September 25, 2018

Today’s digest presents reviews covering potential of microbiome in olfactory communication and oral-gut microbiome axis in rheumatoid arthritis; articles on association of human gut microbiome with different diseases; news on antibiotics and scientific data on personality types in humans.

General microbiome

Review: The Extended Genotype: Microbially Mediated Olfactory Communication – Alexandra J.R. Carthey – Trends in Ecology and Evolution

Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Commmentary: Regulating stool for microbiota transplantation – Pilar N Ossorio – Gut microbes

Proteomics and the microbiome: pitfalls and potential – Huafeng Lin – Expert Review of Proteomics

Pregnancy and early life

Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children – Mon H. Tun – Canadian Medical Association Journal

Human gut microbiome

Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes, MODY2, and Healthy Control Subjects: A Case-Control Study – Isabel Leiva-Gea – Diabetes Care

Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China – Mengxiang Zhang – Scientific Reports

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer – Marta Mangifesta – Scientific Reports

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation – Christopher Staley – Microbiome

Could fecal phenylacetic and phenylpropionic acids be used as indicators of health status? – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemisty

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet – Neurogastroenterology and Motility

Animal experiments

Melatonin reprogramming of gut microbiota improves lipid dysmetabolism in high fat diet-fed mice – Jie Yin – Journal of Pineal Research

Water and extremophile microbiome

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake – Keith Arora-Williams – Microbiome

Probiotics/Prebiotics

The Impact of Probiotic Supplements on Cognitive Parameters in Euthymic Individuals with Bipolar Disorder: A Pilot Study – Eva Z Reininghaus – Neuropsychobiology

Microbes in the news

The case for expensive antibiotics – http://www.wired.com

Crucial antibiotics still used on US farms despite public health fear – The Guardian

Non-microbiology picks

A robust data-driven approach identifies four personality types across four large data sets – Martin Gerlach – Nature Human Behaviour

September 15, 2018

Posted on September 15, 2018 by JP Cardenas

Have a nice weekend! Today, we have several papers, covering different aspects of the microbiome! Some highlights (in bold): the role of microbiota in cancer immunotherapy success; interesting study about the lung microbiota and smoking; changes in gut microbiota in asthma patients, microbiota changes in high-salt feces; an interesting article about the potential effect of dogs in veteran rehabilitation; a review about periodontitis and the microbiome; a ecophylogenetic study about mammalian microbiome, and more!

Human and General Microbiome

Metagenomic Approaches for Understanding New Concepts in Microbial Science – Luana de Fátima Alves – International Journal of Genomics

Review: Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring – Yuanyuan Li – Frontiers in Genetics

Review: NLRP3 inflammasome in colitis and colitis-associated colorectal cancer – Agampodi Promoda Perera – Mammalian Genome

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study – He Xu – Frontiers in Microbiology

Review: Roles of intestinal microbiota in response to cancer immunotherapy – Jing Cong – European Journal of Clinical Microbiology & Infectious Diseases

Intestinal dysbiosis and hormonal neuroendocrine secretion in the fibromyalgic patient: Relationship and correlations – Giovanni Tomasello – Biomedical Papers

Macroecology to Unite All Life, Large and Small – Ashley Shade – Trends in Ecology and Evolution

Dichotomous development of the gut microbiome in preterm infants – Thao T. B. Ho – Microbiome

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

A metagenome-wide association study of gut microbiota in asthma in UK adults – Qi Wang – BMC Microbiology

The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing – Taylor R. Johnson – International Journal of Molecular Sciences

Phthalate Exposure and Odds of Bacterial Vaginosis Among U.S. Reproductive-Aged Women, NHANES 2001-2004 – Ruth J.Geller – Reproductive Toxicology

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria – Ian J. Passmore – PLoS Pathogens

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans – E. H. Seck – International Journal of Obesity

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota – Z.F. Kispal – Journal of Pediatric Urology

The Gut-Brain Axis in Alzheimer’s Disease and Omega-3. A Critical Overview of Clinical Trials – Francesca La Rosa – Nutrients

Associations between Flavonoid Intakes and Gut Microbiota in a Group of Adults with Cystic Fibrosis – Li Li – Nutrients

Review: Insights into the Human Virome Using CRISPR Spacers from Microbiomes – Claudio Hidalgo-Cantabrana – Viruses

Review: Probiotics in the Treatment of Colorectal Cancer – Robert Hendler – Medicines

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease – Shu Mei Teo – Cell Host and Microbe

Human skin volatiles: Passive sampling and GC × GC-ToFMS analysis as a tool to investigate the skin microbiome and interactions with anthropophilic mosquito disease vectors – Alexis P. Roodt – Journal of Chromatography B

Commentary: Regulating stool for microbiota transplantation – Pilar N. Ossorio – Gut Microbes

Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – Gastrointestinal and Liver Physiology

Exploring service dogs for rehabilitation of veterans with PTSD: A microbiome perspective – Andrew J.,Billera Hoisington – Rehabilitation Psychology

Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells – Nicholas A. Zumwalde – Breast Cancer Research

Periodontitis and the microbiome: a systematic review and meta-analysis – Fabrizio Guerra – Minerva Stomatologica

Formal Comment: The microbiome and the human: A reply to Parke and colleagues – Tobias Rees – PLoS Biology

Microbiota-gut-brain research: a critical analysis – Katarzyna B. Hooks – Behavioral and Brain Sciences

Animal Microbiome

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota – Christopher A. Gaulke – mBio

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis – Agnieszka D. Truax – Cell Host and Microbe

American ginseng microbial metabolites attenuate DSS-induced colitis and abdominal pain – Chong-Zhi Wang – International Immunopharmacology

Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome – Heidi Pauer – PLoS ONE

Bacterial community composition in the salivary glands of triatomines (Hemiptera: Reduviidae) – Michele Souza Lima – PLoS Neglected Tropical Diseases

Postnatal Administration of Lactobacillus rhamnosus HN001 Ameliorates Perinatal Broad-Spectrum Antibiotic-Induced Reduction in Myelopoiesis and T cell Activation in Mouse Pups – Eva Fuglsang – Molecular Nutrition and Food Research

Absorption of Codonopsis pilosula Saponins by Coexisting Polysaccharides Alleviates Gut Microbial Dysbiosis with Dextran Sulfate Sodium-Induced Colitis in Model Mice – Yaping Jing – BioMed Research International

Tributyrin Supplementation Protects Immune Responses and Vasculature and Reduces Oxidative Stress in the Proximal Colon of Mice Exposed to Chronic-Binge Ethanol Feeding – B. Glueck – Journal of Immunology Research

Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced Microbiome Changes in Growing Pigs – Michaela P. Trudeau – Frontiers in Veterinary Science

Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets – Jinqiang Xu – Frontiers in Microbiology

Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves – Renjia Du – Frontiers in Microbiology

The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish – Jacquelyn Jones – Frontiers in Microbiology

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets – Yuan Li – Frontiers in Microbiology

Review: Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture – Olav Vadstein – Frontiers in Microbiology

Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement – H. Myint – Beneficial Microbes

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australian Journal of Animal Sciences

The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLoS ONE

Food Microbiome

Lactic Acid Bacterium Population Dynamics in Artisan Sourdoughs Over One Year of Daily Propagations Is Mainly Driven by Flour Microbiota and Nutrients – Fabio Minervini – Frontiers in Microbiology

Effect of Pressure, Reconstituted RTE Meat Microbiota, and Antimicrobials on Survival and Post-pressure Growth of Listeria monocytogenes on Ham – Januana S. Teixeira – Frontiers in Microbiology

Plant Microbiome

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla – Mohamed S. Sarhan – Microbes and Environments

Root exudates drive the soil-borne legacy of aboveground pathogen infection – Jun Yuan – Microbiome

Review: Mycorrhizal microbiomes – Mika T. Tarkka – Mycorrhiza

Bioinformatics

GePMI: A statistical model for personal intestinal microbiome identification – Zicheng Wang – npj Biofilms and Microbiomes

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes – Suzanne M. Kosina – BMC Microbiology

Other

Temporal variability and stability of the fecal microbiome: the Multiethnic Cohort Study – Benjamin C Fu – Cancer Epidemiology, Biomarkers & Prevention

A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria – Samuel H. Light – Nature

September 5, 2018

Posted on September 5, 2018 by xinhuang7

Today’s Digest is not short of articles from all aspects of microbiome research. Highlights include a study on population dynamics during cycles of feast and famine, guidelines for FMT, and a 7-year experiment on the effect of warming and elevated carbon dioxide on soil carbon dynamics.

General microbiology

Microalgae-bacteria symbiosis in microalgal growth and biofuel production: a review – Shuo Yao et al. – Journal of Applied Microbiology

Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles – Zhanshan (Sam) Ma – Microbial Ecology

** Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt & Seppe Kuehn – Physical Review Letters

Review: Ecological effects of cellular computing in microbial populations – Maia Baskerville et al. – Natural Computing

Antibiotics/Antibiotic resistance

Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria – Lisa Mahler et al. – Scientific Reports

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer – Xue Zhou et al. – Science of The Total Environment

Comparative network analysis revealing the mechanisms of antibiotic resistance genes removal by leachate recirculation under different hydraulic loadings – Yinglong Sun et al. – Science of The Total Environment

Do plastics serve as a possible vector for the spread of antibiotic resistance? First insights from bacteria associated to a polystyrene piece from King George Island (Antarctica) – Pasqualina Laganà et al. – International Journal of Hygiene and Environmental Health

Forensic microbiome

Combining human STR and microbial population profiling: two case reports – Frederike C.A. Quaak et al. – FSI Genetics

Human lung microbiome

Review: The Genetics and Genomics of Asthma – Saffron A.G. Willis-Owen et al. – Annual Review of Genomics and Human Genetics

Human gut microbiome

In vitro: Impact of combining acerola by-product with a probiotic strain on a gut microbiome model – Fernanda Bianchi et al. – International Journal of Food Sciences and Nutrition

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village – Kelly V. Ruggles et al. – mSphere

Letter: Primum non nocere: is faecal microbiota transplantation doing harm to patients with IBS? – Paul Enck – Gut

Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study – Yongzhen Zhang et al. – BMC Microbiology

** The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H. Mullish et al. – Journal of Hospital Infection

Fecal microbiota transplantation: a promising strategy in preventing the progression of non-alcoholic steatohepatitis and improving the anti-cancer immune response – Vaihere Delaune et al. – Expert Opinion on Biological Therapy

Review: Modulation of the immune system by the gut microbiota in the development of Type 1 Diabetes – James A. Pearson et al. – Human Vaccines & Immunotherapeutics

Human gut-microbiome-brain axis

Altered Schaedler flora mice: An old defined microbiota animal model to study the new science of microbiota-gut-brain axis – J.M.Lyte et al. – Behavioural Brain Research

Animal experiments

Molecular networks affected by neonatal microbial colonization in porcine jejunum, luminally perfused with enterotoxigenic Escherichia coli, F4ac fimbria or Lactobacillus amylovorus – Paolo Trevisi et al. – PLoS One

Effects of Natural Flavonoid-Isoorientin on Growth Performance and Gut Microbiota of Mice – Li Xuan et al. – Journal of Agricultural and Food Chemistry

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota – Berra Erkosar et al. – Ecology and Evolution

Animal microbiome

Effects of clove (Syzygium aromaticum) oil on quail growth, carcass traits, blood components, meat quality, and intestinal microbiota – Mohamed M A Hussein et al. – Poultry Science

The effect of lavender (Lavandula angustifolia) essential oil as a drinking water supplement on the production performance, blood biochemical parameters, and ileal microflora in broiler chickens – Michalina Adaszyńska-Skwirzyńska & Danuta Szczerbińska – Poultry Science

Review: Factors Influencing Individual Variation in Farm Animal Cognition and How to Account for These Statistically – Emily V. Bushby et al. – Frontiers in Veterinary Science

Broad Bean (Vicia faba L.) Induces Intestinal Inflammation in Grass Carp (Ctenopharyngodon idellus C. et V) by Increasing Relative Abundances of Intestinal Gram-Negative and Flagellated Bacteria – Zhifei Li et al. – Frontiers in Microbiology

Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors – Priscila Bascuñán et al. – Microbiome

Alterations in honey bee gut microorganisms caused by Nosema spp. and pest control methods – Tsiri Diaz et al. – Pest Management Science

Plant, root and soil microbiome

** Elevated CO2 and warming cause interactive effects on soil carbon and shifts in carbon use by bacteria – Yolima Carrillo et al. – Ecology Letters

The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review – Stephanie A Yarwood – FEMS Microbiology Ecology

Strong succession in arbuscular mycorrhizal fungal communities – Cheng Gao et al. – ISME J

Manipulation of the rhizosphere bacterial community by biofertilizers is associated with mitigation of cadmium phytotoxicity – Meng Wang et al. – Science of The Total Environment

Multi-substrate induced microbial respiration, nitrification potential and enzyme activities in metal-polluted, EDTA-washed soils – Guixiang Zhou et al. – Scientific Reports

Divergent accumulation of microbial necromass and plant lignin components in grassland soils – Tian Ma et al. – Nature Communications

Microbial Community Composition In Take-All Suppressive Soils – Paola Duran et al. – Frontiers in Microbiology

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient – Matteo Montagna et al. – Molecular Ecology

Water and extremophile microbiome

Steep redox gradient and biogeochemical cycling driven by deeply sourced fluids and gases in a terrestrial mud volcano – Yueh-Ting Lin et al. – FEMS Microbiology Ecology

Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean – Dapeng Xu – Environmental Microbiology

Biofilm Formation and Degradation of Commercially Available Biodegradable Plastic Films by Bacterial Consortiums in Freshwater Environments – Tomohiro Morohoshi et al. – Microbes and Environments

Dynamics and Functional Potential of Stormwater Microorganisms Colonizing Sand Filters – Andrea Naimah Fraser et al. – Water

Review: Lignin depolymerization and utilization by bacteria – Rong Xu et al. – Bioresource Technology

Microbes in the industry

From systems biology to metabolically engineered cells — an omics perspective on the development of industrial microbes – Judith Becker &Christoph Wittmann – Current Opinion in Microbiology

Phages and viruses

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems – Yulin Wang et al. – Environmental Science & Technology

Technology

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities – Ashley R. Coenen & Joshua S. Weitz – mSystems

A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms – Ting L. Luo et al. – Scientific Reports

A steam-based method to investigate biofilm – Jason Tasse et al. – Scientific Reports

August 7, 2018

Posted on August 7, 2018 by xinhuang7

Today’s Digest features a lot of soil and plant microbiome articles. Highlights include an opinion piece on hypothesis-driven microbiome research, a study on the spread of MCR-3 colistin resistance in China, and a consortium of bacteria to protect plants from pathogents.

General microbiology

** Are microbiome studies ready for hypothesis-driven research? – Anupriya Tripathi et al. – Current Opinion in Microbiology

Mitracarpus frigidus: A promising antifungal in the treatment of vulvovaginal candidiasis – Lara M. Campos et al. – Industrial Crops and Products

Isolation, growth, enzyme assay and identification via 16S rRNA full sequencing of cellulolytic microbes from Nepal for biofuel production – Binayak Raj Pandey et al. – Renewable Energy

Review (Uncorrected Proof): From hairballs to hypotheses – biological insights from microbial networks – Lisa Röttjers & Karoline Faust – FEMS Microbiology Reviews

Review: Barriers and opportunities in bio-based production of hydrocarbons – Yongjin J. Zhou, Eduard J. Kerkhoven & Jens Nielsen – Nature Energy

Antibiotic resistance

** Spread of MCR-3 Colistin Resistance in China: An Epidemiological, Genomic and Mechanistic Study – Yongchang Xu et al. – EBioMedicine

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize – Qing-Lin Chen et al. – Science of The Total Environment

Carbapenem resistance in bacteria isolated from soil and water environments in Algeria – Katia DJENADI et al. – Journal of Global Antimicrobial Resistance

Human respiratory microbiome

Prospective study of timing and pattern of bacteria and viruses in the nasopharyngeal microbiome in a birth cohort – J.L.Mathew et al. – International Journal of Infectious Diseases

Human gut microbiome

Population changes of colon lumen microbiota in patients with chronic hepatitis C – A. Sydorchuk et al. – International Journal of Infectious Diseases

Multi-site human microbiome

Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria – S. H. Kose et al. – Scientific Reports

Food microbiology

Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process – Louise Vermote et al. – International Dairy Journal

Exploring core functional microbiota responsible for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine – Zi-Rui Huang et al. – Food Microbiology

Review: Spoilage yeasts: What are the sources of contamination of foods and beverages? – A. Hernández et al. – International Journal of Food Microbiology

Animal experiments

Consumption of virgin coconut oil in Wistar rats increases saturated fatty acids in the liver and adipose tissue, as well as adipose tissue inflammation – Marianade Moura e Dias et al. – Journal of Functional Foods

Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz et al. – Nature Medicine

Animal microbiome

Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract – Nicole A. Lloyd, Sylvie Nazaret & TamarBarkay – Marine Pollution Bulletin

Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray – Benthobatis moresbyi – Tina Kollannoor Johny et al. – Ecological Genetics and Genomics

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart et al. – American Journal of Veterinary Research

Plant, root and soil microbiome

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems – Madangchanok Imchen et al. – Scientific Reports

Structural development and assembly patterns of the root-associated microbiomes during phytoremediation – Yanmei Chen et al. – Science of The Total Environment

A Method for Collecting Atmospheric Microbial Samples From Set Altitudes for Use With Next-Generation Sequencing Techniques to Characterize Communities – Allison M Spring et al. – Air, Soil and Water Research

Plant-microbe interactions drive denitrification rates, dissolved nitrogen removal, and the abundance of denitrification genes in stormwater control measures – Natalie R Morse et al. – Environmental Science & Technology

Short- and long-term warming alters soil microbial community and relates to soil traits – Hongying Yu et al. – Applied Soil Ecology

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils – Yuqian Tang et al. – Science of The Total Environment

Wheat rhizosphere harbors a less complex and more stable microbial co-occurrence pattern than bulk soil – Kunkun Fan et al. – Soil Biology and Biochemistry

Influence of biochars on the accessibility of organochlorine pesticides and microbial community in contaminated soils – Neelum Ali et al. – Science of The Total Environment

Structure and activity of soil microbial communities in three Mediterranean forests – Felicia Grosso et al. – Applied Soil Ecology

Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria – Srinivasa R. Chaluvadi & Jeff Bennetzen – Frontiers in Plant Science

Review: Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture – D. Maurer et al. – Plant Biology

** Nutrient-and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen – Maureen Berg & Britt Koskella – Current Biology

Network Analyses Can Advance Above-Belowground Ecology – Kelly S.Ramirez et al. – Trends in Plant Science

Minireview: Microbial anaerobic Fe(II) oxidation – ecology, mechanisms and environmental implications – C Bryce et al. – Environmental Microbiology

Phages and viruses

No detectable effect of Wolbachia wMel on the prevalence and abundance of the RNA virome of Drosophila melanogaster – Mang Shi et al. – Proceedings B

Co-Infection Patterns in Individual Ixodes scapularis Ticks Reveal Associations between Viral, Eukaryotic and Bacterial Microorganisms – Shaun T. Cross et al. – Viruses

Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff et al. – Scientific Reports

Microbes in the news

Endophytes: Study Shows GMO Corn Has No Impact On Good Bacteria – Science 2.0

August 6, 2018

Posted on August 6, 2018 by Alyson

In today’s digest, look for probiotic trials for renal insufficiency and metabolic syndrome, experimental dysbiosis in SIV-infected primates, bacterial and fungal network analyses in soils, and recombination in the human virome. Plus, bacteria in the popular press, hints for scientists using Twitter, the first stem cell therapies for Parkinson’s Disease, and more!

Human gut microbiome
Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease – Linda Stewart – Clinical and Experimental Immunology

Animal experiments
Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz – Nature Medicine

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs – Marion Lemaire – Scientific Reports

Animal microbiome
Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs – Sara C. Bell – Frontiers in Microbiology

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart – American Journal of Veterinary Research

Plant, root, and soil microbiome
Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes – Andrew T. Nottingham – Ecology

Soil bacterial networks are less stable under drought than fungal networks – Franciska T. de Vries – Nature Communications

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits – Miguel A. Redondo – The ISME Journal

Variations in microbial community and di-(2-ethylhexyl) phthalate (DEHP) dissipation in different rhizospheric compartments between low- and high-DEHP accumulating cultivars of rice (Oryza sativa L.) – Xue-Xue Chen – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Evaluation of performance and microbial community successional patterns in an integrated OCO reactor under ZnO nanoparticle stress – Zhenghui Liu – RSC Advances

Screening of quorum quenching activity of the bacteria isolated from dairy industry waste activated sludge – J. Kaur – International Journal of Environmental Science and Technology

Food Microbiology
Identification of Mesophilic Spore-formers in Whey Powder using Shotgun Metagenomic Sequencing – Aoife J. McHugh – Applied and Environmental Microbiology

Probiotics/Prebiotics
An open-label, randomized, placebo-controlled study on the effectiveness of a novel probiotics administration protocol (ProbiotiCKD) in patients with mild renal insufficiency (stage 3a of CKD) – Mariadelina Simeoni – European Journal of Nutrition

Probiotic and synbiotic supplementation could improve metabolic syndrome in prediabetic adults: A randomized controlled trial – Nazila Kassaian – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Phages and viruses
Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff – Scientific Reports

Microbes in the news
Hong Kong Subway Study Shows How Quickly Bacteria Travel Across a City – Gizmodo

Bacteria hysteria
Please Don’t Give Up Your Pet Over The Fear Of Dog-Lick Bacteria – Huffington Post

Science, publishing, and career
Scientists on Twitter: Preaching to the choir or singing from the rooftops? – Isabelle Côté – Facets

Alyson’s non-microbiology picks
‘Reprogrammed’ stem cells to be tested in people with Parkinson’s

These tiny, stretchy speakers and microphones let your skin play music

July 02, 2018

Posted on July 2, 2018 by ashokksharma08

Good morning! Today’s Microbiome Digest will cover the general microbiome, HIV infection and multi-site bacterial microbiota, crucial role of lung microbiome in asthma, gut microbiome in type 1 diabetes, Link between diet and metabolic syndrome, Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes, HmmUFOtu: a tool for taxonomic assignment and OTU picking and a news on plastic eating bacteria …

Events and jobs

Post-Doctoral Research Position, Oregon State University, with Dr. Stephen Giovannoni

Postdoctoral Researcher Position Characterizing Microbial Candidate Phlya at Stanford University

General microbiome

Issue: The microbiome: more than a gut reaction – John R. Wingard – Blood

Evaluation at scale of microbiome-derived metabolites as biomarker of flavan-3-ol intake in epidemiological studies – Javier I. Ottaviani – Scientific Reports

All disease begins in the gut: Influence of gastrointestinal disorders and surgery on oral drug performance – Grace B. Hatton – International Journal of Pharmaceutics

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Multi-site human microbiome

HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa – Heidi Tuominen – Scientific Reports

Human respiratory microbiome

State of the Art: Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human vaginal microbiome

Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth – Aline C. Freitas – Microbiome

Human gut microbiome

Review: Gut microbiome in type 1 diabetes: A comprehensive review – Zheng P – Diabetes Metab Res Rev

Review: Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T – Metabolic Syndrome and Related Disorders

Chapter: Microbiota, Obesity and NAFLD – Louis H. S. Lau – Obesity, Fatty Liver and Liver Cancer

Chapter: The Influence of Gut Microbial Metabolism on the Development and Progression of Non-alcoholic Fatty Liver Disease – Wei Jia – Obesity, Fatty Liver and Liver Cancer

Method: Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Ancient Thali Diet: Gut Microbiota, Immunity, and Health – Kaitlyn Shondelmyer – Yale Journal of Biology & Medicine

Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet – Yunjian Zhang – Epilepsy Research

The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Review: The Gut Microbiome Alterations and Inflammation-Driven Pathogenesis of Alzheimer’s Disease—a Critical Review – Marta Sochocka – Molecular Neurobiology

The controversial role of Enterococcus faecalis in colorectal cancer – Carolina Vieira de Almeida – Therapeutic Advances in Gastroenterology

Animal experiments

Pea-protein alginate encapsulation adversely effects development of clinical signs of Citrobacter rodentium-induced colitis in mice treated with probiotics – Natallia Varankovich – Canadian Journal of Microbiology

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets – Chuanshang Cheng – Applied and Environmental Microbiology

Overlapping community composition of gut and fecal microbiomes in lab-reared and field-collected German cockroaches – Madhavi L. Kakumanu – Applied and Environmental Microbiology

TRIF deficiency protects non-obese diabetic mice from type 1 diabetes by modulating the gut microbiota and dendritic cells – Elke Gülden – Journal of Autoimmunity

Mucosal homeostasis is altered in the ileum of gnotobiotic mice – Chasen J. Greig – Journal of Surgical Research

Animal microbiome

Factors influencing bacterial microbiome composition in a wild non-human primate community in Taï National Park, Côte d’Ivoire – Jan F. Gogarten – The ISME Journal

Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes – Pablo Tsukayama – mSystems

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian – Sarah M. Griffiths – The ISME Journal

Plant, root, and soil microbiome

Review: Multifaceted Impacts of Bacteriophages in the Plant Microbiome – Britt Koskella – Annual Review of Phytopathology

‘Concord’ grapevine nutritional status and chlorosis rank associated with fungal and bacterial root zone microbiomes – R.W.Lewis – Plant Physiology and Biochemistry

Draft Genome Sequences of Two Novel Cellulolytic Streptomyces Strains Isolated from South African Rhizosphere Soil – Mobolaji F. Adegboye – Genome Announcements

Differences in microbial key players in anaerobic degradation between biogas and sewage treatment plants – Christian Buettner – International Biodeterioration & Biodegradation

Water and extremophile microbiome

The impact of the Deepwater Horizon blowout on historic shipwreck-associated sediment microbiomes in the northern Gulf of Mexico – Leila J. Hamdan – Scientific Reports

Stoichio-Metagenomics of ocean waters: a molecular evolution approach to trace the dynamics of nitrogen conservation in natural communities – Hannes Dittberner – Frontiers in Microbiology

Probiotics / prebiotics

Review: Impact of Prebiotics on Poultry Production and Food Safety – Steven C. Ricke – Yale Journal of Biology & Medicine

Isolation and Partial Characterization of Lactic Acid Bacteria from the Gut Microbiota of Marine Fishes for Potential Application as Probiotics in Aquaculture – Sergio Alonso – Probiotics and Antimicrobial Proteins

Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder – Jose-Walter Huaman – Gastroenterology

Bioinformatics

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies – Qi Zheng – Genome Biology

Techniques

Review: Culturing the human microbiota and culturomics – Jean-Christophe Lagier – Nature Reviews Microbiology

Microbes in the news

Plastic-eating bacteria discovered by student could help solve global pollution crisis

Sewage microbes make a fuel booster

Our intestinal microbiome influences metabolism — through the immune system

Ashok’s non-microbiology picks

Efficacy and Safety of Dupilumab in Glucocorticoid-Dependent Severe Asthma – Klaus F. Rabe – The NEW ENGLAND JOURNAL of Medicine

June 27, 2018

Posted on June 27, 2018 by TinaS

In today’s Microbiome Digest you can read about: cyanobacterial blooms by J. Huisman, designer microbial consortia by W. Kong, the significance of the intestinal microbiome for vaccinology by Vanessa C. Harris, indigenous microbes residing in oil sands by Xiaoxuan Yu, effects of sliver nanoparticles on soil microbiome by J.Y. Xu, WHAM!: a web-based visualization tool for metagenomics by J.C. Devlin. Yet another interesting read you can find in Science & Publishing –> “Death of scientific journals after 350 years” by S. Silver. Enjoy!

General microbiome

Designing microbial consortia with defined social interactions – Wentao Kong – Nature Chemical Biology

Pregnancy and early life

Antibiotics in early life: dysbiosis and the damage done – Hadar Neuman – FEMS Microbiology Reviews

Human ear microbiota

The unsolved problem of otitis media in indigenous populations: A systematic review of upper respiratory and middle ear microbiota in indigenous children – Andrea Coleman – bioRxiv

Human respiratory microbiome

Does lung microbiome play a causal or casual role in asthma? – Maria Di Cicco – Pediatric Pulmonology

Human gut microbiome

Alterations in the gut bacterial microbiome in fungal Keratitis patients – Sama Kalyana Chakravarthy – PLOS One

Altered intestinal microbiota composition, antibiotic therapy and intestinal inflammation in children and adolescents with cystic fibrosis – Maiara Brusco de Freitas – PLOS One

Nonaplex PCR using Cliffhanger primers to identify diarrhoeagenic Escherichia coli from crude lysates of human faecal samples – Uffe Vest Schneider – PLOS One

Review: The Significance of the Intestinal Microbiome for Vaccinology: From Correlations to Therapeutic Applications – Vanessa C. Harris – Drugs

Review: Update on the Gastrointestinal Microbiome in Systemic Sclerosis – Chiara Bellocchi – Current Rheumatology Reports

Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics – Emiro Buendía – Scientific Reports

Role of Microbiota and Tryptophan Metabolites in the Remote Effect of Intestinal Inflammation on Brain and Depression – Barbora Waclawiková – Pharmaceuticals

The study of bacteria in biopsies from Slovak colorectal adenoma and carcinoma patients – L. Wachsmannova- Neoplasma

Amplification of Antimicrobial Resistance in Gut Flora of Patients Treated with Ceftriaxone – J. Meletiadis – Antimicrobial Agents and Chemotherapy

Animal experiments

Metabolome disruption of pregnant rats and their offspring resulting from repeated exposure to a pesticide mixture representative of environmental contamination in Brittany – Nathalie Bonvallot – PLOS One

Dietary supplementation with raspberry extracts modifies the fecal microbiotain obese diabetic db/db mice – Jose F. Garcia-Mazcorro – Journal of Microbiology and Biotechnology

Effects of dietary yeast nucleotides supplementation on intestinal barrier function, intestinal microbiota, and humoral immunity in specific pathogen-free chickens – Che Wu – Poultry Science

Magnesium lithospermate B improves the gut microbiome and bile acid metabolic profiles in a mouse model of diabetic nephropathy – Jing Zhao – Acta Pharmacologica Sinica

Animal microbiome

Evaluation of the impact of dental prophylaxis on the oral microbiota of dogs – Rebecca Flancman – PLOS One

Improving the standards for gut microbiome analysis of fecal samples: insights from the field biology of Japanese macaques on Yakushima Island – Takashi Hayakawa – Primates

Plant, root, and soil microbiome

Indigenous microorganisms residing in oil sands tailings biodegrade residual bitumen – Xiaoxuan Yu – Chemosphere

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars – Shobit Thapa – Archives of Microbiology

Large-scale replicated field study of maize rhizosphere identifies heritable microbes – William A. Walters – PNAS

Long-term effects of sliver nanoparticles on the abundance and activity of soil microbiome – Jing Yang Xu – Journal of Environmental Sciences

Long-term effects of environmentally relevant concentrations of silver nanoparticles on microbial biomass, enzyme activity, and functional genes involved in the nitrogen cycle of loamy soil – Anna-Lena Grün – Journal of Environmental Sciences

Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L. – Xing-Kui Zhou – International Journal of Systematic and Evolutionary Microbiology

Effects of Bacillus subtilis and nanohydroxyapatite on the metal accumulation and microbial diversity of rapeseed (Brassica campestris L.) for the remediation of cadmium-contaminated soil – Wei Liu – Environmental Science and Pollution Research

Water and extremophile microbiome

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity – Jose Flores-Uribe – bioRxiv

Comparative genomics analyses indicate differential methylated amine utilisation trait within the member of the genus Gemmobacter – Eileen Kröber – bioRxiv

Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance – Wana Lailan Oliveira da Costa – PLOS One

Factors affecting infection of corals and larval oysters by Vibrio coralliilyticus – Blake Ushijima – PLOS One

“Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell ‘omics” – Xyrus X Maurer-Alcalá – Genome Biology and Evolution

Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride – Xikun Liu – FEMS Microbiology Ecology

Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation – Jian Guo – Nature Microbiology

Warming and oligotrophication cause shifts in freshwater phytoplankton communities – Laura Verbeek – Global Change Biology

Review: Cyanobacterial blooms – Jef Huisman – Nature Reviews Microbiology

Research letter: Airborne Microbes Contribute to N2 Fixation in Surface Water of the Northern Red Sea – Eyal Rahav – Geophysical Research Letters

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S. Graf – Environmental Microbiology

Extensive nitrification and active ammonia oxidizers in two contrasting coastal systems of the Baltic Sea – Elisabeth Happel – Environmental Microbiology

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice‐covered lakes – Patricia Tran – Environmental Microbiology

Rapid thermal adaptation in a marine diatom reveals constraints and tradeoffs – Daniel R. O’Donnell – Global Change Biology

A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses – Qiang Zheng – Frontiers in Microbiology / Virology

Built environment

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales – Mikayla A. Borton – PNAS

Phages and viruses

Two point mutations in the Hantaan virus glycoproteins afford the generation of a highly infectious recombinant vesicular stomatitis virus vector – Megan M Slough – bioRxiv

ΦCrAss001, a member of the most abundant bacteriophage family in the human gut, infects Bacteroides – Andrey Shkoporov – bioRxiv

In silico characterisation of the two-component system regulators of Streptococcus pyogenes – Sean J. Buckley- PLOS One

Host-microbiome interactions

Opinion: Classic Models for New Perspectives: Delving into Helminth–Microbiota–Immune System Interactions – Alba Cortés – Trends in Parasitology

Review: Helminth–Bacterial Interactions: Cause and Consequence – Alexis Rapin – Trends in Immunology

Bioinformatics

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data – Joseph C. Devlin – BMC Genomics

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples – Ehsaneddin Asgari – Bioinformatics

Science, publishing, and career

The Impact of Grant Funding on the Publication Activity of Awarded Applicants: A Systematic Review of Comparative Studies and Meta-analytical Estimates – Ruslan Saygitov – bioRxiv

Death of scientific journals after 350 years – Simon Silver – FEMS Microbiology Letters

June 19, 2018

Posted on June 19, 2018 by TinaS

In today’s digest you can read about: the field of CRISPR-CAS antimicrobials by E. Pursey, “microbiota influencers” by G. Rizzatti, bioplastic producing bacterial communities by V. Kumar, mixotrophic behavior of the harmful benthic dinoflagellate by B. Lee and many many diverse and interesting articles. Enjoy!

General microbiome

CRISPR-Cas antimicrobials: Challenges and future prospects – Elizabeth Pursey – PLOS Pathogens

Considering Microbial CO2 during Microbe-Plant Cocultivation – Birgit Piechulla – Plant Physiology

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss – Colin P. McNally – BMC Systems Biology

Pregnancy and early life

Prevalence of antibiotic resistance in commensal Escherichia coli among the children in rural hill communities of Northeast India – Ashish Kumar Singh – PLOS One

Shared and Distinct Features of Human Milk and Infant Stool Viromes – Pia S. Pannaraj – Frontiers in Microbiology

Preterm infant gut microbial patterns related to the development of necrotizing enterocolitis – Tristan P. Lindberg – The Journal of Maternal-Fetal & Neonatal Medicine

Human respiratory microbiome

Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4 – Irene Jiménez-Munguía – PeerJ

Human gut microbiome

Addendum: “I will survive”: A tale of bacteriophage-bacteria coevolution in the gut – Luisa De Sordi – Gut Microbes

The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – Melbert T Schwarz – bioRxiv

Prioritizing and modelling of putative drug target proteins of Candida albicans by systems biology approach – Tariq Ismail – Acta Biochimica Polonica

Antibiotic and Modulation of Microbiota: A New Paradigm? – Gianenrico Rizzatti – Journal of Clinical Gastroenterology

Streptomyces, shared microbiome member of soil and gut, as “old friends” against colon cancer – Alireza Bolourian – FEMS Microbiology Ecology

Gut Microbial-related Choline Metabolite Trimethylamine-N-oxide is Associated with Progression of Carotid Artery Atherosclerosis in HIV Infection – Zhilei Shan – The Journal of Infectious Diseases

Role of Microbiota in Sexually Dimorphic Immunity – Marlies Elderman – Frontiers in Immunology

Early results of fecal microbial transplantation protocol implementation at a community-based university hospital – Rodrigo Duarte-Chavez – Journal of Global Infectious Diseases

Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism – Marion Soto – Molecular Psychiatry

The Rise and Rise of Eosinophilic Gut Diseases Including Eosinophilic Esophagitis Is Probably Not Explained by the Disappearance of Helicobacter pylori, so Who or What’s to Blame? – Nicholas J. Talley – The American Journal of Gastroenterology

Effect of administration of a probiotic preparation on gut microbiota and immune response in healthy women in India: an open-label, single-arm pilot study – Ankita Singh – BMC Gastroenterology

Animal experiments

Toxin-positive Clostridium difficile latently infect mouse colonies and protect against highly pathogenic C. difficile – Lucie Etienne-Mesmin – Gut microbiome

Animal microbiome

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach – Sarayu Bhogoju – PLOS One

Tracking sources of Clostridium botulinum type E contamination in seal meat – Daniel Leclair – International Journal of Circumpolar Health

Plant, root, and soil microbiome

Applying predictive models to decipher rhizobacterial modifications in common reed die-back affected populations – Giovanni Bacci – Science of The Total Environment

Bioplastic reservoir of diverse bacterial communities revealed along altitude gradient of Pangi-Chamba trans-Himalayan region – Vijay Kumar – FEMS Microbiology Letters

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp – Valentina Maggini – FEMS Microbiology Ecology

Divergent Responses of the Diazotrophic Microbiome to Elevated CO2 in Two Rice Cultivars – Yongjie Yu – Frontiers in Microbiology

Synthesis and detoxification of nitric oxide in the plant beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 and its effect on biofilm formation – Xiaoyan Dong – Biochemical and Biophysical Research Communications

Understanding the Strategies to Overcome Phosphorus–Deficiency and Aluminum–Toxicity by Ryegrass Endophytic and Rhizosphere Phosphobacteria – Patricio J. Barra – Frontiers in Microbiology

Soil viruses are underexplored players in ecosystem carbon processing – Gareth Trubl – bioRxiv

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities – Eric M Bottos – FEMS Microbiology Ecology

Changes of soil microbial and enzyme activities are linked to soil C, N and P stoichiometry in afforested ecosystems – F.Z. Zhao – Forest Ecology and Management

Responses of soil microbial communities to nutrient limitation in the desert-grassland ecological transition zone – Cui Y – The Science of the Total Environment

Observed metabolic asymmetry within soybean root nodules reflects unexpected complexity in rhizobacteria-legume metabolite exchange – Dušan Veličković – The ISME Journal

Antibacterial activity of soil bacteria isolated from Kochi, India and their molecular identification – Davis Gislin – Journal of Genetic Engineering and Biotechnology

Brassica napus Growth in Lead-Polluted Soil: Bioaccumulation in Plant Organs at Different Ontogenetic Stages and Lead Fractionation in Soil – Gisele V. Ferreyroa – Water, Air, & Soil Pollution

Editorial: “Plant-Microbe-Insect Interaction: Source for Bio-fertilizers, Bio-medicines and Agent Research” – Gero Benckiser – Frontiers in Plant Science

Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere – Fernando Uriel Rojas-Rojas – Microbiology

Improvement of Ni phytoextraction by Alyssum murale and its rhizosphere microbial activities by applying nitrogen fertilizer – Ali Kanso – Ecological Research

Water and extremophile microbiome

Abundance determines the functional role of bacterial phylotypes in complex communities – Damian W. Rivett – Nature Microbiology

Metabolic Diversity within the Globally Abundant Marine Group II Euryarchaea Drives Ecological Patterns – Benjamin J Tully – bioRxiv

Diversity of bacterial communities and dissolved organic matter in a temperate estuary – Helena Osterholz – FEMS Microbiology Ecology

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms – Zhi-Ping Zhong – Frontiers in Microbiology

Genetic diversity and co-occurrence patterns of marine cyanopodoviruses and picocyanobacteria – Yingting Sun – Applied and Environmental Microbiology

Proteome response of a metabolically flexible anoxygenic phototroph to Fe(II) oxidation – Casey Bryce – Applied and Environmental Microbiology

Genome rearrangement shapes Prochlorococcus ecological adaptation – Wei Yan – Applied and Environmental Microbiology

High CO2 Under Nutrient Fertilization Increases Primary Production and Biomass in Subtropical Phytoplankton Communities: A Mesocosm Approach – Nauzet Hernández-Hernández – Frontiers in Microbiology

Genetic Analyses of the rbcL and psaA Genes From Single Cells Demonstrate a Rhodophyte Origin of the Prey in the Toxic Benthic Dinoflagellate Ostreopsis – Bora Lee – Frontiers in Marine Science

Ubiquitous abundance distribution of non-dominant plankton across the global ocean – Enrico Ser-Giacomi – Nature Ecology & Evolution

Copiotrophic marine bacteria are associated with strong iron‐binding ligand production during phytoplankton blooms – Shane L. Hogle – Limnology and Oceanography

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling – David M. Needham – The ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom – Yuanyuan Xue – The ISME Journal

Coral Microbiomes as Bioindicators of Reef Health – Sofia Roitman – Population Genomics

Microbial community structure and functional potential along a hypersaline gradient – Jeffrey A. Kimbrel – Frontiers in Microbiology

Comparative genomics of Pseudomonas sp. strain SI-3 associated with macroalga Ulva prolifera, the causative species for green tide in the Yellow Sea – Huihui Fu – Frontiers in Microbiology

Probiotics / prebiotics

Pilot assessment of probiotics for pregnant women in Rwanda – Amy McMillan – PLOS One

Phages and viruses

Low spatial structure and selection against secreted virulence factors attenuates pathogenicity in Pseudomonas aeruginosa – Elisa T Granato – bioRxiv

Identification of anti-norovirus genes in mouse and human cells using genome-wide CRISPR activation screening – Robert Orchard – bioRxiv

Biotechnology

Simultaneous autotrophic removal of sulphate and nitrate at different voltages in a bioelectrochemical reactor (BER): Evaluation of degradation efficiency and characterization of microbial communities – Hao Xua – Bioresource Technology

Evaluation of A Novel Split-Feeding Anaerobic/Oxic Baffled Reactor (A/OBR) For Foodwaste Anaerobic Digestate: Performance, Modeling and Bacterial Community – Shaojie Wang – Scientific Reports

Viewpoint: Synthetic Biology for Natural Compounds – Xinrui Zhao – Biochemistry

Bioinformatics

iMetaLab 1.0: A web platform for metaproteomics data analysis – Bo Liao – Bioinformatics

Taxonomy annotation and guide tree errors in 16S rRNA databases – Robert Edgar – PeerJ

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level – Luis M Rodriguez-R – Nucleic Acids Research

Techniques

Whole-Cell MALDI-TOF MS Versus 16S rRNA Gene Analysis for Identification and Dereplication of Recurrent Bacterial Isolates – Michal Strejcek – Frontiers in Microbiology

Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things – Ivan Merelli – Future Generation Computer Systems

Microbes in the news

Unique microbe could thrive on Mars, help future manned missions

In a Warming World, Deadly Bacteria Are More Resistant to Antibiotics

Microbes on the market

Startup aims to make allies of human gut’s microbes

Department of Energy Announces $40 Million for Bio-Based Research

Tina’s non-microbiology picks

Towards an Evolutionary Perspective in Teaching and Popularizing Microbiology – Fernando Bueno Ferreira Fonseca de Fraga – Journal of Microbiology & Biology Education

June 8, 2018

Posted on June 8, 2018 by xinhuang7

A short Digest today with primarily preprints. A policy piece on diabetic patient care in the UK, Wolbachia strains never found before in Anopheles mosquitoes, and fecal pollution contributing to antibiotic resistant genes in waste water.

Jobs

Postdoctoral Fellowship in Microbiome Data Science – Johns Hopkins University

General microbiology

Preprint: DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth – Emily Sarah Melzer et al. – bioRxiv

Preprint: Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA – David G Welkie et al. – bioRxiv

Preprint: The fungal-specific Hda2 and Hda3 proteins regulate morphological switches in the human fungal pathogen Candida albicans – Misty Peterson et al. – bioRxiv

Preprint: Chance and pleiotropy dominate genetic diversity in complex bacterial environments – Lianet Noda-Garcia et al. – bioRxiv

Preprint: Molecular basis for the evolution of species-specific hemoglobin capture by pathogenic Staphylococcus – Jacob E Choby et al. – bioRxiv

Antibiotic resistance

Preprint: Comparison of trimethoprim-sulfamethoxazole versus ciprofloxacin monotherapy in Stenotrophomonas maltophilia bloodstream infections in children – Ahu Aksay et al. – bioRxiv

Preprint: The reduced prevalence of macrolide resistance in Mycoplasma pneumoniae clinical isolates from pediatric patients in Beijing in 2016 – Xiu jun Tian et al. – bioRxiv

Preprint: The key lethal effect existed in the antibacterial behavior of short, medium, and long chain fatty acid monoglycerides on Escherichia coli – Song Zhang et al. – bioRxiv

Human oral microbiome

Preprint: The stress hormone cortisol induces virulence in the oral microbiome – Ana Emilia Duran-Pinedo et al. – bioRxiv

Human gut microbiome

** Policy: Diabetes UK nutrition guidelines: reinforcing the foundations of diabetes care – Mark Greener – Practical Diabetes

Animal microbiome

** Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Preprint: The effect of susceptible and resistant potato cultivars on bacterial communities in the tuberosphere of potato in soil suppressive or conducive to common scab disease – Marketa Sagova-Mareckova et al. – bioRxiv

Preprint: Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit – Peter McAtee et al. – bioRxiv

Water and extremophile microbiome

** Preprint: Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments – Antti Karkman et al. – bioRxiv

Phages and viruses

Preprint: Adomaviruses: an emerging virus family provides insights into DNA virus evolution – Nicole L Welch et al. – bioRxiv

Preprint: Epstein-Barr Virus May Contribute to Central Nervous System Involvement in HIV-positive Individuals – Tommaso Lupia et al. – bioRxiv

Bioinformatics

Preprint: PorSignDB: a database of in vivo perturbation signatures for dissecting clinical outcome of PCV2 infection – Nicolaas Van Renne et al. – bioRxiv

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Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Resistome

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