. Whisner, Calcified Tissue International

Human gut microbiome

Gut dysbiosis breaks immunological tolerance toward the central nervous system during young adulthood – Sudhir K. Yadav, PNAS

Clostridium difficile in Older Adults – Curtis J. Donskey, Infectious Disease Clinics of North America

The Microbiome That Shapes Us: Can It Cause Obesity? – Endashaw Omer, Current Gastroenterology Reports

Human oral microbiome

Infection’s Sweet Tooth: How Glycans Mediate Infection and Disease Susceptibility – Steven L. Taylor, Trends in Microbiology

Animal experiments

Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs – Laura Glendinning, Microbiome

Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome-from days to weeks – Bruno Tilocca, Microbiome

Hindgut mucosa-associated microbiome interacting with host regulating Escherichia coli O157:H7 shedding in cattle – Ou Wang, Applied and Environmental Microbiology

Plant, root, and soil microbiome

Divergent responses of forest soil microbial communities under elevated CO2 in different depths of upper soil layers – Hao Yu, Applied and Environmental Microbiology

Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils – Alexandra Schwarz, Microbial Ecology

Identification of heterotrophic zinc mobilization processes among bacterial strains isolated from wheat rhizosphere (Triticum aestivum L) – Benjamin Costerousse, Applied and Environmental Microbiology

Seed defense biopriming with bacterial cyclodipeptides triggers immunity in cucumber and pepper – Geun Cheol Song, Scientific Reports

Characterization and potential of plant growth promoting rhizobacteria isolated from native Andean crops – Katty Ogata-Gutiérrez, World Journal of Microbiology and Biotechnology

Water and extremophiles microbiome

Biodegradation of dispersed oil in seawater is not inhibited by a commercial oil spill dispersant – Odd G. Brakstad, Marine Pollution Bulletin

Functional characteristics and influence factors of microbial community in sewage sludge composting with inorganic bulking agent – Ke Wang, Bioresource Technology

Food microbiology

Yeast microbiota in artisanal cheeses from Corrientes, Argentina – Marina C. Cardozo, Revista Argentina de Microbiología

Flavonoids as detoxifying and pro-survival agents: What’s new? – Geir Bjørklund, Food and Chemical Toxicology

Techniques

Impact of DNA extraction, sample dilution, and reagent contamination on 16S rRNA gene sequencing of human feces – Eliana P. Velásquez-Mejía, Applied Microbiology and Biotechnology

Microbes in the News

How a 672,000-Gallon Oil Spill Was Nearly Invisible – CHRISTINA CARON, New York Times

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 24, 2018

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Today’s digest is full of REALLY cool science and features including a 3D image of the human lung microbiome and metabolome, how gut microbiome of wild mice promotes fitness, and an interesting perspective piece on how environmental filtering applies to microbiomes.

General microbiome

Environmental Filtering Is a Relic. A Response to Cadotte and Tucker.

Aguilar-Trigueros CA- Trends in Ecology and Evolution

Gut microbiome

The Leaky Gut and Altered Microbiome in Chronic Kidney Disease.

Lau WL- Journal of Renal Nutrition

Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

Tasnim N- Frontiers in Microbiology

Skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs.

Zeng B- Frontiers in Microbiology

Lung microbiome

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

Garg N- Cell Host and Microbe

Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Rosshart SP- Cell

Plant and soil microbiome

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter

Yuan Q- Soil Biology and Biochemistry

Bacterial communities in soil become sensitive to drought under intensive grazing

Jurburg SD- Science of the Total Environment

Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.

Xie K- Scientific reports

Marine and inland water microbiome

Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling

Lee MD-Applied and Environmental Microbiology

Dynamic microbial populations along the Cuyahoga River.

Cannon MV-  PloS one

Preprint

High degree of virulence gene diversity in Streptococcus pyogenes isolated in Central Italy

Bencardino D- BioRxiv

Microbiome News

I Wish I’d Known This Before I Gave Birth

-mindbodygreen.com