August 21, 2017

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

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August 3, 2017

The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature

July 26, 2017

General microbiome

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species – Massimiliano Cardinale – Scientific Reports

Review: The mother–offspring dyad: microbial transmission, immune interactions and allergy development – Maria C. Jenmalm – Journal of Internal Medicine

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross – mSystems

Animal microbiome

Influence of Host Plant on Thaumetopoea pityocampa Gut Bacterial Community – Cinzia P. Strano – Microbial Ecology

The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs – Erin E. Donaldson – PeerJ

Plant, root, and soil microbiome

Review: Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution – Michael Gatheru Waigi – Trends in Biotechnology

Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient – Michael S. Strickland – Applied Soil Ecology

Changes of soil microbial communities during decomposition of straw residues under different land uses – Hong Zhang – Journal of Arid Land

Water and extremophile microbiome

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su – Microbiome

An anaerobic ~3400 Ma shallow-water microbial consortium: presumptive evidence of Earth’s Paleoarchean anoxic atmosphere – J. William Schopf – Precambrian Research

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir – Pan Pan – Applied Microbiology and Biotechnology

Food Microbiology

Editorial: Microbiology of Ethnic Fermented Foods and Alcoholic Beverages of the World – Jyoti P. Tamang – Frontiers in Microbiology

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Phages and viruses

Review : The Human Virome – Implications for Clinical Practice in Transplantation Medicine – Susanna K. Tan – Journal of Clinical Microbiology

Anitha’s non-microbiology picks

Quantum tunneling takes time, new study shows

Perovskites power up the solar industry

Scientists develop fast chemistry that unlocks a new class of polymers

Medicine’s Movable Feast: What Jumping Genes Can Teach Us about Treating Disease

July 19, 2017

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

July 5, 2017

General microbiome

Letter to the editor: Introducing the sporobiota and sporobiome – George Tetz – Gut Pathogens

Human oral microbiome

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Hai-Yue Liu – Frontiers in Microbiology

Human respiratory microbiome

Review: Respiratory microbiota and lower respiratory tract disease – Miguel Lanaspa – Expert Review of Anti-infective Therapy

Human gut microbiome

Review: Feeding the microbiota: transducer of nutrient signals for the host – Fergus Shanahan – Gut

Animal microbiome

Early Postnatal Diets Affect the Bioregional Small Intestine Microbiome and Ileal Metabolome in Neonatal Pigs – Brian D Piccolo – The Journal of Nutrition

Variation between the oral and faecal microbiota in a free-living passerine bird, the great tit (Parus major) – Lucie Kropáčková – Plos One

Temperature variation, bacterial diversity, and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Early-Life Diet Affects Host Microbiota and Later-Life Defenses Against Parasites in Frogs – Sarah A. Knutie – Integrative & Comparitive Biology

Animal experiments

Relative variations of gut microbiota in disordered cholesterol metabolism caused by high-cholesterol diet and host genetics – Tao Bo – Microbiology Open

Plant, root, and soil microbiome

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities – Kelly Gravuer – Frontiers in Microbiology

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere – Ubiana C. Silva – Frontiers in Microbiology

Global change and the soil microbiome: A human-health perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

Contrasting bacterial communities in two indigenous Chionochloa (Poaceae) grassland soils in New Zealand – Jocelyn C. Griffith – Plos One

Water and extremophile microbiome

Bacterial diversity and population shifts driven by spotlight wastewater micropollutants in low-temperature highly nitrifying activated sludge – Antonina Kruglova – JScience of The Total Environment

Probiotics / prebiotics

The potential synergistic behaviour of inter- and intra-genus probiotic combinations in the pattern and rate of short chain fatty acids formation during fibre fermentation – Warnakulasuriya M. A. D. B. Fernando – International Journal of Food Sciences and Nutrition

Review: Structural features underlying prebiotic activity of conventional and potential prebiotic oligosaccharides in food and health – Subin R. C. K. Rajendran – Journal of Food Biochemistry

Phages and viruses

Case control comparison of enteric viromes in captive rhesus macaques with acute or idiopathic chronic diarrhea – Beatrix Kapusinszky – Journal of Virology

A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections – Samuele Bovo – Plos One

Bioinformatics

Does colorectal cancer significantly influence the assembly of gut microbial communities? – Lin Dai – PeerJ

Review: Using metagenomics to investigate human and environmental resistomes – Johan Bengtsson-Palme – Journal of Antimicrobial Chemotherapy

RRmix: A method for simultaneous batch effect correction and analysis of metabolomics data in the absence of internal standards – Stephen Salerno Jr – Plos One

Predicting the ecological quality status of marine environments from eDNA metabarcoding data using supervised machine learning – Tristan Cordier – Environmental Science and Technology

Anitha’s non-microbiology picks

AI is changing how we do science. Get a glimpse

Scientists explain ancient Rome’s long-lasting concrete

June 15, 2017

Today’s digest is full of plant, animal, and soil microbiome studies as well as a nice serving of human gut science, specifically about FMT.

Events and jobs

Visiting Assistant Professor of Microbiology – Methodist University, North Carolina

GENEWIZ Week – many small events, contests, giveaways, and webinars (including mine on using Metagenomics for Biomarker Discovery posted here on Sunday’s blog post. Since my webinar was yesterday, it will be archived and can be downloaded from genewiz.com, starting next week – don’t forget to check it out!)

General microbiome

* Comprehensive analysis of microorganisms accompanying human archaeological remains – Anna Philips – Gigascience

Pregnancy and early life

Relationships Among Microbial Communities, Maternal Cells, Oligosaccharides, and Macronutrients in Human Milk – Williams JE – Journal of Human Lactation

Human oral microbiome

Targeted Antimicrobial Therapy in the Microbiome Era – Victoria N. Stone – Molecular Oral Microbiology

Human gut microbiome

* Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile – Ranjit Kumar – npj Biofilms and Microbiomes

* Fecal microbiota transplantation in metabolic syndrome: History, present and future – P. F. de Groot – Gut microbes

Intestinal microbiota, fecal microbiota transplantation, and inflammatory bowel disease – Weingarden AR – Gut Microbes

Faecal microbiota study reveals specific dysbiosis in spondyloarthritis – Maxime Breban – Annals of Rheumatic Diseases

Metaproteomic analysis of human gut microbiota: where are we heading? – Pey Yee Lee – Journal of Biomedical Science

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage – Minh Thuy Tang – Applied Microbiology and Biotechnology

Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population – A. Divani – Animal Physiology and Animal Nutrition

Chronic treatment with prebiotics, probiotics and synbiotics attenuated cardiac dysfunction by improving cardiac mitochondrial dysfunction in male obese insulin-resistant rats – Tunapong W – European Journal of Nutrition

Amelioration of obesity-related characteristics by a probiotic formulation in a high-fat diet-induced obese rat model – Joo-Hyun Shin – European Journal of Nutrition

Early Gut Microbiota Intervention Suppresses DSS-Induced Inflammatory Responses by Deactivating TLR/NLR Signalling in Pigs – Yi Xiao – Scientific Reports

* Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Animal microbiome (for animals in the wild)

[PrePrint] Ecophysiology of freshwater Verrucomicrobia inferred from genomes recovered through time-series metagenomics – Shaomei He – bioRxiv

Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals – Shan-Hua Yang – Aquatic Microbiology (Frontiers in Microbiology)

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome – Eugeni Belda – Scientific Reports

Social odours covary with bacterial community in the anal secretions of wild meerkats – Sarah Leclaire – Scientific Reports

Plant, root, and soil microbiome

Imidacloprid application changes microbial dynamics and enzymes in rice soil – Bibhab Mahapatra – Ecotoxicology and Environmental Safety

Comparison of ammonia oxidation bacteria community structure in paddy soil with different utilized years – Zhao WeiYe – Southwest China Journal of Agricultural Sciences

[MS Thesis] Variation of Soil Microbial Communities within a Consociation Soil Map Unit and a Vegetative Transect through an Oak Motte – Sarah Elizabeth Shawver – Tarleton State University

Effects of different intercropping patterns on rhizosphere soil bacteria colony characteristics and flue-cured tobacco yield and quality – Wei Jun – Guangxi Academy of Agricultural Sciences

Rhizospheric bacteria diversity of Cypripedium macranthum estimated via high throughput sequencing – Zhang Jian -Southwest China Journal of Agricultural Sciences

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils – Lopez-Lozano NE – Antonie van Leeuwenhoek

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera – Amandine Le Van – PeerJ

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China – Jing Zhou – Scientific Reports

A next generation sequencing approach with a suitable bioinformatics workflow to study fungal diversity in bioaerosols released from two different types of composting plants – Hamza Mbareche – Science of The Total Environment

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment – Granzow S – Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries – Mikel Aguirre – PLOS ONE

Food microbiology

Metagenomics insights into food fermentations – Francesca De Filippis – Microbial Biotechnology

Probiotics / prebiotics

Effect of probiotic Lactobacillus on lipid profile: A systematic review and meta-analysis of randomized, controlled trials – Yuncheng Wu – PLOS ONE

Growing Literature but Limited Evidence: A Systematic Review regarding Prebiotic and Probiotic Interventions for those with Traumatic Brain Injury and/or Posttraumatic Stress Disorder – Lisa A. Brenner – Brain, Behavior, Immunity

Microbes on the market

$10 million gift boosts gut microbiome research at Wash U

Ed’s non-microbiology picks 

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site – Eva-Maria Strauch – Nature Biotechnology

Aberrant telomere length and mitochondrial DNA copy number in suicide completers –  Ikuo Otsuka – Scientific Reports

Impact of nutrition on social decision making – Sabrina Strang – PNAS

Oral vitamin D rapidly attenuates inflammation from sunburn: an interventional study – Jeffrey F. Scott – JID

Adaptive self-organization of Bali’s ancient rice terraces – J. Stephen Lansing – PNAS

Ravens remember the nature of a single reciprocal interaction sequence over 2 days and even after a month – J. J. A. Muller – Animal Behaviour

May 17, 2017

Today’s digest includes a few studies of the interactions between microbes (and synergy in metabolism and other processes), a filling of human gut microbiology, and interesting insights into probiotics both in animals and humans.  Also, check out my post later in the day reviewing microbiome related talks at BioData World West 2017 (late April)

Events and jobs

Scientist – Microbiomics – ZymoResearch

PhD in microbiology – Université Catholique de Louvain (UCL)

Microbiology Laboratory Technologist – Yukon Hospital Corporation – Whitehorse, YT

General microbiome

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities – Margaret F Romine – The ISME Journal

Identification of the potentiating mutations and synergistic epistasis that enabled the evolution of inter-species cooperation – Sarah M. Douglas – PLOS ONE

Pregnancy and early life

PrePrint – Gut dysbiosis following C-section instigates higher colonisation of toxigenic Clostridium perfringens in infants – Nagpal R – Benef Microbes

The influence of dietary immunomodulatory factors on development of food allergy in children – Sardecka I – Postepy Dermatol Alergol.

 

Human oral microbiome

The microbiome of site-specific dental plaque of children with different caries status – Richards VP – Infection and Immunity

Human gut microbiome

Healthy gut microbiota can resolve undernutrition – Emmanuel Hermann – HBSN

The Gut Microbiota and Autism Spectrum Disorders – Qinrui Li – Frontiers in Cellular Neuroscience

The ecological community of commensal, symbiotic, and pathogenic gastrointestinal microorganisms – an appraisal – Haque SZ – Dovepress

Comparative Effectiveness of Faecal Microbiota Transplant by Route of Administration – Nathan D. Gundacker – The Journal of Hospital Infection

Fecal microbiota transplantation in recurrent Clostridium difficile infection in a patient with concomitant inflammatory bowel disease – Gravito-Soares M – Rev Esp Enferm Dig

Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections – Panliang Wang – Journal of Pediatric Surgery

* The Gastric Microbiome and Its Influence on Gastric Carcinogenesis: Current Knowledge and Ongoing Research – Chao Zhang – Hematology/Oncology Clinics of North America

Insights into the role of the intestinal microbiota in colon cancer – Oke S – Therapeutic Advances in Gastroenterology

Gut microbiota changes as a risk factor for obesity – Kvit KB – Wiad Lek.

Animal experiments 

Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions – Mark Trinder – Frontiers in Microbiology

Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice – Guiping Guan – Mediators of Inflammation

Changes in the intestinal bacterial community, short-chain fatty acid profile, and intestinal development of preweaned Holstein calves. 2. Effects of gastrointestinal site and age – J.J. Castro – Journal of Dairy Science

The microbiome regulates amygdala-dependent fear recall – Hoban AE – Molecular Psychiatry

Animal microbiome

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures – Stéphanie Céline Michl – PLOS ONE

The influence of a probiotic supplementation on memory in quail suggests a role of gut microbiota on cognitive abilities in birds – Severine Parois – Behavioural Brain Research

Gut microbial communities of American pikas (Ochotona princeps): evidence for phylosymbiosis and adaptations to novel diets – Kevin D. Kohl – Journal of Animal Ecology

This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth-Microbiota Interactions in Veterinary Species – Peachey LE – Trends in Parasitology

Convergence of gut microbiotas in the adaptive radiations of African cichlid fishes – Baldo L – ISME

Plant, root, and soil microbiome

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire – Sang-Hoon Lee – The ISME Journal

Prokaryotic Communities at Different Depths between Soils with and without Tomato Bacterial Wilt but Pathogen-Present in a Single Greenhouse – Chol Gyu Lee – Microbes and Environments

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – The ISME Journal

A bacterial community-based index to assess the ecological status of estuarine and coastal environments – Eva Aylagas – Marine Pollution Bulletin

The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay – Yile Tao – Marine Pollution Bulletin

The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats – Johanne Aubé – Marine Pollution Bulletin

Changes in microbial community during hydrogen and methane production in two-stage thermophilic anaerobic co-digestion process from biowaste – S. Zahedi – Waste Management

Comparative analysis of microbial diversity in two hot springs of Bakreshwar, West Bengal, India – Chaudhuri B – Genomics Data

Built environment (subways, indoor surfaces)

Characterizing bacterial communities in paper production-troublemakers revealed – Zumsteg A – MicrobiologyOpen

 

Probiotics / prebiotics

Dairy Propionibacteria: Versatile Probiotics – Rabah H – Microorganisms

Contribution of anthocyanin-rich foods in obesity control through gut microbiota interactions – Jamar G – BioFactors

Positive Effect of Probiotics on Constipation in Children: A Systematic Review and Meta-Analysis of Six Randomized Controlled Trials – Huang R – Frontiers in Cellular and Infection Microbiology

Mechanisms of Action of Probiotics and the Gastrointestinal Microbiota on Gut Motility and Constipation – Dimidi E – Advances in Nutrition

Bioinformatics

PrePrint – MetaMeta: Integrating Metagenome Analysis Tools To Improve Taxonomic Profiling – Vitor C. Piro – bioRxiv

Using null models to infer microbial co-occurrence networks – Nora Connor – PLOS ONE

Techniques

Characterization of microbial mixtures by mass spectrometry – Sandrin TR – Mass Spectrometry Reviews

Microbes in the news 

Cork scientists link gut bacteria to anxiety disorders

New tick bacteria in Australia being investigated as possible cause of Lyme disease-type illness

Optical nanofiber ‘hears’ bacteria swim, cancer cells move

Microbes on the market 

BiomX raises $24 million to boost bacteria based drugs

 

Ed’s non-microbiology picks

Breakthrough in delirium research ‘solves 2,500-year-old mystery’

Novel tissue-engineered islet transplant achieves insulin independence in type 1 diabetes – Bioengineering of an Intraabdominal Endocrine Pancreas -David A. Baidal – New England Journal of Medicine

High levels of exercise linked to nine years of less aging (at the cellular level)

Migratory birds bumped off schedule as climate change shifts spring

PrePrint – Using Social Network Analysis to Better Understand Compulsive Exercise Behavior among a Sample of Sorority Members –  Megan S. Patterson – Human Kinetics

Edible insects could play key role in cutting harmful emissions – EurkAlert!