Category Archives: Pregnancy and birth

August 27, 2017

Posted on by

Quite a few reviews and news pieces to supplement your Sunday. Separation of mom and infant shortly after birth may run afoul of our evolutionary history, the gut-microbiome-brain axis is hot today, and can we use bacteria to generate electricity for us?

General microbiology

Review: Plant Hormones: Key Players in Gut Microbiota and Human Diseases? – Emilie Chanclud and Benoît Lacombe – Trends in Plant Science

Review: Microbe-mitochondrion crosstalk and health: An emerging paradigm – Prashant Bajpai et al. – Mitochondrion

Food microbiology

Diversity of bacterial communities in French chicken cuts stored under modified atmosphere packaging – Amélie Rouger et al. – Food Microbiology

Pregnancy and early life

*Review: Mother-newborn separation at birth in hospitals: A possible risk for neurodevelopmental disorders? – Noémi Császár-Nagy and István Bókkon – Neuroscience & Biobehavioral Reviews

Cancer and microbiome

Review: Probiotic species in the modulation of the anticancer immune response – Luciana Marinelli and Gian Carlo Tenore – Seminars in Cancer Biology

Human gut microbiome

Special Issue on Crohn’s Disease – Gastroenterology Clinics of North America

Review: Insights into defective serological memory after acute lymphoblastic leukaemia treatment: The role of the plasma cell survival niche, memory B-cells and gut microbiota in vaccine responses – Shanie Saghafian-Hedengren et al. – Blood Reviews

Review: Circadian Clocks and Metabolism: Implications for Microbiome and Aging – Georgios K. Paschos and Garret A. FitzGerald – Trends in Genetics

Human gut-microbiome-brain axis

*Microbial regulation of microRNA expression in the amygdala and prefrontal cortex – Alan E. Hoban et al. – Microbiome

Press: Feeling anxious? Your gut bacteria might be to blame – Honor Whiteman – Medical News Today

Review: The microbiota–gut–brain axis in obesity – Cristina Torres-Fuentes and Harriët Schellekens et al. – The Lancet Gastroenterology & Hepatology

Commentary: The Microbiome as a Key Regulator of Brain, Behaviour and Immunity: Commentary on the 2017 Named Series – Michael T. Bailey and John F. Cryan – Brain, Behavior, and Immunity

Animal experiments

Probiotics Modulete Gut Microbiota and Improve Insulin Sensitivity in DIO Mice: Probiotics Modulete Microbiota and Insulin Action – Renata A. Bagarolli et al. – The Journal of Nutritional Biochemistry

*Mice: Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption – Kymberleigh A. Romano et al. – Cell Host & Microbe

*Mice: An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate – Luisella Spiga and Maria G. Winter et al. – Cell Host & Microbe

Piglets: Gut antimicrobial effects and nutritional value of black soldier fly (Hermetia illucens L.) prepupae for weaned piglets – Thomas Spranghers et al. – Animal Feed Science and Technology

Plant, root and soil microbiome

Preprint: Plant genes influence microbial hubs that shape beneficial leaf communities – Benjamin Brachi et al. – bioRxiv

Tree roots select specific bacterial communities in the subsurface critical zone – O. Nicolitch et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Product quality and microbial dynamics during vermicomposting and maturation of compost from pig manure – Iria Villar et al. – Waste Management

Phages and viruses

Immobilization of bacteriophage in wound-dressing nanostructure – Frederico Nogueira et al. – Nanomedicine: Nanotechnology, Biology and Medicine

Microbes in the news

Hunter-gatherer gut microbes change with seasons, researchers say – Andrew Joseph – STAT

Top stories: Life-saving mini-organs, seasonal gut bacteria, and the world’s smallest antennas – Giorgia Guglielmi – Science

Does gut bacteria cause autism? Pathogens in the stomach alter the brain’s development and may increase the risk of condition – Alexandra Thompson – Daily Mail

President Trump’s proposed budget would kill Florida’s beach bacteria testing program – Amy Bennett Williams – News-Press

*Could Cyborg Bacteria Help Us Turn Sunlight into Fuel? – Steve Williams – Care2

Researchers suggest microbiological version of “Anna Karenina principle” – Xinhua Net

Trillions of Bacteria in Your Body are Alien to Science, Study Finds – WSP

Could you go a month without bathing? – Yvonne van Dongen – Stuff

Without fecal transplant, life can be a pain in the butt – Travis Paterson – Victoria News

August 24, 2017

Posted on by

Bacterial paleontology of iron formations, gene expression from bacteria and archaea in the Amazon River, indoles promote a “youthful” gene expression profile in their host.

Events and jobs

Podcast: Branding Bacteria – Carla Brown

General microbiome

Preprint: Metabolic Model-Based Analysis of the Emergence of Bacterial Cross-Feeding through Extensive Gene Loss – Colin P McNally – bioRxiv

Pregnancy and early life

Breast Milk Transforming Growth Factor β Is Associated With Neonatal Gut Microbial Composition – Alexandra R Sitarik – Journal of Pediatric Gastroenterology and Nutrition

Human gut microbiome

Increased Tryptophan Metabolism is Associated With Activity of Inflammatory Bowel Diseases – Susanna Nikolaus – Gastroenterology

Animal experiments

Indoles from commensal bacteria extend healthspan – Robert Sonowal – PNAS

Plant, root, and soil microbiome

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities – Alessandro Florio – Scientific Reports

Changes in Soil Microbial Community and Its Effect on Carbon Sequestration Following Afforestation on the Loess Plateau, China – Yun Xiang – International Journal of Environmental Research and Public Health

Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island – Giuseppe Concheri – Scientific Reports

Influence of film mulching on soil microbial community in a rainfed region of northeastern China – Wenyi Dong – Scientific Reports

Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE) – Serena Fraraccio – Scientific Reports

Adaptive evolution of rhizobial symbiotic compatibility mediated by co-evolved insertion sequences – Ran Zhao – The ISME Journal

Micropredator niche differentiation between bulk soil and rhizosphere of an agricultural soil depends on bacterial prey – Lu Zhang – FEMS Microbiology Ecology

Water and extremophile microbiome

Predicting blooms of toxic cyanobacteria in eutrophic lakes with diverse cyanobacterial communities – Aleksandra Bukowski – Scientific Reports

Patterns of Bacterial and Archaeal Gene Expression through the Lower Amazon River – Brandon M Satinsky – Frontiers in Marine Science

Probiotics/prebiotics

Protocol for a randomised, placebo-controlled pilot study for assessing feasibility and efficacy of faecal microbiota transplantation in a paediatric ulcerative colitis population: PediFETCh trial – Nikhil Pai – Gastroenterology and Hepatology

More microbes

Bacterial paleontology of the Neoarchean banded iron formations of Karelia and the Kola Peninsula – M M Astafieva – Paleontological Journal

Microbes in the news

Cyborg bacteria covered in solar panels can beat plants at photosynthesis – Angela Chen – The Verge

Gut bacteria influence the brain indirectly, study shows – Maria Cohut – Medical News Today

Scientists uncover two-layer identification among soil bacteria – Amy Wallace – UPI.com

We May Have Just Found The Hormone That Lets Gut Bacteria Talk to The Brain – Peter Duckbill – Science Alert

August 21, 2017

Posted on by

New Microbiome Digest and many many interesting articles: metagenome analysis as a powerful tool for enzyme bioprospecting, application of DGGE on oral bacterial community; labeling of prokaryotic mRNA in live cells with FISH-TAMB…
While in non-microbiology picks read and join very interesting project Scientist Selfies. This project explores how scientists use Instagram and how scientists’ IG posts can potentially change public perceptions of scientists’.

Events and jobs

Postdoc position for Cell Factory Construction, Novozymes, Denmark

IBS-Nature Conference on Frontiers in Genome Engineering

General microbiome

Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer – Frances Tran – Scientific Reports

Review: Archaea Are Interactive Components of Complex Microbiomes – Christine Moissl-Eichinger – Trends in Microbiology

 

Pregnancy and early life

Human Milk Oligosaccharides Exhibit Antimicrobial and Antibiofilm Properties against Group B Streptococcus – Dorothy L. Ackerman – ACS Infectious Diseases

Review: Development of the gut microbiota in infancy and its impact on health in later life – Masaru Tanaka –  Allergology International

Maternal microbiomes in preterm birth: Recent progress and analytical pipelines – Lindsay A. Parnell – Seminars in Perinatology

Oral microbiology

Application of denaturing gradient gel electrophoresis to the analysis of bacterial communities associated with asymptomatic and symptomatic pericoronitis –  Xin Zhang – Journal of Oral and Maxillofacial Surgery

 

 

Human gut microbiome

Review: Food contact materials and gut health: Implications for toxicity assessment and relevance of high molecular weight migrants – Ksenia J. Groh – Food and Chemical Toxicology

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota – Clémence Defois – Frontiers in Microbiology

Animal experiments

AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut – Kevin Cadwell – BMC Genomics

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Rebecca A. Ober – Veterinary Microbiology

Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks – Kirsty Dougal – Frontiers in Microbiology

Animal microbiome

Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness – Suyeon Kim – LWT – Food Science and Technology

Diet and gut microbiota of two supralittoral amphipods Orchestia montagui and Talitrus saltator living in different microhabitats – Khaled F.A. Abdelrhman – Estuarine, Coastal and Shelf Science

Gut microbiome analysis as a tool for developing new probiotic products – Daniel Ramón – Journal of Biotechnology

Review: Human genetic variation and the gut microbiome in disease – Andrew Brantley Hall – Nature Reviews  Genetics

Plant, root, and soil microbiome

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems – Madangchanok Imchen – Scienfic Reports

Microbial community structure and function respond more strongly to temporal progression than to the application of slurry in an Irish grassland – Aaron Fox – Applied Soil Ecology

Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens – John B. Bruce – Evolution

Water and extremophile microbiome

Differences in temperature and water chemistry shape distinct diversity patterns in thermophilic microbial communities – Cecilia M. Chiriac –  Applied nad Environmental Microbiology

Planococcus ruber sp. nov., isolated from a polluted farmland soil sample – Xu Wang – International Journal of Systematic and Evolutionary Microbiology

Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka – Andrey V. Mardanov – Antonie van Leeuwenhoek

Aura-biomes are present in the water layer above coral reef benthic macro-organisms – Kevin Walsh – PeerJ

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov – Jiro F Mori – The ISME

Food microbiology

Restoration of GABA production machinery in Lactobacillus brevis by accessible carbohydrates, anaerobiosis and early acidification – Qinglong Wu – Food Microbiology

Development of non-pathogenic bacterial biofilms on the surface of stainless steel which are inhibitory to Salmonella enterica – Yoonbin Kim – Food Microbiology

 

Bioinformatics

Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting – Aravind Madhavan –  Applied Biochemistry and Biotechnology

Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process – Karolina Elżbieta Kaczor-Urbanowicz – Bioinformatics

Biotechnology

Biogas production from brewery spent grain as a mono-substrate in a two-stage process composed of solid-state anaerobic digestion and granular biomass reactors – Mario Panjičko – Journal of Cleaner Production

Revealing sludge and biofilm microbiomes in membrane bioreactor treating piggery wastewater by non-destructive microscopy and 16S rRNA gene sequencing – Tomohiro Inaba – Chemical Engineering Journal

Techniques

Characterization of syntrophic Geobacter communities using ToF-SIMS – Wenchao Wei – Biointerphases

Labeling of prokaryotic mRNA in live cells using fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB) – Rachel Harris – bioRxiv

Microbes in the news

No guts no glory: Harvesting the microbiome of athletes

Oil-eating bacteria help sea life thrive

Tina’s (non-microbiology) picks

 Research project “To Selfie or Not to Selfie” – How Can Scientists Foster Public Trust on Instagram? 

Is there enough transparency in #peerreview? Join the debate #PeerRevWk17

August 17, 2017

Posted on by

After two days of holidays on Microbiome Digest, today our blog is a bit longer with many papers in the part of water, soil and gut microbiome. Moreover, check new tools which can be used to deal with microbiome data (MicrobiomeDB and MetaMeta) and some interesting news about microbes in the “Microbes in the news” section. Enjoy the summer (in the lab or on the beach) while reading what is new in microbial world.

Events and jobs

Quality Control Manager, Microbiology, Technical Operations, Marlborough, Massachusetts, US

Assistant/Associate Professor – Microbiology and Immunology (Job ID #83258), Chicago, US

General microbiome

A macroecological theory of microbial biodiversity – William R. Shoemaker – Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms – Jonathan Friedman – Nature Ecology & Evolution

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla – Eric Becraft – bioRxiv

Review: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life – Anja Spang – Science

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria – Arnauld Vinçon-Laugier – Frontiers in Microbiology

Advances in the analysis of “less-conventional” human body fluids: an overview of the ce- and hplc-ms applications in the years 2015–2017 – Monica Di Venere – Electrophoresis

Pregnancy and early life

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly A.Lackey – Journal of Microbiological Methods

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants – Danping Zhu – Scientific Reports

Multi-site human microbiome

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid –  Philipp Kirstahler – bioRxiv

Oral microbiome

Oral microbial community assembly under the influence of periodontitis – Hongju Chen – PLOS One

Subgingival Microbiome of Gingivitis in Chinese Undergraduates – Ke Deng – Chinese Journal of Dental Research

Human skin microbiome

Review: What is new in the pathophysiology of acne, an overview – B. Dréno – Journal of the European Academy of Dermatology and Venerology

The Role of the Skin and Gut Microbiome in Psoriatic Disease – Di Yan – Current Dermatology Reports

Human vaginal microbiome

The Vaginal Microbiome and its Potential to Impact Efficacy of HIV Pre-exposure Prophylaxis for Women –  Jennifer Velloza – Current HIV/AIDS Reports

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment – Cornelia Gottschick – Microbiome

 

Human gut microbiome

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – bioRxiv

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska- Gut Pathogens

Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism –  Wenzhen Ji – Molecular Medicine Reports

Brain-gut-microbiota axis and mental health – Timothy G. Dinan – Psychosomatic Medicine

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells – Mei San Tang – Inflamatory Bowel Diseases

Gut microbiome response to short-term dietary interventions in reactive hypoglycemia subjects – Sara Quercia –  Diabetes Metabolism Research and Reviews

The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces – Donjete Statovci –  Frontiers in Immunology

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects – Elena Buelow – Microbiome

Future prospect of faecal microbiota transplantation as a potential therapy in asthma – Y Kang  – Allergologia et Immunopathologia

Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients With Rheumatoid Arthritis – Annalisa Pianta – Arthritis & Rheumatology

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska – Gut Pathogens

The impact of age and gut microbiota on Th17 and Tfh cells in K/BxN autoimmune arthritis – Fei Teng – Arthritis Research & Therapy

Amoxapine Demonstrates Incomplete Inhibition of β-Glucuronidase Activity from Human Gut Microbiota – Wei Yang –  SLAS Discovery

Animal experiments 

Role of intestinal microbiome in American ginseng-mediated colon cancer protection in high fat diet-fed AOM/DSS mice –  C.-Z. Wang –  Clinical and Translational Oncology

The influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens – Zifeng Han – Infection and Immunity

Animal microbiome 

Microbiota of little penguins and short-tailed shearwaters during development – Meagan L. Dewar – PLOS One

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLOS One

Brief Communication: Climate warming reduces gut microbiota diversity in a vertebrate ectotherm – Elvire Bestion – Nature Ecology & Evolution

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Andrea Springer – Ecology and Evolution

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLOS One

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community – Marcus J. Pennington – Scientific Reports

Plant, root, and soil microbiome

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach – Thanyaporn Ruangdech – Agriculture and Natural Resources

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient – Eric J. Chapman – European Journal of Soil Biology

Bacteria from the rhizosphere and tissues of As-hyperaccumulator Pteris vittata and their role in arsenic transformation – Yong-HeHan – Chemosphere

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize – LinChen – Pedosphere

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates – Yanglei Yi – Frontiers in Microbiology

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants – Anna C. Santamans – PLOS One

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China – Guangyu Li – International Journal of Environmental Research and Public Health

Microbial volatile compounds alter the soil microbial community – Jun Yuan –  Environmental Science and Pollution Research

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G. Marshall – Marine Genomics

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils – Ruo-Nan Wu – Microbial Ecology

Biophysical processes supporting the diversity of microbial life in soil – Robin Tecon – FEMS Microbiology Reviews

Water and extremophile microbiome 

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond – Patrick J. Kearns – Aquatic Microbial Ecology

Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques –  Samuel Bryson – Thesis, Oregon State University

Effects of alkali types on waste activated sludge (WAS) fermentation and microbial communities – Xiaoling Li – Chemosphere

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern –  María José León –  International Journal of Systematic and Evolutionary

Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis – Emad I. Hussein – Microbiology Open

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters – Dahe Zhao – Applied Microbiology and Biotechnology

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing – M Jongman – Journal of Applied Microbiology

Report: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga – Haim Treves – Current Biology

The effects of morphology and neighbouring seaweeds on macroalgal microbiota – Thesis, The University of British Columbia

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system – Jing-Zhe Jiang – PLOS One

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre – Stephanie A. Sommer – Molecular Ecology

Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem – Mohd Ezhar Mohd Noor –  bioRxiv

The organizing effects of elevated CO2 on competition among estuarine primary producers – Craig S. Young – Scientific Reports

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation – Mamoru Oshiki – Genome Announcements

Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology

Early photosynthetic eukaryotes inhabited low-salinity habitats – Patricia Sánchez-Baracaldo – PNAS

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs – Sunita J.Varjani – Bioresource Technology

Probiotics / prebiotics

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure – Gurjeet Kaur – Journal of Proteomics

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Phages and viruses

Phage in urban wastewater have the potential to disseminate antibiotic resistance – Gayathri Upeksha Gunathilaka – International Journal of Antimicrobial Agents

Bioinformatics

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments – Francislon Silva de Oliveira – bioRxiv

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling – Vitor C. Piro – Microbiome

A bioarchitectonic approach to the modular engineering of metabolism – Cheryl A. Kerfeld – Philosophical Transactions of the Royal Society B

Techniques

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems – Joanne B. Emerson – Microbiome

A Note: A simple methodology to collect culturable bacteria from feces of Anopheles darlingi (Diptera: Culicidae) – Andrelisse Arruda – Journal of Microbiological Methods

Biotechnology

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks – Keaton Larson – Environmental Science & Technology

Microbial communities as biosensors for monitoring urban environments – Fangqiong Ling – Microbial Biotechnology

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Review: Purification and reuse of non-point source wastewater via Myriophyllum-based integrative biotechnology: A review – Liu F – Bioresource Technology

Improvements in algal lipid production: a systems biology and gene editing approach –  Avik Banerjee – Critical Reviews in Biotechnology

Microbes in the news 

Scientists Make Food From Bacteria, Water, Electricity, and a Whole Lot of Patience

Are you lonesome tonight? Why we, like Elvis, turn to food for comfort

Scientists See Bacteria Responding Electrically to Physical Stimuli for the First Time

Killing bacteria by hacking plastics with silver and electricity

Human Gut Microbes May Help Suppress MS, New Research Suggests 

Unexpected Microbial Life in Glacial Clay Could Offer Antibiotic Solutions

 

 

 

August 14, 2017

Posted on by

A burst of articles for your Monday digest. Quite a few highlights emerge from this Digest. There can be racial disparity in gastrointestinal cancer risk. The stress we experience now might influence our children’s aging in the future. And you might want to think twice about choosing between 16S and metagenomic sequencing, depending on the type of samples you have.

Jobs

Research Technician – Molecular Biology and Microbiology Department – Tufts University

General microbiology

*Letter: Pilot study to determine whether microbial contamination levels in hospital washrooms are associated with hand-drying method – M.H. Wilcox et al. – Journal of Hospital Infection

History matters: heterotrophic microbial community structure and function adapt to multiple stressors – Alexander Feckler et al. – Global Change Biology

Pregnancy and early life

Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates – Alicja Nogacka et al. – Microbiome

Pregnancy-induced changes in metabolome and proteome in ovine uterine flushings – Jared J. Romero – Biology of Reproduction

Evolution of newborns urinary metabolomic profiles according to age and growth – Aurélien Scalabre et al. – Journal of Proteome Research

Human oral microbiome

Effect of fermented milk containing Lactobacillus rhamnosus SD11 on oral microbiota of healthy volunteers: A randomized clinical trial – P. Rungsri et al. – Journal of Dairy Science

Human lung microbiome

Microbiome in lung explants of idiopathic pulmonary fibrosis: a case-control study in patients with end-stage fibrosis – Kitsios GD – Thorax

Human gut microbiome

**Racial Disparity in Gastrointestinal Cancer Risk – Hassan Ashktorab et al. – Gastroenterology

Master Thesis: A study of the effects of diet on human gut microbial community structure and mercury metabolism – Ria Saha – University of Ottawa

*Investigation into the stability and culturability of Chinese enterotypes – Yeshi Yin
et al. – Scientific Reports

Bangladesh Environmental Enteric Dysfunction (BEED) study: protocol for a community-based intervention study to validate non-invasive biomarkers of environmental enteric dysfunction – Mahfuz M – BMJ Open

Metabolomics

“Omics” in Human Colostrum and Mature Milk: Looking to Old Data with New Eyes – Flaminia Bardanzellu et al. – Nutrients

Animal experiments

Stability and efficacy of frozen and lyophilized fecal microbiota transplant (FMT) product in a mouse model of Clostridium difficile infection (CDI) – Zhi-Dong Jiang et al. – Anaerobe

Rat: The activity of Hou-Po-Da-Huang-Tang is improved through intestinal bacterial metabolism and Hou-Po-Da-Huang-Tang selectively stimulate the growth of intestinal bacteria associated with health – Xing-Yan Liu et al. – Biomedicine & Pharmacotherapy

Mouse: Navy and black bean supplementation primes the colonic mucosal microenvironment to improve gut health – Jennifer M. Monk et al. – The Journal of Nutritional Biochemistry

Mouse: Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease – Ashutosh Mangalam et al. – Cell Reports

Mouse: Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition – Michail Mamantopoulos et al. – Immunity

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice – Koji Yasuda et al. – mSystems

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome – Timothy A. Johnson et al. – mBio

Animal microbiome

*The Effects of Captivity on the Mammalian Gut Microbiome – Valerie J. McKenzie et al. – Integrative and Comparative Biology

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep – Janine Kamke et al. – BMC Research Notes

High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales – Patrick M. Erwin et al. – Scientific Reports

Virome comparisons in wild-diseased and healthy captive giant pandas – Wen Zhang and Shixing Yang et al. – Microbiome

Gut microbiomes of free-ranging and captive Namibian cheetahs: diversity, putative functions, and occurrence of potential pathogens – Wasim uddin et al. – Molecular Ecology

Plant, root and soil microbiome

Ecological and functional effects of fungal endophytes on wood decomposition – Lauren C. Cline et al. – Functional Ecology

Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems – Yasir Arafat et al. – International Journal of Molecular Sciences

Book chapter: The Rhizosphere and Plant Nutrition Under Climate Change – Tarek Alshaal et al. – Essential Plant Nutrients

Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems – Elham A. Kazerooni et al. – Frontiers in Microbiology

Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans – Zongzhuan Shen et al. – Microbial Ecology

*Characterisation and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in soils and plants around e-waste dismantling sites in southern China – Yujie Wang et al. – Environmental Science and Pollution Research

Water and extremophile microbiome

**Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing – Michael Tessler et al. – Scientific Reports

Interplay of hydrology, community ecology and pollutant attenuation in the hyporheic zone – Ignacio Peralta-Maraver et al. – Science of The Total Environment

Responses of coral-associated bacterial communities to local and global stressors – Jamie McDevitt-Irwin et al. – Frontiers in Marine Science

Built environment microbiome

Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio – Kanistha Coombs et al. – Science of The Total Environment

Food microbiome

Bacterial diversity of the Colombian fermented milk “Suero Costeño” assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons – Karina Edith Motato – Food Microbiology

Bioinformatics

*Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson et al. – Briefings in Bioinformatics

Big data management challenges in health research—a literature review – Xiaoming Wang et al. – Briefings in Bioinformatics

Microbes in the news

*FDA: Don’t use these liquid drug or dietary supplement products for infants – Sara Nealeigh – Bradenton Herald

Core bacteria in the gut of horses showed some stability over time in study – HorseTalk

Are Doctors Wrong About Finishing Your Antibiotics? – Paul A. Offit – Daily Beast

*Bacteria at the beach: High levels found at nearly a dozen locations in past two weeks – Sarah Reese – NWI Times

Microbes on the market

OptiBiotix Health PLC (OPTI) Rating Reiterated by FinnCap – Anthony Sawyer – Week Herald

Non-microbiology picks

**Review: Transgenerational Effects of Early Environmental Insults on Aging and Disease Incidence – Mirela Ambeskovic et al. – Neuroscience & Biobehavioral Reviews

Air-quality implications of widespread adoption of cool roofs on ozone and particulate matter in southern California – Scott A. Epstein et al. – PNAS

August 13, 2017

Posted on by

Read about commensal fungi, the “nemabiome,” and a follow-up NYT article on the common topic of dirty sponges.

General microbiome

Commensal Fungi in Health and Disease – Jose J. Limon, Cell Host & Microbe

Circadian Coordination of Antimicrobial Responses – Paola Tognini, Cell Host & Microbe

Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities – Alejandra L. Ibáñez de Aldecoa, Frontiers in Microbiology

Pregnancy and early life

Culture independent assessment of human milk microbial community in lactational mastitis – Shriram H. Patel, Scientific Reports

Human gut microbiome

The Gut Microbiota, Food Science, and Human Nutrition: A Timely Marriage – Michael J. Barratt, Cell Host & Microbe

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis, Cell Host & Microbe

Gut microbial profile in primary biliary cholangitis: Towards bioindicators – Sara Lemoinne, Clinics and Research in Hepatology and Gastroenterology

Human oral microbiome

Microbes and Host Response: A relationship in health and disease – Alpdogan Kantarci, Oral Diseases

Human nearly-sterile sites

Profiling the Urinary Microbiome in Men with Positive versus Negative Biopsies for Prostate Cancer – Eva Shrestha, The Journal of Urology

Animal experiments

Beef, Chicken, and Soy Proteins in Diets Induce Different Gut Microbiota and Metabolites in Rats – Zhu Y, Frontiers in Microbiology

Commentary: Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome – Blessing O. Anonye, Frontiers in Immunology

Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies – Emily L Pascoe, ISME

Animal microbiome

The use of nemabiome metabarcoding to explore gastro-intestinal nematode species diversity and anthelmintic treatment effectiveness in beef calves – Russell W. Avramenko, International Journal for Parasitology

Plant, root, and soil microbiome

Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils – Qing Cao, Environmental Pollution

Compatible Rhizosphere-Competent Microbial Consortium Adds Value to the Nutritional Quality in Edible Parts of Chickpea – Sudheer K. Yadav, Journal of Agricultural and Food Chemistry

Isolation and Characterization of a Phosphorus-Solubilizing Bacterium from Rhizosphere Soils and Its Colonization of Chinese Cabbage (Brassica campestris ssp. chinensis) – Zhen Wang, Frontiers in Microbiology

Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research – Julia A. Vorholt, Cell Host & Microbe

Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation – Papa M. S. Ndour, Frontiers in Plant Science

Water and extremophile microbiome

Phylogenetically conserved resource partitioning in the coastal microbial loop – Samuel Bryson, ISME

Probiotics/Prebiotics

Characterization of the Culturable Subpopulations of Lactobacillus in the Chicken Intestinal Tract as a Resource for Probiotic Development – Bishnu Adhikari, Frontiers in Microbiology

Microbes in the news

We Need to Talk Some More About Your Dirty Sponges – Joanna Klein, New York Times

University of California at San Francisco Recruiting MS Patients for Gut Bacteria Study – Carolina Henriques, Multiple Sclerosis News Today

This paper battery is powered by bacteria in your spit – Jeremy Deaton, Popular Science

August 8, 2017

Posted on by

Our daily digest for you, with highlights on gut microbiota signatures in Japanese infants with food allergy, salt mash communities affected by the Deepwater Horizon oil spill and a proposed stricter P value for claiming a ‘significant’ result.

Jobs

Microbiology Laboratory Technicians – Australian Clinical Labs

General microbiology

Light controlled 3D micromotors powered by bacteria – Gaszton Vizsnyiczai et al. – Nature Communications

Press: Herding Bacteria Brings Power to 3D-Printed Micromotors – Michael Molitch-Hou – Engineering.com

Review: Zika Virus Protease: An Antiviral Drug Target – Congbao Kang et al. – Trends in Microbiology

Call for papers: Advances in Understanding and Controlling Bacteria-Material Interactions, with a Focus on how Bacteria Sense a Surface – Frontiers

Preprint: Saccharomyces cerevisiae strain YH166: a novel wild yeast for the production of tropical fruit sensory attributes in fermented beverages – Kara Osburn – bioRxiv

Pregnancy and early life

Review: Early-life adversity, epigenetics, and visceral hypersensitivity – S. Liu et al. – Neurogastroenterology & Motility

*Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka et al. – FEMS Microbiology Ecology

Animal experiments

Mouse: Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract – Xiaochen Yin et al. – Scientific Reports

Abstract: A commensal Bifidobacterium longum strain improves gluten-related immunopathology in mice through expression of a serine protease inhibitor – McCarville JL et al. – Applied Environmental Microbiology

Carrageenan-induced colitis is associated with decreased population of anti-inflammatory bacterium, Akkermansia muciniphila, in the gut microbiota of C57BL/6J mice – Qingsen Shang et al. – Toxicology Letters

Mouse: Estrogen protection against EAE modulates the microbiota and mucosal-associated regulatory cells – Gil Benedek et al. – Journal of Neuroimmunology

Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken – Pengfei Gao, Chen Ma and Zheng Sun et al. – Microbiome

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning – Christopher Staley et al. – Microbiome

Animal microbiome

Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces effect of necrotic enteritis caused by Clostridium perfringes in chickens – Dafei Yin et al. – Scientific Reports

Plant, root and soil microbiome

Impact of Land-use Change on Vertical Soil Bacterial Communities in Sabah – Hoe Seng Tin et al. – Microbial Ecology

Water and extremophile microbiome

Pilot-scale investigation of sludge reduction in aerobic digestion system with endospore-forming bacteria – Kyu Won Seo et al. – Chemosphere

*Abstract: Salt marsh bacterial communities before and after the Deepwater Horizon oil spill – Engel AS et al. – Salt marsh bacterial communities before and after the Deepwater Horizon oil spill

Phages and viruses

A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation – Emmanuelle Bille & Julie Meyer et al. – PLoS Pathogens

Microbes in the news

Cleaning a Dirty Sponge Only Helps Its Worst Bacteria, Study Says – Joanna Klein – NYT

McDonald’s, KFC, Burger King drinks test positive for fecal bacteria – WHDH

Congrats, happy couples: You really do share everything, even skin bacteria – Ellen Scott – Metro

Seasonal bacteria causes odd taste in Sacramento water – KCRA Staff – KCRA3

IIT Delhi team develops a new antibacterial drug-delivery system – R. Prasad – The Hindu

Antibiotics use by India’s poultry farms endangering human lives, says expert – Charu Bahri – Hindustan Times

Can We Encode Medical Records Into Our DNA? – Cathy Cassata – Healthline

Papaya Outbreak Grows to 109 Infected People. But How Does Salmonella Get Inside Produce? – Heather Williams – UnsafeFoods

Microbes on the market

PhoneSoap uses a UV sanitizing system to keep your phone bacteria-free – Ricci Rox – NoteBookCheck

Non-microbiology pick

*The Reproducibility Of Research And The Misinterpretation Of P Values – David Colquhoun – bioRxiv

July 29, 2017

Posted on by

Enjoy perusing this beefy Microbiome Digest, which is heavy on information about plant/root/soil microbes, water/extremophile microbes, and new microbial techniques.

Events and jobs

Microbiome Symposium 2017 – September 11, Quadras Conference Center

General microbiome

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells – E.S. Heidrich, Bioelectrochemistry

Effect of glucose on nitrogen removal and microbial community in anammox-denitrification system – Yujie Qin, Bioresource Technology

Horizontal Gene Transfer and Ecosystem Function Dynamics – Maarten van de Guchte, Trends in Microbiology

Pregnancy and early life

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective – Isabelle Laforest-Lapointe, Frontiers in Microbiology

Maternal Gut Microbiome Biodiversity in Pregnancy – Marcela C. Smid, American Journal of Perinatology

Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case–control study – Kohei Hasegawa, BMC Research Notes

Adverse events in women and children who have received intrapartum antibiotic prophylaxis treatment: a systematic review – Farah Seedat, BMC Pregnancy and Childbirth

Human skin microbiome

Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease – Chloé Van Leuvenhaege, PLoS ONE

Human oral microbiome

16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients – Wu X., Journal of Oral Microbiology

Porphyromonas gingivalis disturbs host-commensal homeostasis by changing complement function – Olsen I., Journal of Oral Microbiology

Human gut microbiome

The Present Status of Fecal Microbiota Transplantation and Its Value in the Elderly – Yao-Wen Cheng, Current Treatment Options in Gastroenterology

Fecal total iron concentration is inversely associated with fecal Lactobacillus in preschool children – Sasank Kalipatnapu, Gastroenterology

Long-term irritable bowel syndrome symptom control with reintroduction of selected FODMAPs – Ruth M. Harvie, World Journal of Gastroenterology

Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis – Lukas Bajer, World Journal of Gastroenterology

Eubiotic properties of rifaximin: Disruption of the traditional concepts in gut microbiota modulation – Francesca Romana Ponziani, World Journal of Gastroenterology

Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer’s disease: 10 pitfalls of microbiome studies – Ah-Mee Park, Clinical and Experimental Neuroimmunology

Partners of patients with ulcerative colitis exhibit a biologically relevant dysbiosis in fecal microbial metacommunities – Guang-Lan Chen, World Journal of Gastroenterology

Animal Experiments

Oral administration of live- or heat-killed Candida albicansworsened cecal ligation and puncture sepsis in a murine model possibly due to an increased serum (1→3)-β-D-glucan – Wimonrat Panpetch, PLoS ONE

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lambliaand enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens

Animal microbiome

Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus2 (CyHV-2) Infection – Rong She, Current Microbiology

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef – Vanessa R. Marcelino, Molecular Ecology

Characterization of feather-degrading bacterial populations from birds’ nests – Potential strains for biomass production for animal feed – Maria Saarela, International Biodeterioration & Biodegradation

The impact of the bovine fecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle – Minseok Kim, Journal of Applied Microbiology

Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring – Shantanu P. Shukla, Molecular Ecology

Plant, root, and soil microbiome

Elevated CO2 and nitrogen addition have minimal influence on the rhizospheric effects of Bothriochloa ischaemum – Lie Xiao, Scientific Reports

Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata – Casper N. Kamutando, Scientific Reports

Biotoxic impact of heavy metals on growth, oxidative stress and morphological changes in root structure of wheat (Triticum aestivum L.) and stress alleviation by Pseudomonas aeruginosa strain CPSB1 – Asfa Rizvi, Chemosphere

Use of microbial indicators combined with environmental factors coupled to metrology tools for discrimination and classification of Luzhou-flavored pit muds – Q.Y. Zhang, Journal of Applied Microbiology

Fertilization decreases compositional variation of paddy bacterial community across geographical gradient – Ruirui Chen, Soil Biology and Biochemistry

Effects of snow cover plus straw mulching on microorganisms in paddy soil during winter – Hao Zhang, Applied Soil Ecology

The Contribution of Pyrene Degrading Bacteria and Chemical Reagents to Scirpus triqueterPhytoremediation of Pyrene and Ni Co-contaminated Soil – Xiaoxin Hu, Water, Air, & Soil Pollution

Investigating whether light intensity can modify decomposition rates in peatlands through control of the ‘enzymic latch’ – Christian Dunn, Ecological Engineering

Analysis of microbiota in rhizosphere, water and gut of grass carp (Ctenopharyngodon idella) in ponds treated with artificial floating beds – Jian Li, Water and Environment Journal

Scaling from the growth chamber to the greenhouse to the field: Demonstration of diminishing effects of mitigation of salinity in peppers inoculated with plant growth-promoting bacterium and humic acids – Macario Bacilio, Applied Soil Ecology

Disease management of tomato through PGPB: current trends and future perspective – Vipin Kumar Singh, 3 Biotech

Soil bacteria and archaea change rapidly in the first century of Fennoscandian boreal forest development – Stephanie A. Yarwood, Soil Biology and Biochemistry

Leaf litterfall decomposition of pedunculate (Quercus robur L.) and sessile (Q. petraea [Matt.] Liebl.) oaks and their hybrids and its impact on soil microbiota – Girmantė Jurkšienė, Dendrobiology

On the controls of abundance for soil-dwelling organisms on the Tibetan Plateau – Ke Zhao, Ecosphere

Water and extremophile microbiome

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence – John K. Pearman, Scientific Reports

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community – Marcelo Monteiro Pedroso, Metallomics

Polycyclic aromatic hydrocarbons (PAHs) enrich their degrading genera and genes in human-impacted aquatic environments – Ke Yuan, Environmental Pollution

Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence – Jack L. Darcy, FEMS Microbiology Ecology

Eco-friendly and efficient in situ restoration of the constructed sea stream by bioaugmentation of a microbial consortium – Jangyeon Yoo, Korean Journal of Microbiology

Identification of two organohalide-respiring Dehalococcoidiaassociated to different dechlorination activities in PCB-impacted marine sediments – Andrea Nuzzo, Microbial Cell Factories

Draft genome sequence of the halophilic Halobacillus mangroviKTB 131 isolated from Topan salt of the Jeon-nam in Korea – Mingyeong Woo, Genomics Data

First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile – Antonio E. Serrano, Extended Genome Report

Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes – Robert Cardoso de Freitas, Marine Biotechnology

Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman – Janina C. Vogt, Microbial Ecology

Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting – Huhe, Microbiology Open

Built environment

Bioprotection of the built environment and cultural heritage – Geoffrey Michael Gadd, Microbial Biotechnology

Food microbiology

Food waste conversion to microbial polyhydroxyalkanoates – Chad Nielsen, Microbial Biotechnology

Insect frass in stored cereal products as a potential source of Lactobacillus sanfranciscensis for sourdough ecosystem – Federica Boiocchi, Journal of Applied Microbiology

Probiotics

Evaluation of Probiotic Diversity from Soybean (Glycine max) Seeds and Sprouts Using Illumina-Based Sequencing Method – Yali Huang, Probiotics and Antimicrobial Proteins

Bioinformatics

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture – Syafiq Kamarul Azman, BMC Bioinformatics

Techniques

Inferring Past Environments from Ancient Epigenomes – David Gokhman, Microbial Ecology and Evolution

Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR – Libera M. Dalla-Costa, Journal of Microbiological Methods

Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity – Marine Baudin, Journal of Microbiological Methods

Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species – S. Arbefeville, Journal of Microbiological Methods

The feasibility of improved live-dead distinction in qPCR-based microbial source tracking – Laura Seidel, Journal of Microbiological Methods

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo, Journal of Microbiological Methods

Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii – Rebecca L. Lindsey, Journal of Microbiological Methods

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data – David Paez-Espino, Nature Protocols

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree – John R. Stevens, Computational and Structural Biotechnology Journal

July 24, 2017

Posted on by

Here’s our Digest to start your Monday. The importance of managing the antibiotic resistance in perinatal and neonatal care, review on the plant-microbiota holobiont and poo bacteria found in three big fast food chains.

Jobs

Microbiology Lab Technician – Johnson County Community College – Overland Park, KS

Research Fellow – Microbiome Program Job – Mayo Clinic, Rochester MN

Pregnancy and infant microbiome

Book Chapter: Bacterial Infections in the Neonate – Morven S. Edwards & Carol J. Baker – Principles and Practice of Pediatric Infectious Diseases (Fifth Edition)

**Review: Antibiotic stewardship in perinatal and neonatal care – Jayashree Ramasethu & Tetsuya Kawakita – Seminars in Fetal and Neonatal Medicine

Human liver microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu et al. – Hepatology

Human gut microbiome

Comparative phenotypic analysis of “Clostridium neonatale” and Clostridium butyricum isolates from neonates – S. Schönherr-Helleca and G. Klein et al. – Anaerobe

The association of type II diabetes with gut microbiota composition – Fatemeh Navab-Moghadama et al. – Microbial Pathogenesis

The role of intestinal bacteria in the development and progression of gastrointestinal tract neoplasms – Kosuke Mima & Shuji Ogino et al. – Surgical Oncology

Review: The Microbiome in Crohn’s Disease : Role in Pathogenesis and Role of Microbiome Replacement Therapies – Sahil Khanna & Laura E. Raffals – Gastroenterology Clinics of North America

Review: The Gastric and Intestinal Microbiome: Role of Proton Pump Inhibitors – Artem Minalyan – Current Gastroenterology Reports

Animal experiments

The aerial parts of Salvia miltiorrhiza Bge. strengthen intestinal barrier and modulate gut microbiota imbalance in streptozocin-induced diabetic mice – Jun-Fei Gu et al. – Journal of Functional Foods

Intervention of probiotic L. reuteri fermented milk as an adjuvant to combat protein energy malnourishment induced gut disturbances in albino mice – S. Garg et al. – Journal of Functional Foods

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K. Jena et al. – The American Journal of Pathology

The title seems an overstatement: Microbial regulation of hippocampal miRNA expression: Implications for transcription of kynurenine pathway enzymes – Gerard M. Moloney et al. – Behavioural Brain Research

Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation – Jiani N. Chai et al. – Science Immunology

Press: How ‘Bad’ Gut Bacteria Can Change Their Evil Ways – Christopher Wanjek – LiveScience

Animal microbiome

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs – Ursula M. McCormack et al. – Applied and Environmental Microbiology

Press: PIG MICROBIOME MAKEUP MAY INFLUENCE ANIMAL GROWTH RATE – Julie Wolf – ASM

Plant, root and soil microbiome

Review: Insights into plant phosphate sensing and signaling – Byung-Kook Ham et al. – Current Opinion in Biotechnology

Responses of rice paddy micro-food webs to elevated CO2 are modulated by nitrogen fertilization and crop cultivars – Zhengkun Hu et al. – Soil Biology and Biochemistry

**Review: Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares et al. – Current Opinion in Microbiology

Water and extremophile microbiome

Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome – Ran Mei et al. – Water Research

Preprint: Cytosine methylation within marine sediment microbial communities: potential epigenetic adaptation to the environment – Ian M. Rambo – bioRxiv

Phages and viruses

Bacteriophages in the human gut: our fellow travelers throughout life and potential biomarkers of heath or disease – Babak Bakhshinejad & Saeedeh Ghiasvand – Virus Research

Microbes in the news

Florida man contracts flesh-eating bacteria through blisters from hiking –
Cherise Leclerc – WMUR9

Florida Seawater Bacteria Case Count Rises – Sherri Lonon – Patch

Shock as lab tests find of poo bacteria in products at McDonald’s, KFC and Burger King – Zara Whelan – Daily Post

Vaginal Probiotics Could Slow Zika & Other STD Infections – Sheryl Wood – Invisiverse

NASA Identifies What Kind of Fungi Could Grow in a Mars Habitat – Cynthia Wallentine – Invisiverse

July 19, 2017

Posted on by

Today’s digest is a long one! There is high diversity of studies, with a high abundance of gut microbiome studies, a few publications on fecal transplant, and some very interesting early life/pregnancy/mother-infant science.  A normal serving of animal studies, of course a nice colony of environmental microbial studies, and a study reporting the presence of bacteria in Alzheimer’s post-mortem brains.

Events and jobs

Postdoctoral research fellow in translational microbiome research – Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet

General microbiome

Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

[Review]  The human microbiome – Hubert E. Blum – Advances in Medical Sciences

Microbiome and Metabolome Data Integration Provides Insight Into Health and Disease – Michael Shaffer – Translational Research

Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge – Neelam Devpura – International Biodeterioration & Biodegradation

Impact of the Microbiota on Bacterial Infections during Cancer Treatment – Jessica Galloway-Peña – Trends in Microbiology

Pregnancy and early life

** The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut – Elana Biagi – Frontiers in Microbiology | Evolutionary and Genomic Microbiology

* What’s Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings – Lorena Ruiz – Frontiers in Immunology | Nutritional Immunology

Microbiome Associated with Severe Caries in Canadian First Nations Children – M. Agnello – Journal of Dental Research

* Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes – Ronan M. Doyle – PLoS One

Human oral microbiome

Characterization of Oral Microbiota in Removable Dental Prosthesis Users: Influence of Arterial Hypertension – Leila Maria Marchi-Alves – BioMed Research International

Human vaginal microbiome

The association between ethnicity and vaginal microbiota composition in Amsterdam, the Netherlands – Hanneke Borgdorff – PLoS One

Human nearly-sterile sites

** 16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain – David C. Emery – Frontiers in Aging Neuroscience

Human gut microbiome

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia – Sayaka Fujio-Vejar – Frontiers in Microbiology | Microbial Symbioses

*[Review] Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients – Hoda M. Eid – Frontiers in Pharmacology | Ethnopharmacology

MOLECULAR CHARACTERIZATION OF FECAL MICROBIOTA OF HEALTHY CHINESE TOBACCO SMOKER SUBJECTS IN SHAANXI PROVINCE, XI’AN CHINA – Ishaq HM – Journal of Ayub Medical College

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

The Impact of Gut Microbiota on Gender-Specific Differences in Immunity – Floris Fransen – Frontiers in Immunology | Nutritional Immunology

Involvement of gut microbiota in the association between gastrointestinal motility and 5‑HT expression/M2 macrophage abundance in the gastrointestinal tract – Mo Yang – Molecular Medicine Reports

Correspondence: Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial – Benjamin H Mullish – Hepatology

Going to the Bank: Fecal Microbiota Transplantation in Pediatrics – Elaine Barfield – Clinical Pediatrics

INTERRELATIONSHIPS BETWEEN GUT MICROBIOTA AND HOST: Paradigms, Role in Neurodegenerative Diseases and Future Prospects – Villarraso JC – CNS & Neurological Disorders Drug Targets

Faecal microbiota transplant: a novel biological approach to extensively drug-resistant organism-related non-relapse mortality – Innes AJ – Bone Marrow Transplantation

* Gut microbiota is critical for the induction of chemotherapy-induced pain – Shiqian Shen – Nature Neuroscience

Relationships between Gastrointestinal Microbiota and Blood Group Antigens – Anuhya Gampa – Physiological Genomics

[Masters Thesis] Evaluating the Effectiveness of Select Bacteria Against Clostridium difficile – Choquette, Kelsey Rose – Iowa State University, ProQuest Dissertations Publishing

* Potential and active functions in the gut microbiota of a healthy human cohort – Alessandro Tanca – Microbiome

[Letter to Editor] The necessity of gut microbiome characterization in diseases prevention and therapy – Sama Rezasoltani – Gastroenterology and Hepatology from Bed to Bench

[Review Article] The Intricate Interaction between Enteric Microbiota and Brain: Principles and Clinical Implications – Giovanni Gherardi – Journal of Digestive Diseases and Hepatology

Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults – K Lippert – Beneficial Microbes

Animal experiments

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K – The American Journal of Pathology

Grape pomace improves performance, antioxidant status, fecal microbiota and meat quality of piglets – I. Kafantaris – Animal

Animal microbiome

Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans – Lobos O – Italian Journal of Food Safety

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations – Xiaoping He – Microbial Ecology

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change – Cheng-Yu Chen – PLoS One

Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny – François-Étienne Sylvain – Scientific Reports

Microbiome overview in swine lungs – Franciele Maboni Siqueira – PLoS One

Plant, root, and soil microbiome

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops – Zhaojin Chen – Ecotoxicology and Environmental Safety

Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology – Davide Francioli – Microbial Ecology

* Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers – Alastair W. Tait – Frontiers in Microbiology | Extreme Microbiology

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil – Mengting M. Yuan – Global Change Biology

[PrePrint] Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome 

Performance and bacterial community structure of a 10-years old constructed mangrove wetland – Tingting Tian – Marine Pollution Bulletin

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields – Hai-liang Wang – PLoS One

Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania – Cecilia M. Chiriac – Microbiology of Aquatic Systems

Built environment

Pilot study to determine if microbial contamination levels in hospital washrooms are associated with hand drying method – Mark H. Wilcox – Journal of Hospital Infection

Probiotics / prebiotics

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – BBA

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic – Rebeca Martin – Frontiers in Microbiology | Food Microbiology

Bioinformatics

* Abundance estimation and differential testing on strain level in metagenomics data – Martina Fischer – Bioinformatics

Techniques

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures – Lucía Vázquez – Frontiers in Microbiology | Food Microbiology

Next-generation Sequencing of the DNA Virome from Fecal Samples – Monaco CL – Bio-protocol

Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery – Yutong Shi – Environmental Microbiology

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly – K. S. Zadesenets – Russian Journal of Genetics

Microbes on the market

Microbiome Sequencing Services Market: trends, analysis, Overview, forecast up to 2021

Ed’s non-microbiology picks

Heavy metal accumulation by Saccharomyces cerevisiae cells armed with metal binding hexapeptides targeted to the inner face of the plasma membrane – Lavinia Liliana Ruta –Applied Microbiology and Biotechnology

Fracking can contaminate rivers and lakes with radioactive material, study finds

Subacute normobaric oxygen and hyperbaric oxygen therapy in drowning, reversal of brain volume loss: a case report – Paul G Harch – Medical Gas Research

No Effect of Commercial Cognitive Training on Neural Activity During Decision-Making – Joseph W. Kable – Journal of Neuroscience

Health Insurance Expansion and Incidence of Out‐of‐Hospital Cardiac Arrest: A Pilot Study in a US Metropolitan Community – Eric C. Stecker – Journal of the American Heart Association