Category Archives: Fungi

August 6, 2018

Posted on by

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

August 5, 2018

Posted on by

Have a good sunday! Today, in Microbiome Digest: several reviews focused in clinical aspects of the microbiome, associations between malnutrition and dysbiosis, a study observing the effect of prebiotics on autism spectrum disorders, influence of the microbiome on mouse brain, the impact of storage and DNA extraction on microbiota analysis, and much more!

 

Human and General Microbiome

Review: The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human – Anthony P. Corfield – Microorganisms

Review: Next generation microbiology and cystic fibrosis diagnostics: are we there yet? – Claus Moser – Current Opinion in Pulmonary Medicine

Review: Proton Pump Inhibitors: Risks and Rewards and Emerging Consequences to the Gut Microbiome –  Amandeep Singh – Nutrition in Clinical Practice

Review: The Gut Microbiome in Patients with Intestinal Failure: Current Evidence and Implications for Clinical Practice – Esther Neelis – Journal of Parenteral and Enteral Nutrition

Review: The Esophageal Microbiome in Health and Disease – Brooke Corning – Current Gastroenterology Reports

Review: Microbiota issue in CKD: how promising are gut-targeted approaches? – Carmela Cosola – Journal of Nephrology

Review: Neuroimmunophysiology of the gut: advances and emerging concepts focusing on the epithelium – Keith A. Sharkey – Nature Reviews Gastroenterology & Hepatology

Commentary: The Perturbance of Microbiome and Gut-Brain Axis in Autism Spectrum Disorders – Greta Fowlie – International Journal of Molecular Sciences

Comment: Causality in dietary interventions-building a case for gut microbiota – Yan Y. Lam – Genome Medicine

Emergent simplicity in microbial community assembly – Joshua E. Goldford – Science

Contraception: Influence on Vaginal Microbiota and Identification of Vaginal Lactobacilli Using MALDI-TOF MS and 16S rDNA Sequencing – Sonia E. Fosch – The Open Microbiology Journal

Gut Microbiota Dysbiosis is Associated with Malnutrition and Reduced Plasma Amino Acid Levels: Lessons from Genome-Scale Metabolic Modeling – Manish Kumar – Metabolic Engineering

Photobiomodulation of the microbiome: implications for metabolic and inflammatory diseases – Brian Bicknell – Lasers in Medical Science

Roxithromycin regulates intestinal microbiota and alters colonic epithelial gene expression – Cheng Zhang – Applied Microbiology and Biotechnology

Whole Cell Cross-Linking to Discover Host-Microbe Protein Cognate Receptor/Ligand Pairs – Bart C. Weimer – Frontiers in Microbiology

 

Animal Microbiome

The gut microbiota drives the impact of bile acids and fat source in diet on mouse metabolism – Sarah Just – Microbiome

Changes in feeding habits promoted the differentiation of the composition and function of gut microbiotas between domestic dogs (Canis lupus familiaris) and gray wolves (Canis lupus) – Tianshu Lyu – AMB Express

The effect of dietary lipid on gut microbiota in a senescence-accelerated prone mouse model (SAMP8) – Kazushi Yamamoto – Biogerontology

Moderate Dietary Protein Restriction Optimized Gut Microbiota and Mucosal Barrier in Growing Pig Model – Xiyue Chen – Frontiers in Cellular and Infection Microbiology

Effects of Sub-Chronic MPTP Exposure on Behavioral and Cognitive Performance and the Microbiome of Wild-Type and mGlu8 Knockout Female and Male Mice – Eileen Ruth S. Torres – Frontiers in Behavioral Neuroscience

Microbiota influence the development of the brain and behaviors in C57BL/6J mice – Jing Lu – PLoS ONE

Intestinal Microbiota Lipid Metabolism Varies across Rainbow Trout (Oncorhynchus mykiss) Phylogeographic Divide – Christina C. Yildirimer – Journal of Applied Microbiology

Chronic refined low-fat diet consumption reduces cholecystokinin satiation in rats – Mathilde Guerville – European Journal of Nutrition

The dynamics of the piglet gut microbiome during the weaning transition in association with health and nutrition – Robin B. Guevarra – Journal of Animal Science and Biotechnology

 

Methodologies

Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols – Cécile Angebault – PLoS ONE

 

Beneficial Microbes and Compounds

A prebiotic intervention study in children with autism spectrum disorders (ASDs) – Roberta Grimaldi – Microbiome

Chemical Compositions of Cold-pressed Broccoli, Carrot and Cucumber Seed Flours, and Their in Vitro Gut Microbiota Modulatory, Anti-inflammatory and Free Radical Scavenging Properties – Uyory Choe – Journal of Agricultural and Food Chemistry

 

Pathogen Research

Review: Nontuberculous Mycobacteria in Cystic Fibrosis – Brian S. Furukawa – Seminars in Respiratory and Critical Care Medicine

August 2, 2018

Posted on by

In today’s Microbiome Digest you can read about: the connection of mother’s microbiota and development of psychiatric disorders by M.G. Codagnone; pulmonary microbiome by A.N. Costa; microbiome and allergic diseases by M.Pascal; olfactory communication via microbiota in birds by O. Maraci; global topsoil microbiome by M. Bahram and many more. Enjoy your hot summer read!

Pregnancy and early life

Review: Programming Bugs: Microbiota and the Developmental Origins of Brain Health and Disease – Martin G.Codagnone – Biological Psychiatry

Human respiratory microbiome

The pulmonary microbiome: challenges of a new paradigm – André Nathan Costa – Jornal Brasileiro de Pneumologia

Oral microbiology

Are the mutans streptococci still considered relevant to understanding the microbial etiology of dental caries? – Jeffrey A. Banas – BMC Oral Health

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach – Yoshio Nakano – BMC Oral Health

Human skin microbiome

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome – Kang Kang – Cell Reports

Human gut microbiome

Alterations in the Gut Microbiota of Rats Chronically Exposed to Volatilized Cocaine and Its Active Adulterants Caffeine and Phenacetin – Cecilia Scorza – Neurotoxicity Research

Origination, change, and modulation of geriatric disease-related gut microbiota during life – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens – Alexandra E. Livanos – PLOS One

Minireview: Microbiome and Allergic Diseases – Mariona Pascal – Frontiers in Immunology / Mucosal Immunity

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy – Xingming Deng – Frontiers in Microbiology / Antimicrobials, Resistance and Chemotherapy

Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model – Qin Qi – World Journal of Gastroenterology

Helicobacter pylori in human health and disease: Mechanisms for local gastric and systemic effects – Denisse Bravo – World Journal of Gastroenterology

Acquisition of MACPF domain-encoding genes is the main contributor to LPS glycan diversity in gut Bacteroides species – Valentina Laclare McEneany – The ISME Journal

Drivers of Microbiome Biodiversity: A Review of General Rules, Feces, and Ignorance – Aspen T. Reese – mBio

Effects of prebiotic inulin-type fructans on blood metabolite and hormone concentrations and faecal microbiota and metabolites in overweight dogs – Celeste Alexander – British Journal of Nutrition

Standardization of gut microbiota analysis: Variability in samples taken at different times from single case and the effect of the freezing the sample – F. Saglam – International Journal of Infectious Diseases

Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size – Emily C. Hoedt – The ISME journal

Animal experiments 

A Polysaccharide Isolated from Dictyophora indusiata Promotes Recovery from Antibiotic-Driven Intestinal Dysbiosis and Improves Gut Epithelial Barrier Function in a Mouse Model – Sadia Kanwal – Nutrients

High Dose Vitamin D supplementation alters faecal microbiome and predisposes mice to more severe colitis – Simon Ghaly – Scientific Reports

Treatment with camu camu (Myrciaria dubia) prevents obesity by altering the gut microbiota and increasing energy expenditure in diet-induced obese mice – Fernando F Anhê – Gut Microbiota

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures – Matej Medvecky – BMC Genomics

Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations – John B. Gorham – European Journal of Nutrition

Animal microbiome 

A prokaryotic-eukaryotic relation in the fat body of Bombus terrestris – Anneleen Parmentier – Environmental Microbiology Reports

Olfactory Communication via Microbiota: What Is Known in Birds? – Öncü Maraci – Genes

Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism (Ciona robusta) – Alexandria Creasy – Viruses

Plant, root, and soil microbiome

Description of ‘Candidatus Methylocucumis oryzae’, a novel Type I methanotroph with large cells and pale pink colour, isolated from an Indian rice field – Pranitha S. Pandit – Antonie van Leeuwenhoek

Long-term effects of untreated wastewater on soil bacterial communities – Tianlin Shen – Science of The Total Environment

Minireview: Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation – Sara Correa-García – Microbial Biotechnology

Soil pre-fumigation could effectively improve the disease suppressiveness of biofertilizer to banana Fusarium wilt disease by reshaping the soil microbiome – Zongzhuan Shen – Biology and Fertility of Soils

Structure and function of the global topsoil microbiome – Mohammad Bahram – Nature

Globally rising soil heterotrophic respiration over recent decades – Ben Bond-Lamberty – Nature

Water and extremophile microbiome

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current – Flavia Flaviani – Frontiers in Microbiology / Aquatic Microbiology

Evaluation of biomethane potential of waste algal biomass collected from eutrophied lake: effect of source of inocula, co-substrate, and VS loading – Pushpendar Kumar – Journal of Applied Phycology

Distinct molecular signatures in dissolved organic matter produced by viral lysis of marine cyanobacteria – Xiufeng Ma – Environmental Microbiology

Increased biofilm formation due to high-temperature adaptation in marine Roseobacter – Alyssa G. Kent – Nature Microbiology

Adaptive mechanisms that provide competitive advantages to marine bacteroidetes during microalgal blooms – Frank Unfried – The ISME Journal

The anchoring effect—long-term dormancy and genetic population structure – Lisa Sundqvist – The ISME Journal

Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments – Stefan Spring – Environmental Microbiology

The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients – Julia M. Otte – Environmental Microbiology

Temporal and spatial dynamics in microbial community composition within a temperate stream network – Norman Hassell – Environmental Microbiology

Diel dynamics and coupling of heterotrophic prokaryotes and dissolved organic matter in epipelagic and mesopelagic waters of the central Red Sea – Francisca C. García – Environmental Microbiology

Probiotics / prebiotics

The effects of a multispecies probiotic on migraine and markers of intestinal permeability–results of a randomized placebo-controlled study – N M de Roos – European Journal of Clinical Nutrition

Phages and viruses

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis – Tanmoy Chakraborty – Virulence

Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: Insights from a natural arms-race – Amelia McKitterick – bioRxiv

Bioinformatics

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea – Johannes Alneberg – Scientific Data

Bacteria & Art

The Beautiful World of Bacteria

 

July 28, 2018

Posted on by

Have a good weekend! For this Saturday, we have more than 60 articles! 

Including: A set of reviews about mother, delivery and neonate microbiome; relationship between microbiome and cancer and Alzheimer; microbiome in primate models, reviews about pathogens and more…

 

Human and General Microbiome

Review: Gut Mycobiota and Fungal Metabolites in Human Homeostasis – Izabella Mogilnicka – Current Drug Targets

Review: Dietary Protein and Muscle in Aging People: The Potential Role of the Gut Microbiome – Mary Ni Lochlainn – Nutrients

Review: The interplay between neutrophils and microbiota in cancer – Carolyne K. Smith – Journal of Leukocyte Biology

Review: Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut – Siavash Atashgahi – Frontiers in Physiology

Review: Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How? – Sharon Y. Geerlings – Microorganisms

Review: Considering gut microbiota disturbance in the management of Helicobacter pylori infection – Loris R. Lopetuso – Expert Review of Gastroenterology & Hepatology

Microbiome Analyses for Toxicological Studies – Jacquelynn Benjamino – Current Protocols in Toxicology

Editorial: Caesarean-Section and Neonatal Gut Microbiome: Short and Long Term Effects and New Targets for Early Prevention – Giannattasio A. – Annals of Nutrition and Metabolism

Review: C-section and the Neonatal Gut Microbiome Acquisition: Consequences for Future Health – Arboleya S. – Annals of Nutrition and Metabolism

Review: Birth Mode-Related Differences in Gut Microbiota Colonization and Immune System Development – Francino M.P.  – Annals of Nutrition and Metabolism

Review: Intervention for Dysbiosis in Children Born by C-Section – Francavilla R. – Annals of Nutrition and Metabolism

Review: Gut Microbiota Composition in Healthy Japanese Infants and Young Adults Born by C-Section – Nagpal R. – Annals of Nutrition and Metabolism

Review: Dysbiosis in Children Born by Caesarean Section – Salas Garcia M.C. – Annals of Nutrition and Metabolism

 

Human Gut

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link? – Aguayo, Sebastian –  Journal of Alzheimer’s Disease

Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma – Zhigang Ren – Gut

A Multi-omic Association Study of Trimethylamine N-Oxide – Ohad Manor – Cell Reports

Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults – Chad W. MacPherson – Scientific Reports

Cost-effectiveness analysis of ribotype-guided fecal microbiota transplantation in Chinese patients with severe Clostridium difficile infection – Minghuan Jiang – PLoS ONE

Microbiota Quality and Mitochondrial Activity Link with Occurrence of Muscle Cramps in Hemodialysis Patients using Citrate Dialysate: A Pilot Study – Durand P.-Y. – Blood Purification

Gut microbiota, dietary intakes and intestinal permeability reflected by serum zonulin in women – S. Mörkl – European Journal of Nutrition

Analysis of the Enteric Microbiome: First Tentative Steps Towards a Comprehensive Work-up of Prostate Cancer? – Ilaria Cavarretta – European Urology

 

Human Respiratory Tract

Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients – Georgios D. Kitsios – Frontiers in Microbiology

Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients – Laura Iaffaldano – Scientific Reports

 

Newborn and Mother Microbiome

Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study – Naruaki Imoto – Journal of Perinatology

 

Human Urinary/Reproductive Tract

Endocervical and vaginal microbiota in South African adolescents with asymptomatic Chlamydia trachomatis infection – Christina Balle – Scientific Reports

Introduction: Microbes in the female reproductive function, do they matter? – Carlos Simon – Fertility and Sterility

 

Human Skin

Relations between epidermal barrier dysregulation and staphylococci-dominated microbiome dysbiosis in atopic dermatitis – Can Altunbulakli – Atopic Dermatitis Research

 

Animal Microbiome / Animal Experiments

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – Scientific Reports

Diarrhea-Associated Intestinal Microbiota in Captive Sichuan Golden Snub-Nosed Monkeys (Rhinopithecus roxellana) – Hui Zhu – Microbes and Environments

An orally administered oral pathobiont and commensal have comparable and innocuous systemic effects in germ-free mice – Keisuke Sato – Journal of Periodontal Disease

Effects of dietary tryptophan supplementation in the acetic acid-induced colitis mouse model – Shuai Chen – Food and Nutrition

Early-life stress leads to sex-dependent changes in pubertal timing in rats that are reversed by a probiotic formulation – Caitlin S. M. Cowan – Developmental Psychobiology

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway – Emilie U. Andersen-Ranberg – Microorganisms

Gut microbiota influences Alzheimer’s disease pathogenesis by regulating acetate in Drosophila model – Yan Kong – Future Microbiology

Elevated Seawater Temperatures Decrease Microbial Diversity in the Gut of Mytilus coruscus – Yi-Feng Li – Frontiers in Physiology

Microbiome-metabolomics Analysis of the Impacts of Long-term Dietary Advanced Glycation End Products Consumption on the C57BL/6 Mouse Fecal Microbiota and Metabolite Perturbation – Wanting Qu – Journal of Agricultural and Food Chemistry

Papio spp. Colon microbiome and its link to obesity in pregnancy – XuanJi Li – Journal of Medical Primatology

Combination of Aronia, Red Ginseng, Shiitake Mushroom and Nattokinase Potentiated Insulin Secretion and Reduced Insulin Resistance with Improving Gut Microbiome Dysbiosis in Insulin Deficient Type 2 Diabetic Rats – Hye Jeong Yang – Nutrients

Short and long-term effects of a synbiotic on clinical signs, the fecal microbiome, and metabolomic profiles in healthy research cats receiving clindamycin: a randomized, controlled trial – Jacqueline C. Whittemore​ – PeerJ

Lactobacillus plantarum ZDY04 exhibits a strain-specific property of lowering TMAO via the modulation of gut microbiota in mice – Liang Qiu – Food and Function

Diet induced maternal obesity affects offspring gut microbiota and persists into young adulthood – Yanjie Guo – Food and Function

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity – Xue-Song Zhang – eLife

Clostridium butyricum Attenuates Chronic Unpredictable Mild Stress-Induced Depressive-Like Behavior in Mice via the Gut-Brain Axis – Jing Sun – Journal of Agricultural and Food Chemistry

 

Food Microbiome

Analysis of Fish Commonly Sold in Local Supermarkets Reveals the Presence of Pathogenic and Multidrug-Resistant Bacterial Communities – Ama Okyere – Microbiology Insights

Short communication: Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE – Vesna Milanović – International Journal of Food Microbiology

Acyl-homoserine-lactones receptor LuxR of Shewanella baltica involved in the development of microbiota and spoilage of refrigerated shrimp – Jinxin Jie – Journal of Food Science and Technology

 

Beneficial Microbes and Compounds

Review: Probiotics against airway allergy: host factors to consider – Irina Spacova – Disease Model and Mechanisms

Abundance of gut Prevotella at baseline and metabolic response to barley prebiotics – Jonna Sandberg – European Journal of Nutrition

Letter: Effect of Metformin or Chinese Herbal Formula in Patients with Type 2 Diabetes Mellitus and Hyperlipidemia: A Reassessment – Venu Gopal Jonnalagadda – mBio

Coreopsis Tinctoria Modulates Lipid Metabolism by Decreasing Low-Density Lipoprotein and Improving Gut Microbiota – Ren Z. – Cellular Physiology and Biochemistry

 

Pathogen Research

Review: Recent insights into Shigella – Stephen Baker – Current Opinion in Infectious Diseases

Review: Cholera: recent updates – Ana A. Weil – Current Opinion in Infectious Diseases

 

Soil and Plant Microbiome

Microbial community assembly differs across minerals in a rhizosphere microcosm – Thea Whitman – Environmental Microbiology

Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome – Eric J. N. Helfrich – Nature Microbiology

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts – Ming-Yi Chou – Scientific Reports

 

Methods

Methodology: A two-stage microbial association mapping framework with advanced FDR control – Jiyuan Hu – Microbiome

A Comprehensive Study on Predicting Functional Role of Metagenomes Using Machine Learning Methods – Jyotsna Talreja Wassan – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Generalized Linear Models with Linear Constraints for Microbiome Compositional Data – Jiarui Lu – Biometrics

Analyzing differences between microbiome communities using mixture distributions – Konstantin Shestopaloff – Statistics in Medicine

Pathomimetic modeling of human intestinal diseases and underlying host-gut microbiome interactions in a gut-on-a-chip – Woojung Shin – Methods in Cell Biology

 

Other

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems – Magdalena Calusinska – Biotechnology for Biofuels

 

23 July, 2018

Posted on by

Today’s digest includes exciting Microbiome events and brilliant papers on animal microbiomes. Lastly, research exploring the war on gluten.

Events

Microbiome X Regulation 1 Panel discussion on navigating the FDA

Introduction to the 4th International Symposium on Gluten-Free Cereal Products and Beverages.

General Microbiome

Antibiotic Scars Left on the Gut Microbiota from the Stringent Response. Yi H. Trends in Microbiology

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Hua ZS. Nature Communications

Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain.Doyle CJ. Frontiers in Microbiology.

How Microbial Aggregates Protect against Nanoparticle Toxicity.Tang J. Trends in Biotechnology.

Inhibition of microbial spoilage of grass carp (Ctenopharyngodon idellus) fillets with a chitosan-based coating during refrigerated storage. Yu D. International Journal of Food Microbiology

Gut Microbiome

The gut microbiome and irritable bowel syndrome. Menees S. F1000Research

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.Zarrinpar A. Nature Communications

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Zhang X. Nature Communications

Techniques

A rapid PCR-based method to discriminate Macrococcus caseolyticus and Macrococcus canis from closely-related Staphylococcus species based on the ctaC gene sequence. Mazhar S. Journal of Microbiological Methods

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification. Vervier K. Methods in Molecular Biology

Soil, Water, and Air Microbiome

Influence of new agromining cropping systems on soil bacterial diversity and the physico-chemical characteristics of an ultramafic soil. Saad RF. Science of the Total Environment

<i>Pseudomonas chlororaphis</i> produces multiple R-tailocin particles that broaden the killing spectrum and contribute to persistence in rhizosphere communities.Dorosky RJ. Applied and Environmental Microbiology

REVIEW: Microbial diversity and biogeography in Arctic soils.Malard LA. Environmental Microbiology Reports.

Impact of brine and antiscalants on reef-building corals in the Gulf of Aqaba – Potential effects from desalination plants.Petersen KL. Water Research

Mapping the Bacterial Community in Digboi Oil Refinery, India by High-Throughput Sequencing Approach. Dasgupta A.  Current Microbiology.

Chemical-, site-, and taxa-dependent benthic community health in coastal areas of the Bohai Sea and northern Yellow Sea: A sediment quality triad approach. Khim JS. Science of the Total Environment.

Animal Experiments and Microbiome

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda. Zeng Y. Frontiers in Microbiology

REVIEW:The gut microbiota of wild rodents: Challenges and opportunities. Viney M. Laboratory Animals

Genome-wide association studies of inflammatory bowel disease in German shepherd dogs. Peiravan A. PLoS One.

Effects of Rodent Diet Choice and Fiber Type on Data Interpretation of Gut Microbiome and Metabolic Disease Research.Pellizzon MA. Current Protocols in Toxicology

Non-Microbiology Hot Pick

The war on gluten. Servick K. Science.

 

 

11 July, 2018

Posted on by

Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Lundgren SN. Microbiome.

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Das B. Scientific Reports

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice.Wang. PLoS One

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. Ge Y. PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.Pais IS. PLoS Biology

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

June 28, 2018

Posted on by

Microbial adaptation to snake and spider venom, a 1.5-year study of fungi in space at the International Space Station, US National Postdoc Survey results.

General microbiome

Quantitative assessment of individual populations within polymicrobial biofilms – Susana Patrícia Lopes – Scientific Reports

Human nearly-sterile sites

Streptococcus mutans in Umbilical Cord Blood, Peripheral Blood, and Saliva from Healthy Mothers – Marcelly Milhomem Mendes – Current Microbiology

Animal microbiome

Pre-print: Microbial adaptation to venom is common in snakes and spiders – E Esmaeilishirazifard – bioRxiv

Plant, root, and soil microbiome

Colonisation dynamics of arbuscular mycorrhizal fungi and dark septate endophytes in the sugarcane crop cycle – Anders Claassens – Rhizosphere

Response Surface Modelling through Box-Behnken approach to optimize bacterial quorum sensing inhibitory action of Tribulus terrestris root extract – Kayeen Vadakkan – Rhizosphere

Multi ‘omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone – Emily B Graham – Science of the Total Environment

Pre-print: Co-culture of soil biofilm isolates enables the discovery of novel antibiotics – Chun-Hui Gao – bioRxiv

Pre-print: Microbial interkingdom interactions in roots promote Arabidopsis survival – Paloma Duran – bioRxiv

Water and extremophile microbiome

Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill – Candice Y Lumibao – Science of the Total Environment

Microbes in space

Integrity of the DNA and Cellular Ultrastructure of Cryptoendolithic Fungi in Space or Mars Conditions: A 1.5-Year Study at the International Space Station – Silvano Onofri – Life

Food microbiology

Influence of lactate and acetate removal on the microbiota of French fresh pork sausages – Agnès Bouju-Albert – Food Microbiology

Probiotics/prebiotics

The anxiolytic effect of probiotics: A systematic review and meta-analysis of the clinical and preclinical literature – Daniel J Reis – PLOS ONE

Phages and viruses

Pre-print: Megaphage infect Prevotella and variants are widespread in gut microbiomes – Audra E Devoto – bioRxiv

Bacteria art

Fifty Percent Human – how art brings us in touch with our microbial cohabitants – Sonja Bäumel – Microbial Biotechnology

Scottish fashion student who grows dresses from tea brews up storm in fashion world – Daily Record

artist reimagines the human microbiome as an intricately cut paper coral reef – design bloom

The next big home design trend? Bacteria – Co.Design

Science, career, and publishing

Pre-print: Career Choice, Gender, and Mentor Impact: Results of the U.S. National Postdoc Survey – Sean C McConnell – bioRxiv

June 15, 2018

Posted on by

Secondary metabolite biosynthetic genes from novel soil bacteria, a human viral protein cluster metagenomic database, sleep apnea symptoms alter the gut microbiota and metabolome.

Pregnancy and early life

16S ribosomal RNA-based gut microbiome composition analysis in infants with breast milk jaundice – Miao Duan – Open Life Sciences

Human respiratory microbiome

Pre-print: New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for species-level identification of microbiome data from the aerodigestive tract – Isabel Fernández Escapa – bioRxiv

Human oral microbiome

Review: Live and let die: hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome – Sylvio Redanz – Molecular Oral Microbiology

Human nearly-sterile sites

Cultural Isolation and Characteristics of the Blood Microbiome of Healthy Individuals – Stefan Panaiotov – Advances In Microbiology

Human gut microbiome

Sex differences in NSAID-induced perturbation of human intestinal barrier function and microbiota – Shoko Edogawa – The FASEB Journal

Animal experiments

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome – Anupriya Tripathi – mSystems

IL-1R and MyD88 Contribute to the Absence of a Bacterial Microbiome on the Healthy Murine Cornea – Stephanie J Wan – Frontiers in Microbiology

Aflatoxin B1 Disrupts Gut-Microbial Metabolisms of Short-Chain Fatty Acids, Long-Chain Fatty Acids, and Bile Acids in Male F344 Rats – Jun Zhou – Toxicological Sciences

Metabolome and gut microbiota variation with long-term intake of Panax ginseng extracts on rats – Yifan Sun – Food & Function

Animal microbiome

Partial incubation during egg laying reduces eggshell microbial loads in a temperate‐breeding passerine – Patricia B Bollinger – Journal of Avian Biology

Bacterial and Fungal Midgut Community Dynamics and Transfer Between Mother and Brood in the Asian Longhorned Beetle (Anoplophora glabripennis), an Invasive Xylophage – Charles J Mason – Microbial Ecology

Succession of embryonic and the intestinal bacterial communities of Atlantic salmon (Salmo salar) reveals stage‐specific microbial signatures – Jep Lokesh – MicrobiologyOpen

Plant, root, and soil microbiome

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis – Alexander Crits-Christoph – Nature

Environment and host as large-scale controls of ectomycorrhizal fungi – Sietse van der Linde – Nature

Studies on Quantitative Analysis of Rhizosphere and Non-Rhizosphere Mycoflora at Different Stages of Plant Growth in Different Varieties of Pigeon Pea [Cajanus cajan (L.) Millsp.] – V Jalander – International Journal of Pure & Applied Bioscience

The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata – Casper N Kamutando – Microbial Ecology

Review: Plant Growth Promoting Rhizobacteria: Blessing to Agriculture – Twisha S Patel – International Journal of Pure & Applied Bioscience

Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities – Vanessa N Kavamura – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway – Gourvendu Saxena – mSystems

Phages and viruses

The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation – Ali H A Elbehery – Frontiers in Microbiology

Bioinformatics

BioSankey: Visualization of Microbial Communities Over Time – Alexander Platzer – Journal of Integrative Bioinformatics

Pre-print: Understanding trivial challenges of microbial genomics: An assembly example – Delphine Lariviere – bioRxiv

Microbes in the news

Faecal transplants could help preserve vulnerable species – Sara Reardon – Nature

Science, career, and publishing

Pre-print: Researchers preferentially collaborate with same-gendered colleagues across the life sciences – Luke Holman – bioRxiv

Pre-print: Attitudes, Perceptions and Barriers to Research and Publishing among Research and Teaching Staff: A Case Study – Stanley Irobekhian Reuben Okoduwa – bioRxiv

June 13, 2018

Posted on by

Events and jobs

Computational scientists (from post-master to postdoc fellowships) in metagenomics and microbial genomics : Trento, Italy – The Laboratory of Computational Metagenomics

General microbiome

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative – Jun Wang, Microbiome Announcement

Microbial ecology

Everything is not everywhere: a tale on the biogeography of cyanobacteria – Karine Felix Ribeiro, Hydrobiologia

A Meta‐Analysis of Temperature Sensitivity as a Microbial Trait – Charlotte J. Alster, Global Change Biology

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities – John Davison, ISME

Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes – Dehong Zheng, Microbiological Research

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity – Ambrin Sarwar, Plos One

Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes – Claudia Coleine, Frontiers in Microbiology

Pregnancy and early life

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis – Stephen Wandro, mSphere

The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci – Hiie Soeorg, Pediatric Research

Multisite human microbiome

Prion-like Propagation of α-synuclein in the gut-brain axis – Ying Chen, Brain Research Bulletin

Microbiome-Gut-Brain Axis and Toll-Like Receptors in Parkinson’s Disease – Valentina Caputi, International Journal of Molecular Sciences

Current Insights in Microbiome Shifts in Sjogren’s Syndrome and Possible Therapeutic Interventions – Christina Tsigalou, Frontiers in Immunology

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome between Neonatal Intensive Care Unit (NICU) Environments – Suchitra K. Hourigan, Frontiers in Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood, Scientific Reports

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B. Dréno, Journal of the European Academy of Dermatology and Venereology

Characterisation of Cutibacterium acnes phylotypes in acne and in vivo exploratory evaluation of Myrtacine® – S. Pécastaings, Journal of the European Academy of Dermatology and Venereology

Human oral microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise  Tornavoi de Castro, Archives of Oral Biology

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis – Franco Cavalla, Genes

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK – Andrew G Farrer, bioRxiv

Human gut microbiome

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders – Clive H. Wilder-Smith, United European Gastroenterology Journal

The Intersection Between Colonization Resistance, Antimicrobial Stewardship, and Clostridium difficile – Rossana Rosa, Current Infectious Disease Reports

Celiac Disease and Fecal Microbiota Transplantation: A New Beginning? – Shmuel Golfeyz MD, Correspondence

Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial – Yoriko Heianza, Nutrition

Cutting the Gordian Knot of the Microbiota – Kimberly S.Vasquez, Molecular Cell

Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects – Kajetan Trost, Food Research International

Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults – Hee-Young Kim, Journal of Functional Foods

Animal experiments

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang, Molecular Nutrition and Food Research

Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: a meta-analysis of controlled trials – Chhaiden Heak, Asian-Australasian Journal of Animal Sciences

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza, Journal of Functional Foods

The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells – Alexi A. Schoenborn, Gut Microbes

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter – Umer Zeeshan Ijaz, bioRxiv

Microbial quantity impacts Drosophila nutrition, development, and lifespan – Erin S. Keebaugh, iScience

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica) – Narjis Kraimi, Frontiers in Physiology

Animal microbiome

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains – Simona Kraberger, Infection, Genetics and Evolution

Diverse novel resident Wolbachia strains in Culicine mosquitoes from Madagascar – Claire L Jeffries, bioRxiv

Sample treatment optimization for fish stool metabolomics – Takeshi Hano, Journal of Chromatography B

Plant, root, and soil microbiome

Two decades of altered snow cover does not affect soil microbial ability to catabolize carbon compounds in an oceanic alpine heath – E.R. Jasper Wubs, Soil Biology and Biochemistry

Grazing and resource availability control soil nematode body size and abundance‐mass relationship in semi‐arid grassland – W. S. Andriuzzi, Journal of Animal Ecology

Isolation and screening of antibiotic producing actinomycetes from rhizosphere and agricultural soils – Atsede Muleta, African Journal of Biotechnology

Responses of Bougainvillea spectabilis to elevated atmospheric CO2 under galaxolide (HHCB) pollution and the mechanisms of its rhizosphere metabolism – Minzhe Zhang, Journal of Soils and Sediments

Differential effect of the nitrogen form on the leaf gas exchange, amino acid composition, and antioxidant response of sweet pepper at elevated CO2 – María C. Piñero, Plant Growth Regulation

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China – Dan-Ting Yu, Journal of Soils and Sediments

Efficacy of Bacillus subtilis native strains for biocontrol of Phytophthora crown and root rot of pistachio in Iran – Mohammad Moradi, Tropical Plant Pathology

Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants – Allison M. Veach, Plant and Soil

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China – Hao Guan, Bioresource Technology

Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis – Monali C. Rahalkar, 3 Biotech

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil – Xiao-Han Wang, Environmental Pollution

Enhanced removal of nitrate in the maize rhizosphere by plant growth-promoting Bacillus megaterium NCT-2, and its colonization pattern in response to nitrate – Shaohua Chu, Chemosphere

Bioactive luteoloside produced by Myroides odoratimimus, solvent-tolerant bacterium form the rhizosphere of Lonicera japonica –  Y. X. Zhao, Natural Product Research

Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion – Jayanta  Kumar Biswas, Geoderma

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li, Science of The Total Environment

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Analysis on metabolic functions of stored rice microbial communities by BIOLOG ECO microplates – Zhiwen Ge, Frontiers in Microbiology

Effects of discrete bioactive microbial volatiles on plants and fungi – Birgit Piechulla, Plant, Cell, and Environment

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship – Marta Goberna, ISME

Similar soil microbial community structure across different environments after long‐term succession: evidence from volcanoes of different ages – Shangqi Xu, Journal of Basic Microbiology

Water and extremophile microbiome

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network – Wei Huang, Microbiology Open

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant – Zhen Yu, Bioresource Technology

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom – Ivan S. Mikhailov, Microbial Ecology

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra – Maria Väisänen, Microbial Ecology

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) – M. Cellamare, FEMS Microbiology Ecology

Methanogens in the Antarctic Dry Valley Permafrost – Tatiana A. Vishnivetskaya, FEMS Microbiology Ecology

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India – Mingma Thundu Sherpa, Indian Journal of Microbiology

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase – Suhyun Kim, bioRxiv

Assessing the effect of pretreatments on the structure and functionality of microbial communities for the bioconversion of microalgae to biogas – Olivia Córdova, Frontiers in Microbiology

Great Salt Lake microbiology: a historical perspective – Bonnie K. Baxter, International Microbiology

Life from the ashes: survival of dry bacterial spores after very high temperature exposure – Lynda Beladjal, Extremophiles

Microbial and geochemical controls on waste rock weathering and drainage quality – Sharon Blackmore, Science of The Total Environment

Characterization and high-throughput sequencing of a trichlorophenol-dechlorinating microbial community acclimated from sewage sludge – Jiaxiu Song, Journal of Cleaner Production

Impacts of surface-applied residues on N-cycling soil microbial communities in miscanthus and switchgrass cropping systems – Karen A. Thompson, Applied Soil Ecology

Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments – Xiaobo Liu, International Biodeterioration & Biodegradation

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen, Bioresource Technology

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant – Carlos Narciso-da-Rocha, Environment International

Impact of organic waste composition on life cycle energy production, global warming and Water use for treatment by anaerobic digestion followed by composting – Sara A. Pace, Resources, Conservation and Recycling

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms – Boštjan Murovec, Journal of Environmental Management

Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia – Joany Babilonia, Frontiers in Microbiology

Assessing the abundance of fungal populations in a full-scale membrane bioreactor (MBR) treating urban wastewater by using quantitative PCR (qPCR) – P. Maza-Márquez, Journal of Environmental Management

Food microbiology

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa – Marcel Houngbédji, Food Microbiology

Probiotics / prebiotics

Probiotics in IBD: Combining in vitro and in vivomodels for selecting strains with both anti-inflammatory potential as well as a capacity to restore the gut epithelial barrier – Mazen Zaylaa, Journal of Functional Foods

Can prebiotics assist in the management of cognition and weight gain in schizophrenia? – Amy Chia-Ching Kao, Psychoneuroendocrinology

Probiotic potentials of Lactobacillus plantarum isolated from fermented durian (Tempoyak), a Malaysian traditional condiment – Asmariah Ahmad, Food Science and Nutrition

Bioinformatics

Identifying Heritable Communities of Microbiome by Root-Unifrac and Wishart Distribution – Yunfan Tang, bioRxiv

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive – Pedro J. Torres, Bioinformatics

Techniques

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community – Alexandra Perras, bioRxiv

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides – Evan F. Haney, Biomolecules

June 12, 2018

Posted on by

Gut and General Microbiome

Screening for Nonalcoholic Fatty Liver Disease in Inflammatory Bowel Diseases: A Cohort Study Using Transient Elastography – Chiara Saroli Palumbo – Inflammatory Bowel Diseases

Review: A critical appraisal of advances in the diagnosis of diverticular disease – Antonio Tursi – Expert Review of Gastroenterology & Hepatology  

Antimicrobial-Induced Cytopenia and Bone Marrow Hypocellularity in Patients with Cirrhosis – Anupama Patil – Bone Marrow Research

Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia – Ahmed O. Alomair – Gastroenterology Research and Practice

Connecting homocysteine and obesity through pyroptosis, gut microbiome, epigenetics, peroxisome proliferator-activator receptor γ (PPARγ) and zinc finger protein 407 (Zfp407) – Anwesha Laha – Canadian Journal of Physiology and Pharmacology

Review: Sexual dimorphism of cardiometabolic dysfunction: Gut microbiome in the play? – Tzu-Wen L. Cross – Molecular Metabolism

Individuality and convergence of the infant gut microbiota during the first year of life – Eric J. de Muinck – Nature Communications

Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gut – Gabriele Andrea Lugli – Applied and Environmental Microbiology

Commentary: Beyond Oxalobacter: the gut microbiota and kidney stone formation – Gwen Falony – Gut

Nutritional modulation of the intestinal microbiota: future opportunities for the prevention and treatment of neuroimmune and neuroinflammatory disease – Vincent C.Lombardi – The Journal of Nutritional Biochemistry

 

Reproductive and Urinary Tract Microbiome

Review: Implantation failure of endometrial origin: what is new? –  Jose Bellver – Current Opinion in Obstetrics and Gynecology

Detecting viral genomes in the female urinary microbiome – Andrea Garretto – Journal of General Virology

Commentary: Regional Caesarean Delivery Practices, the Maternal-Infant Microbiome, and Risk for Asthma – Rebecca Entz – Journal of Obstetrics and Gynaecology Canada

 

Skin Microbiome

Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil – Paulo E. S. Silva – Scientific Reports

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood – Scientific Reports

 

Oral and Respiratory Microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise Tornavoide Castro – Archives of Oral Biology

Bacterial biogeography of adult airways in atopic asthma – Juliana Durack – Microbiome

Review: Adenotonsillar microbiome: an update – James Jordan Johnston – Postgraduate Medical Journal

 

Animal Microbiome

The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system – Meredith A. J. Hullar – PLOS ONE

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang – Molecular Nutrition & Food Research

Deficiency of BrpA in Streptococcus mutans Reduces Virulence in Rat Caries Model – Zezhang T. Wen – Molecular Oral Microbiology

Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure – Xue-Ying Zhang – Microbiome

Abnormal gut microbiota composition contributes to cognitive dysfunction in SAMP8 mice – Gaofeng Zhan – Aging

The role of regulator FucP in Edwardsiella tarda pathogenesis and the inflammatory cytokine response in tilapia – Jiayan Wu – Fish & Shellfish Immunology

Malassezia pachydermatis from animals: Planktonic and biofilm antifungal susceptibility and its virulence arsenal – Raimunda Sâmia Nogueira Brilhante – Veterinary Microbiology

 

Beneficial Microbes

Oral administration of Bifidobacterium bifidum TMC3115 to neonatal mice may alleviate IgE-mediated allergic risk in adulthood – R.Y. Cheng – Beneficial Microbes

Three-Month Feeding Integration With Bifidobacterium Strains Prevents Gastrointestinal Symptoms in Healthy Newborns – Irene Aloisio – Frontiers in Nutrition

 

Bioinformatics and Genomics

Review: Interrogating the microbiome: experimental and computational considerations in support of study reproducibility – Carine Poussin – Drug Discovery Today

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software – Toby J. Wilkinson – Frontiers in Microbiology

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity – Andrea Hahn – Frontiers in Microbiology

Next-Generation Machine Learning for Biological Networks – Diogo M. Camacho – Cell