Category Archives: Human oral

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 4, 2017

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Today we have many interesting articles,  Marangoni A. evaluates  antifungal properties of Spirulina platensis against  Candida species; J. de Gunzburg  reports on gut microbiome  protection from antibiotics; E. Uhlig writes about removal of Escherichia coli from “ready‐to‐eat” salads .. while in my personal non microbiological pics you can read the study from A.Carter about women’s visibility in academic seminars. Apparently women ask fewer questions than men. Enjoy your winter read.

Events and jobs

Microbiology Professor, College of the Sequoias, San Jose

Postdoctoral Fellow, EMBL,Hinxton, United Kingdom

General microbiome

Review: Multidrug resistant (or antimicrobial-resistant) pathogens – alternatives to new antibiotics? – Anne-Sophie Brunel – Swiss Medical Weekly

Petri dish versus Winogradsky column: a longue durée perspective on purity and diversity in microbiology, 1880s-1980s – Grote M – History and Philosophy of the Life Sciences

Pregnancy and early life

32-week premature rupture of membranes caused by oropharyngeal microbiota – Alberto Hidalgo-Chicharro – Microbiology Society

Bacteriological and Immunological Profiling of Meconium and Fecal Samples from Preterm Infants: A Two-Year Follow-Up Study – Marta Gómez – Nutrients

Human respiratory microbiome

IL-17 and TNF-α Are Key Mediators of Moraxella catarrhalis Triggered Exacerbation of Allergic Airway Inflammation – Safa Alnahas – Frontiers in Immunology

Oral microbiome

Gingivitis and plaque prevention using three commercially available dentifrices: A comparative clinical and microbiological randomized control parallel study – Ramprasad Reddy – International Journal of Pharmaceutical Investigation

Human vaginal microbiome

In vitro activity of Spirulina platensis water extract against different Candida species isolated from vulvo-vaginal candidiasis cases – Antonella Marangoni – PLOS One

Characterization of a New Ezakiella Isolated From the Human Vagina: Genome Sequence and Description of Ezakiella Massiliensis Sp. Nov – K Diop – Current Microbiology

Newly Isolated Lactobacilli Strains From Algerian Human Vaginal Microbiota: Lactobacillus Fermentum Strains Relevant Probiotic’s Candidates – Liza Ouarabi – Probiotics and Antimicrobial Proteins

Human nearly-sterile sites

A comprehensive analysis of breast cancer microbiota and host gene expression – Kevin J. Thompson – PLOS One

Human gut microbiome

Aging Gut Microbiota at the Cross-Road between Nutrition, Physical Frailty, and Sarcopenia: Is There a Gut–Muscle Axis? – Andrea Ticinesi – Nutrients

Adipose Tissue Metabolism and Cancer Progression: Novel Insights from Gut Microbiota? – Benedicte F. Jordan – Current Pathobiology Reports

Protection of the human gut microbiome from antibiotics – Jean de Gunzburg – The Journal of Infectious Diseases

Gut microbiota and colorectal cancer: insights into pathogenesis for novel therapeutic strategies – Yongbo Kang – Zeitschrift für Gastroenterologie

Genomic Analysis of a Pathogenic Bacterium, Paeniclostridium sordellii CBA7122 Containing the Highest Number of rRNA Operons, Isolated from a Human Stool Sample – Joon Yong Kim – Frontiers in Pharmacology

Cellular senescence in gastrointestinal diseases: from pathogenesis to therapeutics – Frey N – Nature Reviews Gastroenterology

Gut Symbiont Bacteroides fragilis Secretes a Eukaryotic-Like Ubiquitin Protein That Mediates Intraspecies Antagonism – Chatzidaki-Livanis M – mBio

Reduction in Gut Microbial Diversity as a Mechanism of Action of Exclusive Enteral Nutrition – Kaakoush NO – The American Journal of Gastroenterology

Adipose Tissue Metabolism and Cancer Progression: Novel Insights from Gut Microbiota? – Jordan BF – Current Pathobiology Reports

Review: A review of metabolic potential of human gut microbiome in human nutrition – Yadav M – Archives of Microbiology

Animal experiments 

Colonization with Escherichia coli EC 25 protects neonatal rats from necrotizing enterocolitis – Debi M. Thomas – PLOS One

Animal microbiome

Bamboo Specialists From Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbe – EA McKenney – Microbial Ecology

Plant, root, and soil microbiome

Organic Amendments in a Long-Term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis – CAO Schmid – Microbial Ecology

Distinctive Soil Archaeal Communities in Different Variants of Tropical Equatorial Forest – D Kerfahi – Microbial Ecology

Water and extremophile microbiome 

Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China – Hongpeng Cui – Current Microbiology

Built environment

Microbial Insight into a Pilot-Scale Enhanced Two-Stage High-Solid Anaerobic Digestion System Treating Waste Activated Sludge – Jing Wu – International Journal of Environmental Research and Public Health

Food microbiology

Effects of household washing on bacterial load and removal of Escherichia coli from lettuce and “ready-to-eat” salads – Elisabeth Uhlig – Food Science & Nutrition

Organic food and the impact on human health – Hurtado-Barroso S – Critical Reviews in Food Science and Nutrition

Probiotics / prebiotics

Probiotics Ingestion Does Not Directly Affect Thyroid Hormonal Parameters in Hypothyroid Patients on Levothyroxine Treatment – Giorgia Spaggiari – Frontiers in Endocronology

Characterization of probiotic potential of Bacillus species isolated from a traditional brine pickle – Ragul K – Journal of Food Science and Technology

 

Bioinformatics

Microbiome Datasets Are Compositional: And This Is Not Optional – Gregory B. Gloor – Frontiers in Microbiology

A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community – Herschend J – Scientific Reports

A 16S rRNA gene sequencing and analysis protocol for the Illumina MiniSeq platform – Monica Pichler – bioRxiv

Techniques

Exploration of Microbial Communities Using the Thermo Scientific Varioskan LUX Multimode Reader and the Invitrogen EVOS FL Cell Imaging System – Anna Hiltunen – BioTechniques

Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria – Giantommaso Scarascia – BMC Microbiology

Microbes in the news

Microorganisms on your scalp, ears and elbows can be turned into music

Microbes on the market

With $1M in funding, Phase Genomics looks to crack genetic codes and discover unknown bacteria

Tina’s non microbiological pics

Women’s visibility in academic seminars: women ask fewer questions than men

 

December 2, 2017

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Events and jobs
PhD Student – Developing and validating a computational model of the gut microbiota–mucosa interactions to replace and reduce animal experiments – Birmingham, UK

Assistant/Associate Professor, Microbiology and Immunology – SUNY Upstate Medical University – Syracuse, NY

Microbiology Manager – Cranleigh Scientific – Kent, England

Adjunct Anatomy and Physiology and Microbiology Instructor – City College – Altamonte Springs, FL

Program Manager – Rutgers, The State University of New Jersey

Assistant Professor, Statistics and Microbiology – The University of Manitoba – Winnipeg, Manitoba, Canada

Human respiratory microbiome
Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients – Stephen Wandro – MSystems

Human skin microbiome
Effects of cosmetics on the skin microbiome of facial cheeks with different hydration levels. – Silvia Esmeralda Pérez-Topete – Microbiology Open

Propionibacterium acnes induces autophagy in keratinocytes: involvement of multiple mechanisms. – Klára Megyeri – The Journal Of Investigative Dermatology

Human oral microbiome
A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods. – K C Anukam – Nigerian Journal Of Clinical Practice

Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers – Brandilyn A. Peters – Cancer Research

Review: Microbial colonization of the periodontal pocket and its significance for periodontal therapy. – Andrea Mombelli – Periodontology 2000

Review: Resilience of the Oral Microbiota in Health: Mechanisms That Prevent Dysbiosis. – B T Rosier – Journal Of Dental Research

Human gut microbiome
Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production. – Nicole Reichardt – The Isme Journal

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients – Andrew Brantley Hall – Genome Medicine

Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy. – Yizhong Wang – Journal Of Crohn’S & Colitis

Antibiotic Resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. – Jie Feng – Environmental Microbiology

Involvement of shared mucosal-associated microbiota in the duodenum and rectum in diarrhea-predominant irritable bowel syndrome. – Gangping Li – Journal Of Gastroenterology And Hepatology

Review: Are the decrease in circulating anti-α1,3-Gal IgG and the lower content of galactosyl transferase A1 in the microbiota of patients with multiple sclerosis a novel environmental risk factor for the disease? – Emmanuel Montassier – Molecular Immunology

Review: Combined therapies to treat complex diseases: The role of the gut microbiota in multiple sclerosis. – Laura Calvo-Barreiro – Autoimmunity Reviews

Review: Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders – Nikolas Dovrolis – Briefings in Bioinformatics

Animal experiments
IL-17 is a protection effector against the adherent-invasive Escherichia coli in murine colitis. – Hai-Jia Zhang – Molecular Immunology

Changes in gut microbiota during development of compulsive checking and locomotor sensitization induced by chronic treatment with the dopamine agonist quinpirole. – Tony D Jung – Behavioural Pharmacology

Potential Impact of Metabolic and Gut Microbial Response to Pregnancy and Lactation in Lean and Diet-Induced Obese Rats on Offspring Obesity Risk. – Heather A Paul – Molecular Nutrition & Food Research

Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut-brain axis. – H Li – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits – Yang Chen – PeerJ

Animal microbiome
Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. – H Pieter J van Veelen – Microbiome

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

Production and biotechnological potentialities of extracellular polymeric substances from sponge-associated Antarctic bacteria – Consolazione Caruso – Applied and Environmental Microbiology

Review: Wild gut microbiota protect from disease. – Francesca S Gazzaniga – Cell Research

Plant, root, and soil microbiome
Symbionts protect aphids from parasitic wasps by attenuating herbivore-induced plant volatiles. – Enric Frago – Nature Communications

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream. – Juanita Mora-Gómez – The Science Of The Total Environment

Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome. – Shobit Thapa – Journal Of Basic Microbiology

Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics. – Katarzyna Ignasiak – Bmc Microbiology

Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi – Stephen J. Mondo – Nature Communications

Organic amendments shift the phosphorus-correlated microbial co-occurrence pattern in the peanut rhizosphere network during long-term fertilization regimes – Yan Chen – Applied Soil Ecology

The interactive effects of arbuscular mycorrhiza and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogens – Alejandro Pérez-de-Luque – Scientific Reports

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil – Lily Pereg – Science of the Total Environment

Review: Yeast population of the Kindo Peninsula lichens – A. V. Kachalkin – Microbiology

Review: Bacterial Endophyte Colonization and Distribution within Plants – Shyam L. Kandel – Microorganisms

Review: Emerging Microbial Biocontrol Strategies for Plant Pathogens – Sharifah Farhana Syed Ab Rahman – Plant Science

Water and extremophile microbiome
Microbial life on a sand grain: from bulk sediment to single grains. – David Probandt – The Isme Journal

Tracking active groundwater microbes with D2 O labeling to understand their ecosystem function. – Martin Taubert – Environmental Microbiology

Variability of the composition of the microbial community of the deep subsurface thermal aquifer in Western Siberia – V. V. Kadnikov – Microbiology

Cyanobacterial community structure in hot water springs of Indian North-Western Himalayas: A morphological, molecular and ecological approach – Yadvinder Singh – Algal Research

Built environment
Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles. – Kristie Tanner – Environmental Microbiology Reports

Microorganisms of low-temperature heavy oil reservoirs (Russia) and their possible application for enhanced oil recovery – T. N. Nazina – Microbiology

Food microbiology
Review: Cereal fiber, fruit fiber, and type 2 diabetes: Explaining the paradox. – Karen M Davison – Journal Of Diabetes And Its Complications

Probiotics / prebiotics
Exploring the Impact of Food on the Gut Ecosystem Based on the Combination of Machine Learning and Network Visualization. – Hideaki Shima – Nutrients

Translational Development of Microbiome-Based Therapeutics: Kinetics of E. coli Nissle and Engineered Strains in Humans and Nonhuman Primates. – Caroline Kurtz – Clinical And Translational Science

Phages and viruses
Distribution and Inferred Evolutionary Characteristics of a Chimeric ssDNA Virus Associated with Intertidal Marine Isopods – Kalia S. I. Bistolas – Viruses

Microbial Ecology
Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists – Alexandra L. McCully – mBio

Review: Cell-cell recognition and social networking in bacteria. – Vera Troselj – Environmental Microbiology

Bioinformatics
Functional sequencing read annotation for high precision microbiome analysis. – Chengsheng Zhu – Nucleic Acids Research

Reader reaction on the fast small-sample kernel independence test for microbiome community-level association analysis. – Bin Guo – Biometrics

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes – Bhavya Papudeshi – BMC Genomics

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota – Aitor Blanco-Míguez – Briefings in Bioinformatics

Techniques
Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics – Zijuan Lai – Nature Methods

Brief guide to the analysis, interpretation and presentation of microbiota data. – Stefan Zalewski – Archives Of Disease In Childhood. Education And Practice Edition

Optimized fluorescent proteins for the rhizosphere-associated bacterium Bacillus mycoides with endophytic and biocontrol agent potential. – Yanglei Yi – Environmental Microbiology Reports

Genome Announcements
Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java, Indonesia. – Anto Budiharjo – Genome Announcements

Mrakia arctica sp. nov., a new psychrophilic yeast isolated from an ice island in the Canadian High Arctic – Masaharu Tsuji – Mycoscience

Microbes in the news
New research provides insights into the skin microbiome – EurekAlert

Lab notes: The vaginal microbiome can predict whether a woman is going to have a premature baby – Scroll.in
Paper link: First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk  (posted Nov 27, 2017)

How Bacteria Help Regulate Blood Pressure – Veronique Greenwood – Quanta Magazine

Gut Bacteria Predict Responses, Survival Time to PD-1 Cancer Immunotherapy – Bryant Furlow – Modern Medicine Network

Synthetic Glycolipids As A New Class Of Antimicrobials To Down-Regulate Cell Wall Functions – Narayanaswamy Jayaraman – Science Trends

The microbiological art of making a better sausage – Phys.Org

Will microbial protein replace meat on the table? – Digital Journal – Tim Sandle

New 3-D printed materials harness the power of bacteria – Maria Temming – Science News

Scientists Have Expanded the Genetic Code in Bacteria – Brad Jones – Futurism

Microbes on the market
Qiagen Joins French Biotech to Build the Next Generation of Microbiome Technology – Alex Dale – European Biotech News

DuPont and Ireland’s APC venture forward in microbiome-inspired pact – Will Chu – Nutra Ingredients

Rebiotix Announces Expansion of Phase 1 Trial of the Company’s Oral Capsule Microbiota Product, RBX7455, Following Successful Completion of Initial Study Arms – Markets Insider

Science, publishing, and career
Five ways to fix statistics – Jeff Leek – Nature

Tiffany’s non-microbiology picks
An Open Letter to the Senate Concerning H.R.1 and the Graduate Student Tax Provision – Alana Van Dervort
# A letter (that you can sign) against one part of the bill that passed this morning

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 23, 2017

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Today we have pretty much diverse Microbiome Digest particularly in the section of General microbiome. Interesting papers on E coli as a model organism for metabolic engineering, influence of exercise on our gut microbiota and influence of antibiotics on genetic diversity of honeybee gut microbiota. Enjoy reading these and many many more articles and news about microbes.

Events and jobs

PhD in Soil Microbiology, Teagasc Johnstown Castle, UK

PhD Fellowship in Molecular Microbiology, Copenhagen, Denmark

Postdoctoral Research Associate – Bacterial Evolutionary Genomics, Missoula, MT, US

Postdoctoral researchers – (Lemon Lab), Cambridge MA, US

Associate Professor/Professor in Microbiology, Nottingham, UK

General microbiome

The Immunomodulatory Drug Glatiramer Acetate is Also an Effective Antimicrobial Agent that Kills Gram-negative Bacteria – Stig Hill Christiansen – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China – Sudhakar G. Bhandare – Genome Announcements

Survival of microbes in Earth’s stratosphere – Priya Das Sarma – Current Opinion in Microbiology

Review: Cable Bacteria Take a New Breath Using Long-Distance Electricity – Filip J.R. Meysman – Trends in Microbiology

Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation – Edgardo Sepulveda – Frontiers in Microbiology

The effect of the 2015 Earthquake on the bacterial community compositions in water in Nepal – Sital R. Uprety – Frontiers in Microbiology

Rokubacteria: genomic giants among the uncultured bacterial phyla – Eric D. Becraft – Frontiers in Microbiology

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

Pregnancy and early life

Microbial Mechanistic Insight into the Role of Inulin in Improving Maternal Health in a Pregnant Sow Model – Pan Zhou – Frontiers in Microbiology

Human respiratory microbiome

A practical molecular identification of nonfermenting Gram-negative bacteria from cystic fibrosis – Carolina Paulino da CostaCapizzani – Brazilian Journal of Microbiology

Oral microbiome

Over-the-counter mouthwash use and risk of pre-diabetes/diabetes – Kaumudi J.Joshipura – Nitric Oxide

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing – Yuan Wang – Frontiers in Microbiology

Exploring the association between Alzheimer’s disease, oral health, microbial endocrinology and nutrition – Alice Harding – Frontiers in Aging Neuroscience

Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet – Florent Lassalle – Molecular Ecology

Human skin microbiome

Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo – K Johani – Journal of Antimicrobial Chemotherapy

Human gut microbiome

Review: Influence of microbiota on intestinal immune system in ulcerative colitis and its intervention – Sailong Zhang – Frontiers in Immunology

Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans – Allen, Jacob M – Medicine & Science in Sports & Exercise

The Kynurenine Pathway As a Novel Link between Allergy and the Gut Microbiome – Aaron P. Van der Leek – Frontiers in Immunology

The gut microbiota: A new potential driving force in liver cirrhosis and hepatocellular carcinoma – Marco Sanduzzi Zamparelli – United European Gastroenterology Journal

Animal experiments 

Aged Gut Microbiota Contributes to Systemical Inflammaging after Transfer to Germ-Free Mice – Floris Fransen – Frontiers in Immunology

Animal microbiome

Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages – Manuela Oliveira Ramalho – PLOS One

Spontaneous body contractions are modulated by the microbiome of Hydra – Andrea P. Murillo-Rincon – Sceintific Reports

Age-related differences in the respiratory microbiota of chickens – Laura Glendinning – PLOS One

A potential new species of porcine Actinobacillus defined by multi-locus sequence analysis – C. Turni – Animal Production Science

Prevalence survey of Toxoplasma gondii in hearts from Western Australian sows – K. Hodgson – Animal Production Science

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome – Kasie Raymann –  Molecular Ecology

Plant, root, and soil microbiome

Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato – Anastasis Antoniou – Frontiers in Plant Science

Exogenous nitrogen addition reduces the temperature sensitivity of microbial respiration without altering the microbial community composition – Hui Wei – Frontiers in Microbiology

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities – Theodore M. Flynn – Frontiers in Microbiology

The effect of Lobelia dortmanna L. on the structure and bacterial activity of the rhizosphere – KatarzynaLewicka-Rataj – Aquatic Botany

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xue-Ying Tian – Frontiers in Microbiology

Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession – Miao Wang – Frontiers in Microbiology

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

Water and extremophile microbiome

Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation – Marta Sebastián – Environmental Microbiology

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods – Alexis L. Pasulka – Environmental Microbiology

Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity – Abigail Tomasek – Frontiers in Microbiology

Chapter 4.1 – The Biota of Intermittent Rivers and Ephemeral Streams: Prokaryotes, Fungi, and Protozoans – Anna M. Romaní – Intermittent Rivers and Ephemeral Streams

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge – Wei Xu – Deep Sea Research Part I

Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems – Dongwei Hou – Frontiers in Microbiology

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams – Ze Ren – Frontiers in Microbiology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology
Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Zhichao Zhou – Frontiers in Microbiology

 

Food microbiology

Novel insights into microbial community dynamics during the fermentation of Central European ice wine – Mária Bučková – International Journal of Food Microbiology

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

Probiotics / prebiotics

Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals – Mia C. Theilmann – mBio

Phages and viruses

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers – Sophie Nguyen – mBio

MVP: a microbe–phage interaction database  – Na L. Gao – Nucleic Acids Research

Biotechnology

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments – Emine Gozde Ozbayram – Applied Microbiology and Biotechnology

Escherichia coli as a model organism for systems metabolic engineering – Paul A.Adamczyk – Current Opinion in System Biology

Bioinformatics

Review: Computational Approaches for Integrative Analysis of the Metabolome and Microbiome – Jasmine Chong – Metabolites

Techniques

Nucleic acid purification from plants, animals and microbes in under 30 seconds – Yiping Zou – PLOS Biology

Lighting Van Leeuwenhoek’s samples – Lesley A. Robertson – FEMS Microbiology Letters

Analysis of Microbiome Data in the Presence of Excess Zeros – Abhishek Kaul – Frontiers in Microbiology

Stripping flow cytometry: How many detectors do we need for bacterial identification? – Peter Rubbens – Cytometry

Microbes in the news 

Plague Bacteria Entered Europe During Neolithic Age, Genetic Analysis Finds 

How the Immune System Identifies Invading Bacteria

Scientists Program Remote-Controlled Nanobots to Kill Cancer

Microbes on the market 

Qualitative Report on Human Microbiome Market 

Microbes and art

Superbugs And Rockets Side By Side At Science Museum

 

 

 

November 11, 2017

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Human Microbiome

Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis – Leonardo Mancabelli – FEMS Microbiology Ecology

Salivary proteins and microbiota as biomarkers for early childhood caries risk assessment – Abdullah S Hemadi – International Journal of Oral Science (Open Article)

Pancreatic cyst fluid harbors a unique microbiome – Shan Li – Microbiome (Open Article)

Minireview: Microbial Therapeutics Designed for Infant Health – Claire Watkins – Frontiers in Nutrition (Open Article)

Exclusive Enteral Nutrition Induces Remission in Pediatric Crohn’s Disease via Modulation of the Gut Microbiota – Dawei Gong – BioMed Research International

Review: Clostridium difficile infection in the elderly: an update on management – Tomefa E Asempa – Clinical Interventions in Aging

Healthy donor faecal transplant for corticosteroid non-responsive severe alcoholic hepatitis – Cyriac Abby Philips – BMJ Case Reports

The gut mycobiome composition is linked to carotid atherosclerosis – M.R. Chacón –  Beneficial Microbes  

Review: T Cell-Mediated Chronic Inflammatory Diseases Are Candidates for Therapeutic Tolerance Induction with Heat Shock Proteins – Ariana Barbera Betancourt – Frontiers in Immunology (Open Article)

Review: Recipe for IBD: can we use food to control inflammatory bowel disease? – Mario Witkowski – Seminars in Immunopathology (Open Article)

Measuring the impact of olive pomace enriched biscuits on the gut microbiota and its metabolic activity in mildly hypercholesterolaemic subjects – Lorenza Conterno  – European Journal of Nutrition (Open Article)

 

Animal Microbiome

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 (Open Article)

Review: Mouse models for human intestinal microbiota research: a critical evaluation – Floor Hugenholtz – Cellular and Molecular Life Sciences (Open Article)

Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca – T. Dulski – Journal of Fish Biology

A High Grain Diet Dynamically Shifted the Composition of Mucosa-Associated Microbiota and Induced Mucosal Injuries in the Colon of Sheep – Yue Wang – Frontiers in Microbiology (Open Article)

Alteration of Gut Microbiota and Inflammatory Cytokine/Chemokine Profiles in 5-Fluorouracil Induced Intestinal Mucositis – Hong-Li Li – Frontiers in Cellular and Infection Microbiology (Open Article)

Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals – M. Chiarello – Scientific Reports (Open Article)

Mitochondrial gene polymorphism is associated with gut microbial communities in mice – Misa Hirose – Scientific Reports (Open Article)

 

Environmental Microbiomes

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities – Theodore M. Flynn – Frontiers in Microbiology (Provisionally accepted article, full text available soon)

Taxonomic and functional differences between microbial communities in Qinghai Lake and its input streams – ze ren – Frontiers in Microbiology (Provisionally accepted article, full text available soon)

 

Bioinformatics

HOMINID: A framework for identifying associations between host genetic variation and microbiome composition – Joshua Lynch – GigaScience (Open Article)

 

Air Microbiome

Microbiota of the ground air layers in natural and industrial zones of the Kola Arctic – Maria V. Korneykova – Journal of Environmental Science and Health, Part A

 

Beneficial Microbes

Whole-Genome Sequencing of Lactobacillus Species from Two Commercial Probiotic Products – Anna Colavecchio – Genome Announcements (Open Article)

November 9, 2017

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Today, we have interesting papers about diet and microbiota both in human and other mammals. We have also papers about urchin and black slug microbiota and gut remediation (use of probiotics to manage metal accumulation).

 

Human Microbiome

State of the art: Manipulating the microbiome: evolution of a strategy to prevent S. aureus disease in children – D F Khamash – Journal of Perinatology

Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications – Shuai Zheng – Scientific Reports

Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota – Gregorio Iraola – Nature Communications

Impact of Lactobacillus reuteri colonization on gut microbiota, inflammation, and crying time in infant colic – Monica L. Nation – Scientific Reports

Outlook: Microbiome: A bag of surprises – Claire Ainsworth – Nature

Research Highlight: Gut microbiota: Oral bacteria: a cause of IBD? – Iain Dickson – Nature Reviews Gastroenterology and Hepatology

Commentary: Different Substrate Preferences Help Closely Related Bacteria To Coexist in the Gut – Petra Louis – mBio

Opinion: How poverty affects diet to shape the microbiota and chronic disease – Christy A. Harrison – Nature Reviews Immunology

Review: Balancing Herbal Medicine and Functional Food for Prevention and Treatment of Cardiometabolic Diseases through Modulating Gut Microbiota – Ming Lyu – Frontiers in Microbiology

Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients – Matteo Soverini – Frontiers in Microbiology

 

Animal Microbiome

Effect of Dietary Forage to Concentrate Ratios on Dynamic Profile Changes and Interactions of Ruminal Microbiota and Metabolites in Holstein Heifers – Jun Zhang –  Frontiers in Microbiology

(Provisionally accepted, Full text available soon) Antibiotic-induced Alterations in Gut Microbiota are Associated with Changes in Glucose Metabolism in Healthy Mice – Richard R. Rodrigues – Frontiers in Microbiology

Phylogeny and Antagonistic Activities of Culturable Bacteria Associated with the Gut Microbiota of the Sea Urchin (Paracentrotus lividus) – Marinella Silva Laport – Current Microbiology

Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice – Matthew J. Dalby – Cell Reports

Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes – Ryan Joynson – Frontiers in Microbiology

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period – Zhigang Zhu – PLoS ONE

Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota – Guolin Li – Cell Metabolism

Nonalcoholic Fatty Liver Disease Is Exacerbated in High-Fat Diet-Fed Gnotobiotic Mice by Colonization with the Gut Microbiota from Patients with Nonalcoholic Steatohepatitis – Chien-Chao Chiu – Nutrients

 

Beneficial Microbes and Molecules

Gut remediation: a potential approach to reducing chromium accumulation using Lactobacillus plantarum TW1-1 – Gaofeng Wu – Scientific Reports

(Provisionally accepted, Full text available soon) Lactobacillus plantarum MYS6 ameliorates fumonisin B1-induced hepatorenal damage in broilers – B V. Deepthi –  Frontiers in Microbiology

(Provisionally accepted, Full text available soon) Wuji Wan formula ameliorates diarrhoea and disordered colonic motility in post-inflammation irritable bowel syndrome rats by modulating the gut microbiota – Ying Chen – Frontiers in Microbiology

Polysaccharides from Chrysanthemum morifolium Ramat ameliorate colitis rats by modulating the intestinal microbiota community – Jin-Hua Tao – Oncotarget

 

Environmental Microbiology

Fungal Community Structure and As-Resistant Fungi in a Decommissioned Gold Mine Site – Silvia Crognale – Frontiers in Microbiology

 

Methods

Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota – Fanjing Meng – Molecular Medicine Reports

 

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 1, 2017

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Happy November everybody! We have an interesting collection of articles today. Co-cultivation of plant beneficial fungi as an effective strategy to modulate the production of bioactive metabolites and a review on the benefits of berries and their phytochemicals on the digestive and immune systems. Enjoy!

Events and jobs

Microbiology Lab Assistant – Seattle, Washington – Labcorp

General microbiome

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Pyschosomatic Medicine

Human respiratory microbiome

Review : CF Airway Microbiome: Overturning the Old, Opening the Way for the New – George A. O’Toole – Journal of Bacteriology

Human oral microbiome

Effect of maltitol-containing chewing gum use on the composition of dental plaque microbiota in subjects with active dental caries – Erica M. Prosdocimi – Journal of Oral Microbiology

Human gut microbiome

The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis – Puneet Puri – Hepatology

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology

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

Review : Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrient – Colette Shortt – European Journal of Nutrition

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro – Hasinika K. A. H. Gamage – Scientific Reports

Animal experiments

Antibiotic treatment disrupts bacterial communities in the colon and rectum of SIV-infected macaques – Alexander S. Zevin – FEMS Microbiology Letters

Ophiopogonin D alleviates high-fat diet–induced metabolic syndrome and changes the structure of gut microbiota in mice – Siyu Chen – The FASEB Journal

Animal microbiome

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques – Corey D. Russo – Microbial Ecology

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits – Ara S. Winter – PeerJ

Analysis of the Microbial Diversity in the Fecal Material of Giraffes – Jessica M. Schmidt – Current Microbiology

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors – Douglas S. Pearce – Microbiome

Metabolomics

Plasma Metabolites From Choline Pathway and Risk of Cardiovascular Disease in the PREDIMED (Prevention With Mediterranean Diet) Study – Marta Guasch-Ferré – Journal of the American Heart Association

Plant, root, and soil microbiome

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

An endophytic Bacillus strain promotes growth of oil palm seedling by fine root biofilm formation – MdHoirul Azri – Rhizosphere

Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants – Guzel R. Kudoyarova – Acta Physiologiae Plantarum

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China – Chuang Zhang – Biogeosciences

Impact of land use change and soil organic carbon quality on microbial diversity in soils across Europe – Márton Szoboszlay – FEMS Microbiology Ecology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens – Cara H. Haney – Molecular Ecology

*Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites – F. Vinale – Scientific Reports

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – Gigascience

Water and extremophile microbiome

Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis – Zheng Xiao – Applied Microbiology and Biotechnology

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant – Seungdae Oh – Water Research

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau – Yong-Liang Chen – Molecular Ecology

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake – Dayong Zhao – FEMS Microbiology Ecology

Food Microbiology

Anti-obesity Effect of Exopolysaccharides Isolated from Kefir Grains – Juha Lim – J. Agric. Food Chem

Modulating Effects of Dicaffeoylquinic Acids from Ilex Kudingcha on Intestinal Microecology in vitro – Minhao Xie – Journal of Agricultural Food Chemistry

*Review of the health effects of berries and their phytochemicals on the digestive and immune systems – Coen Govers – Nutrition Reviews

Probiotics / prebiotics

Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity – G.Karimi – Nutrition, Metabolism and Cardiovascular Diseases

Bioinformatics

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Phages and viruses

Review : Assessing Species Diversity Using Metavirome Data: Methods and Challenges – Damayanthi Herath – Computational and Structural Biotechnology Journal

Microbes in the news

Caves Host Gooey Biofilms Built by Methane-Eating Bacteria

3D Printed Artificial Small Intestine to Advance Research on Gut Bacteria

Enzymes from dangerous bacteria turn into important tools for protein chemistry

Microbes on the market

The University Medical Center Groningen and Novogene announce the start of the 10K Metagenome Project

Science, publishing, and career

Book Chapter : Leading Change in Undergraduate STEM Education – Adam K. Leibovich – Educational and Outreach Projects from the Cottrell Scholars Collaborative Undergraduate and Graduate Education Volume 1

Anitha’s non-microbiology picks

Congratulations Nancy Scherich! The winner of this year’s ‘Dance Your Ph.D.’ contest

ROSINA spectral measurements bring comet’s chemistry to life

Scary as they are, few vampires have a backbone

 

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