Category Archives: General Microbiome

May 7, 2017

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A short digest for Sunday morning. Few interesting gut microbiome articles and Time magazine cover story about the next pandemic and novel detection technologies.

General microbiome

Antibiotics in a general population: Relations with gender, body mass index (BMI) and age and their human health risks – Sisi Liu -Science of the Total Environment

Human gut microbiome

A Clostridium difficile-Specific, Gel-Forming Protein Required for Optimal Spore Germination – ML Donnelly – MBio

The intestinal microbiome and paediatric liver disease – Daniel H Leung, MD – The Lancet

Plant, root, and soil microbiome

Review: Communication in the Phytobiome – Jan E. Leach – Cell

Food microbiology

The impact of nutrition on intestinal bacterial communities – Harry J Flint – Current opinion in Microbiology

Large-scale targeted metagenomics analysis of bacterial ecological changes in 88 kimchi samples during fermentation – Moeun Lee – Food microbiology

Probiotics / prebiotics

Designer probiotics for the prevention and treatment of human diseases – Koon Jiew Chua – Current opinion in chemical biology

Microbes in the news

Time magazine: The world is not ready for the next pandemic

Researchers find link between gut microbiome, osteoarthritis pain

May 6, 2017

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Events and jobs

Trainee Microbiology Analyst – Eurofins Lancaster Laboratories

General microbiome

*Review: Optimizing methods and dodging pitfalls in microbiome research – Dorothy Kim – Microbiome

*Book: Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System – Jack Gilbert, Rob Knight

Human gut microbiome

*Review: Ménage à trois in the human gut: interactions between host, bacteria and phages – Mohammadali Khan Mirzaei – Nature Reviews Microbiology

Animal microbiome

The functional microbiome of arthropods – Mauro Degli Esposti – PLOS ONE

A comparative study of gut microbiota profiles of earthworms fed in three different substrates – Dianfeng Liu – Symbiosis

Plant, root, and soil microbiome

Breaking continuous potato cropping with legumes improves soil microbial communities, enzyme activities and tuber yield – Shuhao Qin – PLOS ONE

Study on the effect of soil beneficial microorganisms on the growth of kiwifruit – Huihe Li – Biomedical Research

Water and extremophile microbiome

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons – Jérôme Comte – Environmental Microbiology

*Review: The life sulfuric: microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Fine stratification of microbial communities through a metagenomic profile of
the photic zone – Jose M. Haro-Moreno – bioRxiv

Probiotics / prebiotics

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens – Alessandra De Cesare – PLOS ONE

Bioinformatics

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation – CC Laczny – Nucleic Acids Research

Techniques

*Highlight: How to see more: double hybridization to reveal ecological differentiation among close bacterial relatives – Stefan Bertilsson – Environmental Microbiology

Comparative analysis of the sensitivity of metagenomic sequencing and PCR to detect a biowarfare simulant (Bacillus atrophaeus) in soil samples – Delphine Plaire – PLOS ONE

Microbes in the news

The Invisible Secret That Will Change Your Skin Forever – Rachel Krause – Refinery29

Improve your skin microbiome – Cassie Shortsleeve – Furthermore

Dormant bacteria trapped in ice could be released by climate change – Alayna Treene – Axios

Microbes on the market

Commense Licenses UBC’s Microbiome Therapeutic for Preventing Childhood Asthma – Genetic Engineering & Biotechnology News

Bacteria Hysteria

Why Bacteria Are More Threatening Than Ever – Alice Park – Time

Science, publishing, and career

Infection and Immunity welcomes the new microbiology – Andreas J. Bäumler – Infection and Immunity

May 1, 2017

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General microbiome

From Gene Annotation to Function Prediction for Metagenomics – F Sharifi – Protein Function Prediction

*Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome – ME Perez-Muñoz – Microbiome

Collateral damage during antibiotic treatment of C. difficile infection in the aged host: insights into why recurrent disease happens – JH Shin – Gut Microbes

 

Human oral microbiome

Oral Treponeme Major Surface Protein: Sequence Diversity and Distributions within Periodontal Niches – M You – Molecular Oral Microbiology

 

Human gut microbiome

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology – J Zhao – European Journal of Clinical Microbiology & Infectious Diseases

Gut Check: The evolution of an educational board game – DA Coil – PLoS Biology

From sensing to shaping microbiota: insights into the role of NOD2 in intestinal homeostasis and progression of Crohn’s Disease – I Balasubramanian – Am. J. Physiol. Gastrointest. Liver Physiol.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients – JR Bedorf – Genome Medicine

 

Animal microbiome

Progressive response of large intestinal bacterial community and fermentation to the stepwise decrease of dietary crude protein level in growing pigs – Y Peng – Applied Microbiology and Biotechnology

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle – GO Ribeiro – Scientific Reports

Impact and consequences of polyphenols and fructooligosaccharide interplay on gut microbiota in rats – CJ Zheng – Food & Function

 

Plant, root and soil microbiome

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity – R O′ Rorke – ISME

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site –  A Durand – Microbial Ecology

Understory Dwarf Bamboo Affects Microbial Community Structures and Soil Properties in a Betula ermanii Forest in Northern Japan – B Kong – Microbes & Environments

Effects of root exudates on denitrifier gene abundance, community structure and activity in a micro-polluted constructed wetland – H Wu – Sci. Total Environ

Contribution of native phosphorous-solubilizing bacteria of acid soils on phosphorous acquisition in peanut (Arachis hypogaea L.) – M Pradhan – Protoplasma

 

Probiotics

Aggregation and Adhesion Activity of Lactobacilli Isolated from Fermented Products In Vitro and In Vivo: a Potential Probiotic Strain – S Grigoryan – Probiotics and Antimicrobial Proteins

 

Built environment microbiology

Three-stage anaerobic co-digestion of food waste and horse manure – J Zhang – Scientific Reports

 

Microbes in news

Undeveloped microbiomes make infants more prone to illness – R Saxena – ARS Technica

Being a guinea pig for science can be a long, slow slog – B Jefferson – SCPR

Pharma pollution fuels resistance to antibiotics, bacteria turns super bug – TNN – The Times of India

Cleaning up Iowa’s beaches – E Jordan – The Gazette

Augusta hospital adopts test to help find treatment for some patients quicker – S Turner – Aiken Standard

Only a superweapon can kill superbacteria, and humanity finally found it – W Nicol – Digital Trends

‘Lab in a cell’ helps crack code on chlamydia – R Shore –  Edmonton Journal

 

 

April 29, 2017

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Events and jobs

Bioinformatics Scientist, Microbiome – Human Longevity Inc.

General microbiome

The hologenome across environments and the implications of a host-associated microbial repertoire – Tyler J. Carrier – Frontiers in Microbiology

Teleosts as Model Organisms to Understand Host-Microbe Interactions – Emily A. Lescak – Journal of Bacteriology

*Review: The Shifting Microbiome in Surgical Stress – Panna A. Codner – Current Surgery Reports

A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations – Marie Marchal – BMC Evolutionary Biology

Human gut microbiome

Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome – Dorottya Nagy-Szakal – Microbiome

Study protocol on the role of intestinal microbiota in colorectal cancer treatment: a pathway to personalized medicine 2.0 – R. Aarnoutse – International Journal of Colorectal Disease

Animal experiments

Differences in microbiota membership along the gastrointestinal tract of piglets and their differential alterations following an early-life antibiotic intervention – Chunlong Mu – Frontiers in Microbiology

Animal microbiome

Biogeographic comparison of Lophelia-associated bacterial communities in the western Atlantic reveals conserved core microbiome – Christina A. Kellogg – Frontiers in Microbiology

Plant, root, and soil microbiome

Response of methanogenic microbial communities to desiccation stress in flooded and rain-fed paddy soil from Thailand – Andreas Reim – Frontiers in Microbiology

Metagenomics of Microbial Communities Associated with the Rhizosphere of the Saudi Desert Medicinal Plants – Mohammed N Baeshen – EC Microbiology

Rhizospheric soil enzyme activities and phytominimg potential of Aeluropus lagopoides and Cyperus conglomeratus growing in contaminated soils at the banks of artificial lake of reclaimed wastewater – Zahid Khorshid Abbas – International Journal of Phytoremediation

*Review: The unseen rhizosphere root-soil-microbe interactions for crop production – Ruifu Zhang – Current Opinion in Microbiology

Water and extremophile microbiome

Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments – Marion H. Stagars – Frontiers in Microbiology

Novel large sulfur bacteria in the metagenomes of groundwater-fed chemosynthetic microbial mats in the Lake Huron basin – Allison M. Sharrar – Frontiers in Microbiology

Microbial population dynamics and ecosystem functions of anoxic/aerobic granular sludge in sequencing batch reactors operated at different organic loading rates – Enikö Szabó – Frontiers in Microbiology

Characteristics of bacterial community in cloud water at Mt Tai: similarity and disparity under polluted and non-polluted cloud episodes – Min Wei – Atmospheric Chemistry and Physics

Built environment

Density assessment and mapping of microorganisms around a biocomposting plant in Sanandaj, Iran – Sanaz Rashidi – Environmental Monitoring and Assessment

Techniques

High throughput and quantitative measurement of microbial metabolome by gas chromatography/mass spectrometry using automated alkyl chloroformate derivatization – Linjing Zhao – Analytical Chemistry

Functional Association Prediction by Community Profiling – Dazhi Jiao – Methods

*Book: Modern Tools and Techniques to Understand Microbes – Ajit Varma

Microbes on the market

Microbiome market competitive landscape technology in 2017 pipeline review published by leading research firm – WhaTech

Science, publishing, and career

Review of 3rd annual Translation Microbiome Conference – James Vitale – Taconic

April 28, 2017

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Quite a few interesting articles and news about microbes: are we colonised with bacteria in utero? What is the relevance of cooperative interactions in microbial biotechnological processes? Microbe colonies  in space? Read more in today’s Microbiome Digest..

General microbiome

Variable habitat conditions drive species covariation in the human microbiota – Charles K. Fisher – PLOS

Pregnancy and early life

*Review: The prenatal gut microbiome: are we colonized with bacteria in utero? – R. W. Walker – Pediatric Obesity

Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study – Mohan Pammi – PLOS
 Human respiratory microbiome

A commensal streptococcus hijacks a Pseudomonas aeruginosa exopolysaccharide to promote biofilm formation – Jessica A. Scoffield – PLOS
Human oral microbiome

A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis – Matthias Munz – Human Molecular Genetics

Human nearly-sterile sites 

A case of polymicrobial anaerobic spondylodiscitis due to Parvimonas micra and Fusobacterium nucleatum – Leanne M Cleaver – JMM Case Reports

Human gut microbiome

Small Molecules from Deep within the Gut – Michael Ehrmann – ChemBioChem

Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis – Jacob Vinita – Inflammatory Bowel Diseases

Fecal Microbiota Transplantation for Refractory Clostridium difficile Colitis in Solid Organ Transplant Recipients – R. J. Friedman-Moraco – American Journal of Transplantation

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses – Konstantin Yarygin – PLOS
Animal experiments

Neonatal mono-colonization of germ-free mice with Lactobacillus casei enhances casein immunogenicity after oral sensitization to cow’s milk – Matieny Aicha Maiga – Molecular Nutrition & Food Research

Shifts in the Gut Microbiota Composition Due to Depleted Bone Marrow Beta Adrenergic Signaling Are Associated with Suppressed Inflammatory Transcriptional Networks in the Mouse Colon – Tao Yang – Frontiers in Physiology

Animal microbiome

Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population – Nádia Conceição-Neto – Ecology and Evolution

The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders – C Karlsen – Journal of Fish Diseases

Plant, root, and soil microbiome

Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content – Pankaj Trivedi – Environmental Microbiology

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco) – Odile Bruneel –  Extremophiles

Water and extremophile microbiome 

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy – Ilenia M. D’Angeli – Science of The Total Environment
Probiotics / prebiotics

Characterization, identification and application of lactic acid bacteria isolated from Leymus chinensis silage – Qing Zhang – Grassland Science
Biotechnology

*Review: Cooperation in microbial communities and their biotechnological applications – Matteo Cavaliere – Environmental Microbiology

Techniques

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data – Achal Dhariwal – Nucleic Acid Research

Microbes in the news

Adaptive Phage Therapeutics – Terminally Ill Patient Successfully Treated With Bacteriophage – BioSpace

Research Links Microbiome Makeup To Remission in Pediatric Crohn’s – Gastroenterology & Endoscopy News

NASA Astronauts Are Close to Identifying Unknown Microbe Colonies That Grow in Space – Sciencealert.com

 

April 26, 2017

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A series of commentary on the effects of microbiota on vaccines, a fascinating news release about a phage therapy against multi-drug resistant bacterial infection, and can our gut microbes tell us what to eat?

General microbiology

Evaluation of serotypes 5 and 8 capsular polysaccharides in protection against Staphylococcus aureus in murine models of infection – Brian L. Cheng – Human Vaccines & Immunotherapeutics

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? If So, Is There Potential for Efficacious Microbiota-Based Vaccines? – Dan R Littman – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Engaging Our Endogenous Adjuvants – Nicholas Collins1 and Yasmine Belkaid – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Issues of Sovereignty, Federalism, and Points-Testing in the Prokaryotic and Eukaryotic Spaces of the Host-Microbial Superorganism – Andrew J. Macpherson – Cold Spring Harbor Perspectives in Biology

Web alert: Microbial therapeutics – Microbial Biotechnology

Human multi-site microbiome

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015 – Marcus J. Drake – Neurourology and Urodynamics

Human gut microbiome

Doctoral Dissertation: The Effects of the Gut Microbiota on the Host Chromatin Landscape – Nicholas Paul Semenkovich – University of Washington, St. Louis

Tissue adaptation: Implications for gut immunity and tolerance – Ana M.C. Faria – Journal of Experimental Medicine

Animal experiments

Doctoral Dissertation, Mouse: The impact of malnutrition on host-microbe interactions in the intestine – Eric Brown – University of British Columbia

Mouse: Deciphering the mechanism of Huang-Lian-Jie-Du-Decoction on the treatment of sepsis by formula decomposition and metabolomics: enhancement of cholinergic pathways and inhibition of HMGB-1/TLR4/NF-κB signaling – Dingqiao Xu – Pharmacological Research

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats – Jing Chen – PLoS One

Commensal bacteria and essential amino acids control food choice behavior and reproduction – Ricardo Leitão-Gonçalves – PLoS Biology

Press: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh – Scientific American

Press: Are Gut Bacteria Driving Your Cravings? – Shayla Love – Vice

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice – Annadora J. Bruce-Keller – PLoS One

Animal microbiome

Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics – Can Song – Scientific Reports

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

New issue of Microbial Biotechnology is available online.

Plant, root and soil microbiome

Microbial communities associated with plants: learning from nature to apply it in agriculture – Fernando Dini Andreote and Michele de Cássia Pereira e Silva- Current Opinion in Microbiology

Life in earth – the root microbiome to the rescue? – Tim H Mauchline, Jacob G Malone – Current Opinion in Microbiology

Unique rhizosphere micro-characteristics facilitate phytoextraction of multiple metals in soil by the hyperaccumulating plant Sedum alfredii – Dandi Hou – Environmental Science & Technology

Water and extremophile microbiome

Doctoral Dissertation: Microbial community variation in an Arctic shelf seafloor – Tan Thi Nguyen – The Arctic University of Norway

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan – Ramganesh Selvarajan – Molecules

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis – Daniel Kurth – Scientific Reports

Probiotics

VSL#3 probiotic differently influences IEC-6 intestinal epithelial cell status and function – Benedetta Cinque – Journal of Cellular Physiology

Phages and viruses

Press Release: Novel phage therapy saves patient with multidrug-resistant bacterial infection – University of California, San Diego

Technology

Preprint: Assessing species biomass contributions in microbial communities via metaproteomics – Manuel Kleiner – bioRxiv

Microbes in the news

Are Probiotics the Answer to Acne? – Kristen Fischer – Healthline News

Are the microbes in our gut affecting how fast we age? – Vincent Maffei – OUPblog

Bacteria May be Reason Some Foods Cause Heart Disease, Stroke – Maggie Fox – NBC News

The Slow-Motion Bacteria Buried Deep in the Ocean’s Floor – Veronique Greenwood – The Atlantic

Bacteria from India’s hot springs could help contain oil spills – Dinesh C Sharma – Firstpost

Bacteria causing diarrhoea deaths in children resists key antibiotic – Syed Akbar – The Times of India

Fat rats, slow sperm, and unhealthy bacteria – Lee Evslin – The Garden Island

April 24, 2017

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General Microbiome

Review: Ecology of the Oral Microbiome: Beyond Bacteria – Jonathon L. Baker – Trends in Microbiology

Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets – Ting Yu – Frontiers in Microbiology

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments –  Matthew L Jenior – BioRxiv

Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods

Protective effects of milk fermented by Lactobacillus plantarum B7 from Brazilian artisanal cheese on a Salmonella enterica serovar Typhimurium infection in BALB/c mice – Journal of Functional Foods

 

Pathogens

Molecular Demonstration of a Pneumocystis Outbreak in Stem Cell Transplant Patients: Evidence for Transmission in the Daycare Center – Frontiers in Microbiology

A New Rabbit-skin Model to Evaluate Protective Efficacy of Tuberculosis Vaccines – Xun Liu – Frontiers in Microbiology

Molecular epidemiology and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus strains in a tertiary hospital in China – Haishen Kong – Frontiers in Microbiology

 

Environmental Microbiology

Microbial community assembly differs by mineral type in the rhizosphere – Thea Whitman – BioRxiv

Interaction between DAPG and HCN producing Pseudomonas brassicacearum LBUM300 and Clavibacter michiganensis subsp. michiganensis in the rhizosphere of tomato – Applied Environmental Microbiology

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean – Tom O. Delmont – BioRxiv

Bacterial communities in boreal forest mushrooms are shaped both by soil parameters and host identity – Mari Pent – Frontiers in Microbiology

 

Genomics

Isoprenoid Pyrophosphate-Dependent Transcriptional Regulation of Carotenogenesis in Corynebacterium glutamicum – Nadja A. Henke – Frontiers in Microbiology

Whole genome sequencing of 7 strains of Staphylococcus lugdunensis allows identification of mobile genetic elements – Xavier Argemi – Genome Biology and Evolution

Pooled CRISPR interference screens enable high-throughput functional genomics study and elucidate new rules for guide RNA library design in Escherichia coli – Tianmin Wang – BioRxiv

 

Evolution

Tunneling through time: Horizontal gene transfer constrains the timing of methanogen evolution –  Joanna M. Wolfe – BioRxiv

 

Bioinformatics

AliTV-interactive visualization of whole genome comparisons – Markus J. Ankenbrand – PeerJ (not peer-reviewed)

TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation – Ali Z Ijaz – PeerJ (not peer-reviewed)

 

Other

Preprinting Microbiology – Patrick D Schloss – BioRxiv

 

Non – Microbiology picks

News: Scientists across the world take to the streets to demand freedom from political interference – The Telegraph (via Yahoo News)

Human umbilical cord plasma proteins revitalize hippocampal function in aged mice – Joseph M. Castellano –  Nature

 

April 22, 2017

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General microbiome

The Microbiome – The Biochemist (full issue)

Human vaginal microbiome

*Review: What fertility specialists should know about the vaginal microbiome: a review – Juan Antonio García-Velascoa – Reproductive BioMedicine Online

Animal experiments

Microbiota-Induced Antibodies Are Essential for Host Inflammatory Responsiveness to Sterile and Infectious Stimuli – Daniel Cisalpino – Journal of Immunology

Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans – Timothy A. Scott – Cell

Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics – Aurian P. García-González – Cell

Examining the role of the microbiome in the effectiveness of colorectal cancer treatment – Jim Fessenden – UMass Medical School Communications

Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens – Yun-Gi Kim – Science

Infant mice lack microbes that help fight intestinal infection – EurekAlert!

Effects of different oligosaccharides at various dosages on the composition of gut microbiota and short-chain fatty acids in mice with constipation – Linlin Wang –  Food & Function

Short Term High Fat Diet Induces Obesity-Enhancing Changes in Mouse Gut Microbiota That are Partially Reversed by Cessation of the High Fat Diet – Yue Shang – Lipids

Animal microbiome

Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature – Andrian P. Gajigan – Microbiology Open

Characterization of the gut microbiota in the golden takin (Budorcas taxicolor bedfordi) – Jun Chen – AMB Express

*Opinion: Mammary microbiota of dairy ruminants: fact or fiction? – Pascal Rainard – Veterinary Research

Determination of the microbial community features of Haemaphysalis flava in different developmental stages by high-throughput sequencing – Deyong Duan – Journal of Basic Microbiology

Plant, root, and soil microbiome

A signature of tree health? Shifts in the microbiome and the ecological drivers of horse chestnut bleeding canker disease – Britt Koskella – New Phytologist

Soil aggregates as massively concurrent evolutionary incubators – Matthias C Rillig – ISME

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment – Qing Wang – Biology and Fertility of Soils

*Editorial: Signalling in the phytomicrobiome: Understanding and harnessing the plant holobiont – Donald L. Smith – Frontiers in Plant Science

Warming enhances old organic carbon decomposition through altering functional microbial communities – Lei Cheng – ISME

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Long-term straw returning affects Nitrospira-like nitrite oxidizing bacterial community in a rapeseed-rice rotation soil – Xuesong Luo – Journal of Basic Microbiology

Water and extremophile microbiome

Attenuation and modification of the ballast water microbial community during voyages into the Canadian Arctic – Mattias L. Johansson – Diversity and Distributions

Prokaryote species richness is positively correlated with eukaryote abundance in wastewater treatment biofilms – Inga Leena Angell – Letters in Applied Microbiology

*Review: The life sulfuric: Microbial ecology of sulfur cycling in marine sediments – Kenneth Wasmund – Environmental Microbiology Reports

Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra – Enrique Zozaya-Valdés – Environmental Microbiology

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds – Christian Wurzbacher – ISME

Built environment

Diversity changes of microbial communities into hospital surface environments – Rika Yano – Journal of Infection and Chemotherapy

Bioinformatics

A Robust Symmetric Nonnegative Matrix Factorization Framework for Clustering Multiple Heterogeneous Microbiome Data – Yuanyuan Ma – Preprints

Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline – Daniel J. White – Journal of Computational Biology

Techniques

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut – Bentley Lim – Cell

‘Genetic scalpel’ can manipulate the microbiome, Yale study shows – Bill Hathaway – Yale News

What is broad-range 16S rDNA PCR? – Amani Patel – Microbiology and Infectious Disease

Microbes in the news

Microbiome: The Body’s Great Conductor –  Conan Milner – Epoch Times

Our Gut Microbes Have Circadian Rhythms, Too — And They Might Own Us – Jesslyn Shields – HowStuffWorks

The Bacteria That Can Help Find Land Mines – Daniel Akst – The Wall Street Journal

Science, publishing, and career

Grant Addresses Computational Challenges in Microbiome Research – Jacobs School of Medicine and Biomedical Science

April 19, 2017

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Exciting papers with locoregional effects of microbiota in a mouse model of colon carcinogenesis, maternal high fat diet detrimentally alterring epigenetic and gut microbiome pathways leading to fatty liver disease in mice.

Events and jobs

ASM Microbe 2017 : New Orleans

QC Microbiology Product Testing Associate – Experis : Irvine, CA
General microbiome

Review: Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Cohort Profile: African Collaborative Center for Microbiome and Genomics Research’s (ACCME) Human Papillomavirus (HPV) and Cervical Cancer Study – Sally N. Adebamowo – International Journal of Epidemiology

Review: Cultured microbes represent a substantial fraction of the human and mouse gut microbiota – Ilias Lagkouvardos – Gut Microbes

Human skin microbiome

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients – Mor Miodovnika – Experimental Dermatology

Human gut microbiome

Review : A psychology of the human brain–gut–microbiome axis – Andrew P. Allen – Social and Personality Psychology Compass

Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs – Sean M P Bennet – Gut

Animal microbiome

Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic- phase newts (Amphibia) – Joana Sabino-Pinto – Environmental Microbiology

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa – Tomeu Viver – Environmental Microbiology

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers – Ilias Chantziaras -Journal of Antimicrobial Chemotherapy

The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and potential metabolic β-diversity – Michael P. Doane – Environmental Microbiology Reports

Animal experiments

Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota – Eliane von Klitzing – PLOS ONE

Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles – J. D. Latorre – Poultry Science

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock – Shengyin Jiao – Journal of the Science of Food and Agriculture

*Locoregional effects of microbiota in a preclinical model of colon carcinogenesis – Sarah Tomkovich – Cancer Research

Selection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet – Yufang Liu – Current Microbiology

*Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations – Umesh D. Wankhade – PLOS ONE

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion – Steven D Mamet- The ISME Journal

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil – Masahito Hayatsu – The ISME Journal

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater – Munawar Sultana – Groundwater

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses – Patricia Moya – Plos ONE

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – Plos ONE

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils – Ian D. E. A. Lidbury – Microbiology Open

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations – M. S. Bray – Gebiology

Water and extremophile microbiome

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats – Dimitry Y Sorokin – The ISME Journal

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system – Laura A Sauder – The ISME Journal

Minireview: Microbial ecology of mountain glacier ecosystems: Biodiversity, ecological connections, and implications of a warming climate – Scott Hotaling – Environmental Microbiology

Probiotics / prebiotics
Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans – M. Mego – Neurogastroenterology and Motility

Techniques

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces – Jialan Cao – Engineering in Life Sciences

Protocol : Metagenomics and CAZyme Discovery – Benoit J. Kunath – Protein-Carbohydrate Interactions : Methods in Molecular Biology

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols – L. Coorevits – European Journal of Clinical Microbiology & Infectious Diseases

Microbes in the news

Study finds amoeba ‘grazing,’ killing bacteria usually protected by film

How Bacteria-Laden Beetle Poop Is Killing American Squash and Melons

Glowing bacteria detect buried landmines

Science, publishing, and career

Saturday, Science Advocates Prepare for a Long March

Anitha’s non-microbiology picks

Research unlocks molecular key to animal evolution and disease

Cumulative culture can emerge from collective intelligence in animal groups – Takao Sasaki – Nature Communications

April 18, 2017

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Today’s digest hosts a number of rhizosphere-related publications as well as a good amount of interesting microbiome-host-health science.  Coming up next week is BioData World West 2017, a conference focused on Genomics/Precision Medicine/AI that I will be attending – I’ll keep an eye out for anything microbiome-related!

Events and jobs

2017 Metagenomics Workshop – Edwards Lab Event (Bioinformatics)

BioData World West 2017 – Precision Medicine, AI, Genomics Conference

General microbiome

Biological Determinants of Health: Genes, Microbes, and Metabolism Exemplars of Nursing Science – Erin P. Ferranti – Nursing Outlook

* Microbiotal-Host Interactions and Hypertension – Sarah Galla – Physiology

Multi-site human microbiome

* The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat – Diana M. Proctor – Cell Host & Microbe

Human respiratory microbiome

* The microbiome in respiratory medicine: current challenges and future perspectives – Rosa Faner – European Respiratory Journal

Human skin microbiome

Living in Peace: Host-Microbiota Mutualism in the Skin – Daniel J. Campbell – Cell Host & Microbe

Human gut microbiome

The Gut Microbiome: Connecting Spatial Organization to Function – Carolina Tropini – Cell Host & Microbe

Lactobacillus casei DG and its postbiotic reduce the inflammatory mucosal response: an ex-vivo organ culture model of post-infectious irritable bowel syndrome – Compare D – BMC Gastroenterology

Animal experiments

Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction – Netusha Thevaranjan – Cell Host & Microbe

Animal microbiome

PrePrint – Succession of embryonic and intestinal bacterial communities of Atlantic salmon – Jep Lokesh – bioRxiv

The Role of Rumen Microbiome on Feed Efficiency of Grazing Cattle [page 138] – Leluo Guan – 28th Annual Florida Ruminant Nutrition Symposium

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages – Carlos Iván Briones-Roblero – PLOS One

Plant, root, and soil microbiome

The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests – Tyler Schappe – Journal of Ecology

Host plant compatibility shapes the proteogenome of Frankia coriariae – Amir Ktari – Frontiers in Microbiology

Managing and manipulating the rhizosphere microbiome for plant health: A systems approach – Matthew D. Wallenstein – Rhizosphere

In vitro and In vivo biofilm formation by Azotobacter isolates and its relevance to rhizosphere colonization – Mohd. Musheer Altaf – Rhizosphere

Metabolism of pyrene through phthalic acid pathway by enriched bacterial consortium composed of Pseudomonas, Burkholderia, and Rhodococcus (PBR) – Sagar Vaidya – 3 Biotech

Effects of titanium dioxide nanoparticles on soil microbial communities and wheat biomass – Janine Moll – Soil Biology and Biochemistry

The effect of simulated warming on root dynamics and soil microbial community in an alpine meadow of the Qinghai-Tibet Plateau – Changting Wang – Applied Soil Ecology

Water and extremophile microbiome

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes, USA – Matt R. Simon – Journals of Soils and Sediments

A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems – Mikkel Stokholm-Bjerregaard – Frontiers in Microbiology

Applicability of cryoconite consortia of microorganisms and glacier-dwelling animals in astrobiological studies – Krzysztof Zawierucha – Contemporary Trends in Geoscience

Built environment

Review – Microbiological diagnosis of device-related biofilm infections – Yijuan Xu – APMIS

Patent Application – MONITORING AND MANAGING A FACILITY MICROBIOME – Dillon, Harrison – Free Patents Online

Microbes in space

Origins of Life on Mars: NASA’s Rovers Were Never Sterilized – Rhawn Gabriel Joseph – Cosmology.com

Phages and viruses

Mini Review Article – Phages in the Human Body – Ferran Navarro – Frontiers in Microbiology

Bioinformatics

* A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes – Wontack Han – Research in Computational Molecular Biology. RECOMB 2017.

Techniques

Effect of environmental variation on estimating the bacterial species richness – Jongjian Chen – Frontiers in Microbiology

Thesis – USE OF MOLECULAR METHODS IN BIOTHREAT PREPAREDNESS – Katja Koskela – National Defense University: Research Publications No. 13

Microbes in the news

Pets During Pregnancy Trigger Gut Bacteria Changes for Infants That May Cut Obesity Risk, Study Finds

Gut microbiome dysregulation implicated in OCD

Microbes on the market

Innovative Microbiome-based IBD Therapeutics to Be Developed Under New Partnership

Microbiome drug candidate prevents recurrence of C. difficile infection

Ed’s non-microbiology picks

Climate change causes glacial river in Yukon to change direction

Self-taught artificial intelligence beats doctors at predicting heart attacks

Stroke rates appear to be rising steadily in young adults

Costs of Selective Attention: When Children Notice What Adults Miss – Daniel J. Plebanek – APS

California Dryness and Recovery Challenge Multi-Century Odds