June 3, 2018

Today’s digest full of great and fun studies including a fungal survey of the atmosphere and links between gut microbiome and MS.

General Microbiome

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Egert M. Methods

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.Cardona C. mSystems

Biohydrogen production from space crew’s waste simulants using thermophilic consolidated bioprocessing.Wang J. Bioresource Technology

Prevalence of <i>Trichomonas vaginalis</i> infection and protozoan load in South African women: a cross-sectional study.de Waaij DJ.BMJ Open

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.Seridi L. PLoS One

Gut Microbiome

A gut feeling about multiple sclerosis.Quintana FJ. Proceedings of the National Academy of Sciences

Dietary fat and gut microbiota: mechanisms involved in obesity control.Coelho OGL. Critical Reviews in Food Science and Nutrition

Probiotic Species in the Modulation of Gut Microbiota: An Overview.Azad MAK J. Biomedical Research International.

The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.Lv Y. Journal of Diabetes Research

The Gut Microbiome Profile in Obesity: A Systematic Review.Castaner O. International Journal of Endocrinology.

The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation.O’Flaherty S. mSphere

Skin Microbiome

Early-life skin microbiota in hospitalized preterm and full-term infants.Younge NE. Microbiome.

Oral Microbiome

Stimulated and unstimulated saliva samples have significantly different bacterial profiles.Gomar-Vercher S. PLoS

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.Presti RM. AIDS

Oral microbiota in youth with perinatally acquired HIV infection. Starr JR. Microbiome

Air and Water Microbiome

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland.Cousins CR. Geobiology

Taxonomic diversity of fungi deposited from the atmosphere.Woo C. ISME Journal.

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.Garcia SL. mSphere.

Animal Experiments and Microbiome

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.Zhang Z. Microbiome

Longevity extension in Drosophila through gut-brain communication.Westfall S. Scientific Reports

Exploring the diversity-stability paradigm using sponge microbial communities.Glasl B. Scientific Reports

Exploring the Microbiome of Callinectes sapidus (Maryland Blue Crab).Ramachandran P. Genome Announcements

Effect of different types of olive oil pomace dietary supplementation on the rumen microbial community profile in Comisana ewes.Mannelli F. Scientific Reports

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period.Salem SE. Scientific Reports

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus).Mekuchi M. PLoS One

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.Herstad KMV.PLoS One

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera). Ziganshina EE. Biomedical Research International.

Plant and Soil Microbiomes

Antibiotic Resistance in Plant-Pathogenic Bacteria. Sundin GW. Annual Review of Phytopathology

Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with <i>Salicornia</i> for Treatment of Marine Aquaculture Effluents.Ma X. Archaea.

Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses.Acevedo FE. Molecular Plant-Microbe Interactions

Multifunctional potential of endophytic and rhizospheric microbial isolates associated with Butia purpurascens roots for promoting plant growth.da Silva CF. Antonie Van Leeuwenhoek

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.Gołębiewski M. Microbial Ecology

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.Bartoli C. ISME Journal.

 

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May 9, 2018

Have a good Wednesday! Today, we have an interesting set of papers about the effect of different compounds on microbiota, as well the effect of some probiotics. We have also a paper about the use binding of  immunoglobulin A by gut microbiota commensals as a potential mechanism for stabilization; we have also papers about virome from urinary and female reproductive tracts, a study a multi-site study of maternal microbiota.

Gut and General Microbiome

Introduction: The host-associated microbiome: Pattern, process and function – Laura Wegener Parfrey – Molecular Ecology (Special Issue: The host-associated microbiome: Pattern, process and function)

Gut microbiota utilize immunoglobulin A for mucosal colonization – G. P. Donaldson – Science

Low Maternal Microbiota Sharing across Gut, Breast Milk and Vagina, as Revealed by 16S rRNA Gene and Reduced Metagenomic Sequencing – Ekaterina Avershina – Genes

Editorial: Bacteria in the ageing gut: Did the taming of fire promote a long human lifespan?Antoine Danchin – Environmental Microbiology

Commentary: Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives – Lijuan Sun – Protein & Cell

Review: Gut microbiota derived metabolites in cardiovascular health and disease – Zeneng Wang – Protein & Cell

Treating Clostridium difficile infections: Should fecal microbiota transplantation be reclassified from investigational drug to human tissue?Mark StuntzContemporary Clinical Trials Communications

Effects of intestinal colonization by Clostridium difficile and Staphylococcus aureus on microbiota diversity in healthy individuals in China – Danfeng Dong – BMC Infectious Diseases

BaiCD gene cluster abundance is negatively correlated with Clostridium difficile infection – Philipp Solbach – PLoS ONE

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science ProjectNatalia S. Klimenko – Nutrients

Respiratory Tract Microbiome

Relation between lower respiratory tract microbiota and type of immune response against tuberculosis – Maede Nakhaee – Microbial Pathogenesis

Microbiome characteristics of induced sputum compared to bronchial fluid and upper airway samples – Shi‐qi An – Pediatric Pulmonology

The association between inflammation, the microbiome and urethane-induced pulmonary adenocarcinoma – Zenghua Deng – Oncology Letters

Urinary/Reproductive Tract Microbiome

Urinary Virome Perturbations in Kidney Transplantation – Tara K. Sigdel – Frontiers in Medicine

The Vaginal Eukaryotic DNA Virome and Preterm Birth – Kristine M. Wylie – American Journal of Obstetrics and Gynecology

Beneficial Microbes and Compounds

Walnut Consumption Alters the Gastrointestinal Microbiota, Microbially Derived Secondary Bile Acids, and Health Markers in Healthy Adults: A Randomized Controlled TrialHannah D Holscher – The Journal of Nutrition

The effect of vitamin D on intestinal inflammation and faecal microbiota in patients with ulcerative colitis – Mayur Garg – Journal of Crohn’s and Colitis

Exopolysaccharide from Bifidobacterium longum subsp. longum 35624™ modulates murine allergic airway responses – E. Schiavi – Beneficial Microbes

Modulatory effect of three probiotic strains on infants’ gut microbial composition and immunological parameters on a placebo-controlled, double-blind, randomised study – J. De Andrés – Beneficial Microbes

Review: Role of Lactobacillus reuteri in Human Health and Diseases – Qinghui Mu – Frontiers in Microbiology

Intake of phytic acid and myo-inositol lowers hepatic lipogenic gene expression and modulates gut microbiota in rats fed a high-sucrose diet – Yukako Okazaki – Biomedical Reports

Animal Microbiome

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – Scientific Reports

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Endophytic Fungi in Species of Artemisia – Andreea Cosoveanu – Journal of Fungi

Tributyltin exposure induces gut microbiome dysbiosis with increased body weight gain and dyslipidemia in mice – Hao Guo – Environmental Toxicology and Pharmacology

Food Microbiome

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms – Van Thi Thuy Ho – International Journal of Food Microbiology

Validation of standard method EN ISO 22964:2017 – Microbiology of the food chain – Horizontal method for the detection of Cronobacter sppAmparo de Benito – International Journal of Food Microbiology

Plant and Soil Microbiome

Mycobiome analysis of asymptomatic and symptomatic Norway spruce trees naturally infected by the conifer pathogens Heterobasidion spp. – Andriy Kovalchuk – Environmental Microbiology Reports

Perspective: Core microbiomes for sustainable agroecosystems – Hirokazu Toju – Nature Plants

Meetings: Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystemsDenis Faure – New Phytologist

Other

Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion – Susanne Theuerl – Bioresource Technology

 

April 24, 2018

Today, after a hiatus, we have a new and big digest. Have a good Tuesday!

Gut Or General Microbiome

Editorial: Metagenomics, culturomics, and the human gut microbiota – Sophie Amrane – Expert Review of Anti-infective Therapy

Review: Disruptions in gut microbial-host co-metabolism and the development of metabolic disorders – Cynthia Rajani – Clinical Science

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – Microbiome

Review: Factors influencing horizontal gene transfer in the intestine – Ximin Zeng – Animal Health Research Reviews

Commentary: Help, hope and hype: ethical considerations of human microbiome research and applications – Yonghui Ma – Protein & Cell

A System Biology Perspective on Environment-Host-Microbe Interactions – Lianmin Chen – Human Molecular Genetics

Comment on: effects of sleeve gastrectomy on the composition and diurnal oscillation of gut microbiota related to the metabolic improvements – Tammy L.Kindel – Surgery for Obesity and Related Diseases

Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine – Francesca De Filippis – Inflammatory Bowel Diseases

Targeting the gut microbiome to treat the osteoarthritis of obesity – Eric M. Schott – JCI Insight

Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: the PROFICEL study – Marta Olivares –  Gut Microbes

Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora – Awa Diop – Microbiology Open

Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions – Michail Mamantopoulos – Gut Microbes

No Significant Association Between the Fecal Microbiome and the Presence of Irritable Bowel Syndrome-type Symptoms in Patients with Quiescent Inflammatory Bowel Disease – Oliver Shutkever –  Inflammatory Bowel Diseases

Research Highlight: Microbiome promotes pancreatic cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Deciphering human gut microbiota-nutrient interactions: a role for biochemistry – Carina Chittim – Biochemistry

Letter: Defining the Impact of Host Genotypes on Microbiota Composition Requires Meticulous Control of Experimental Variables –  Andy Wullaert – Cell Immunity

Review: Engineered Human Gastrointestinal Cultures to Study the Microbiome and Infectious Diseases – Sarah E.Blutt – Cellular and Molecular Gastroenterology and Hepatology

The Role of Macrophage Migration Inhibitory Factor in the Function of Intestinal Barrier – Milica Vujicic- Scientific Reports

Perspective: Urbanization and the gut microbiota in health and inflammatory bowel disease – Tao Zuo – Nature Reviews Gastroenterology & Hepatology

A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer – QuanQiu Wang – Scientific Reports

Review: The human gut microbiota: metabolism and perspective in obesity – Aline Corado Gomes – Gut Microbes

Association between the Dietary Inflammatory Index (DII) and urinary enterolignans and C-reactive protein from the National Health and Nutrition Examination Survey-2003-2008 – Nitin Shivappa – European Journal of Nutrition

Case Report: The Effect of Fecal Microbiota Transplantation on a Child with Tourette Syndrome – Huijun Zhao – Case Reports in Medicine

Current evidence linking diet to gut microbiota and brain development and function – Florencia Ceppa – International Journal of Food Sciences and Nutrition

Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation – Marlena Maziarz – Bioinformatics

Review: Gut microbiota, metabolism and psychopathology: A critical review and novel perspectives – Robin N. Groen – Critical Reviews in Clinical Laboratory Sciences

The Role of Gut Microbiota in Obesity and Type 2 and Type 1 Diabetes Mellitus: New Insights into “Old” Diseases – Igor Alexander Harsch – Medical Sciences

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – PLoS Computational Biology

 

Respiratory Microbiome

Prenatal antibiotic exposure and childhood asthma: a population-based study – Keely Loewen – European Respiratory Journal

Impact of gut colonization with butyrate producing microbiota on respiratory viral infection following allo-HCT – Bastiaan W. Haak – Blood

Oropharyngeal and nasopharyngeal decontamination with chlorhexidine gluconate in lung cancer surgery: a randomized clinical trial – Xavier Benoit D’Journo – Intensive Care Medicine

Impact of Long-Term Erythromycin Therapy on the Oropharyngeal Microbiome and Resistance Gene Reservoir in Non-Cystic Fibrosis Bronchiectasis – Jocelyn M. Choo – mSphere

Neonates colonized with pathogenic bacteria in the airways have a low-grade systemic inflammation – Nadia Rahman Fink – Allergy

Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions – Tatsuo Ichinohe – Frontiers in Immunology

 

Oral Microbiome

Metagenomic analysis of oral microbiome in young children aged 6‐8 y living in a rural isolated Chinese province – Yuan Xu – Oral Diseases

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis – Emily M. Nowicki – mBio

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis – Daniel Hagenfeld – PLoS One

The interplay between oral microbiome, lifestyle factors and genetic polymorphisms in the risk of oral squamous cell carcinoma – Jenn-Ren Hsiao – Carcinogenesis

Dynamic Alterations in Salivary Microbiota Related to Dental Caries and Age in Preschool Children With Deciduous Dentition: A 2-Year Follow-Up Study – Lei Xu – Frontiers in Physiology

 

Reproductive / Urinary tract Microbiome

How uterine microbiota might be responsible for a receptive, fertile endometrium – Marilen Benner – Human Reproduction Update

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota – Krystal Thomas-White – Nature Communications

 

Fecal Microbiota Transplant

Editorial: Is fecal microbiota transplantation a temporary patch for treatment of Clostridium difficile infection or a new frontier of therapeutics? – Alexander Khoruts – Expert Review of Gastroenterology & Hepatology

Case Report: ANCA Vasculitis and Hemophagocytic Lymphohistiocytosis following a Fecal Microbiota Transplant – Adam Amlani – Case Reports in Rheumatology

Regional variability in fecal microbiota transplantation practices: a survey of the Southern Ontario Fecal Microbiota Transplantation Movement – Susy S. Hota – CMAJ Open

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O. Anonye – Frontiers in Cellular and Infection Microbiology

Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice – Quentin Le Bastard – Scientific Reports

 

Animal Microbiome and Animal Experiments

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates – Joshua M. Taylor​​ – PeerJ

Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser – Wen Wang – Journal of Basic Microbiology

Exposure to concentrated ambient PM2.5 alters the composition of gut microbiota in a murine model – Wanjun Wang – Particle and Fibre Toxicology

Imidacloprid decreases honey bee survival but does not affect the gut microbiome – Kasie Raymann – Applied and Environmental Microbiology

Letter: Bile Acids and the Microbiome in the Cow: Lack of Deoxycholic Acid Hydroxylation – Alan F. Hofmann – Lipids

Akkermansia muciniphila can reduce the damage of gluco/lipotoxicity, oxidative stress, and inflammation and normalize intestine microbiota in streptozotocin-induced diabetic rats – Ling Zhang – Pathogens and Disease

The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster – Lisa Jehrke –  Scientific Reports

Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex – Lisanne M G Verschuren – Journal of Animal Science

Discovery of a mcr-1-bearing plasmid in commensal colistin-resistant Escherichia coli from healthy broilers in Faisalabad, Pakistan – Jiali Lv – Virulence

Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection – Laura Markey – Gut Microbes

PCBs-high-fat diet interactions as mediators of gut microbiota dysbiosis and abdominal fat accumulation in female mice – Yulang Chi – Environmental Pollution

Metagenome and Culture-Based Methods Reveal Candidate Bacterial Mutualists in the Southern House Mosquito (Diptera: Culicidae) – Aparna Telang – Journal of Medical Entomology

Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Potent SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents – Fuyong Du – Journal of Pharmacology and Experimental Therapeutics

Similarity of the dog and human gut microbiomes in gene content and response to diet – Luis Pedro Coelho – Microbiome

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology

Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra – Benedikt M. Mortzfeld – Frontiers in Microbiology

The effects of baicalein on cortical pro-inflammatory cytokines and the intestinal microbiome in senescence accelerated mouse prone 8 – Li Gao – ACS Chemical Neuroscience

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi – Zhuoran Han – Microbiology Open

 

Built Environments

A comparison of methods used to unveil the genetic and metabolic pool in the built environment – Cinta Gomez-Silvan – Microbiome

Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter – Mogul Rakesh – Astrobiology

 

Pathogen Research

The Critical Role of Zinc in a New Murine Model of Enterotoxigenic  E. coli 1 (ETEC) Diarrhea – DT Bolick  – Infection and Immunity

Review: Effects of antibiotic resistance (AR) and microbiota shifts on Campylobacter jejuni-mediated diseases – Phillip T. Brooks – Animal Health Research Reviews

A quality improvement initiative to reduce necrotizing enterocolitis across hospital systems – Amy T. Nathan – Journal of Perinatology

Quantitative Simulations Predict Treatment Strategies Against Fungal Infections in Virtual Neutropenic Patients – Sandra Timme – Frontiers in Immunology

Review: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li – Frontiers in Microbiology

Heterogeneous ceramide distributions alter spatially resolved growth of Staphylococcus aureus on human stratum corneum – Joseph M. Cleary – Journal of the Royal Society Interface

 

Viruses

Viral Diversity of House Mice in New York City – Simon H. Williams – mBio

Subclinical cytomegalovirus infection associates with altered host immunity, gut microbiota and vaccine responses – Clarissa Santos Rocha – Journal of Virology

 

Antimicrobial Research

Antimicrobial resistance: from basic science to translational innovation – Jun Lin –  Animal Health Research Reviews

 

Plant/Environment Microbiome

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria – Ling Xu – PNAS

Assessment of toxic impact of metals on proline, antioxidant enzymes, and biological characteristics of Pseudomonas aeruginosa inoculated Cicer arietinum grown in chromium and nickel-stressed sandy clay loam soils – Saima Saif – Environmental Monitoring and Assessment

The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing – Da‐Cheng Hao – Journal of Basic Microbiology

Exposure to nanoplastics disturbs the gut microbiome in the soil oligochaete Enchytraeus crypticus – Bo-Kai Zhu – Environmental Pollution

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region – Katarzyna Siegel-Hertz – Frontiers in Microbiology

 

Food Microbes

Towards better microbial safety of fresh produce: Chlorophyllin-based photosensitization for microbial control of foodborne pathogens on cherry tomatoes – Egle Paskeviciute – Journal of Photochemistry and Photobiology B: Biology

Metaproteomics of Microbiota in Naturally Fermented Soybean Paste, Da‐jiang – Ping Zhang – Journal of Food Science

 

Drugs, Beneficial Microbes and Compounds

Age-Related Changes in the Natural Killer Cell Response to Seasonal Influenza Vaccination Are Not Influenced by a Synbiotic: a Randomised Controlled Trial – Agnieszka Przemska-Kosicka – Frontiers in Immunology

4G-β-D-galactosylsucrose as a prebiotics may improve underweight in inpatients with schizophrenia – Takahiko Nagamine – Nihon Shokuhin Men’eki Gakkai

An approach on the potential use of probiotics in the treatment of skin conditions: acne and atopic dermatitis – Vitória H. M. Mottin – International Journal of Dermatology

Effects of Prebiotic Fiber Xylooligosaccharide in Adenine induced Nephropathy in Mice – Jieping Yang – Molecular Nutrition and Food Research

Anti-inflammatory effect of multistrain probiotic formulation (L. rhamnosus, B. lactis, and B. longum) – Marzia Sichetti – Nutrition

A combination of Lactobacillus mali APS1 and dieting improved the efficacy of obesity treatment via manipulating gut microbiome in mice – Yung-Tsung Chen – Scientific Reports

The Potential Effect of Chinese Herbal Formula Hongqijiangzhi Fang in Improving NAFLD: Focusing on NLRP3 Inflammasome and Gut Microbiota – Shu Liang – Evidence-Based Complementary and Alternative Medicine

Cationic amphiphilic bolaamphiphile-based delivery of antisense oligonucleotides provides a potentially microbiome sparing treatment for C. difficile – Arun K. Sharma – The Journal of Antibiotics

A probiotic modulates the microbiome and immunity in multiple sclerosis – Stephanie K. Tankou – Annals of Neurology

Comprehensive comparison of polysaccharides from Ganoderma lucidum and G. sinense: chemical, antitumor, immunomodulating and gut-microbiota modulatory properties – Li-Feng Li – Scientific Reports

Anti-diabetic mechanism of dietary polysaccharides based on their gastrointestinal functions – Jie-Lun Hu – Journal of Agricultural and Food Chemistry

The Effects of Synbiotic Supplementation on Body Mass Index, Metabolic and Inflammatory Biomarkers, and Appetite in Patients with Metabolic Syndrome: A Triple-Blind Randomized Controlled Trial – Samira Rabiei – Journal of Dietary Supplements

 

Bioinformatics and Methods

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs – Daniel H. Huson – Biology Direct

KDiamend: a package for detecting key drivers in a molecular ecological network of disease – Mengxuan Lyu – BMC Systems Biology

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications – Joost Theo Petra Verhoeven – Canadian Journal of Microbiology

Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members – Vivek Keshri – Genome Biology and Evolution

 

March 22, 2018

Of special note today: A randomized double blind controlled clinical trial on the impacts of probiotics on Alzheimer’s demonstrated an improvement in cognitive function, triglycerides, insulin sensitivity and C reactive protein; and a meta-analysis of the lung microbiome in tuberculosis identified specific species that are characteristic of the disease.

Events and jobs

Research Associate – Kintai Therapeutics – Cambridge, MA

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Human respiratory microbiome

*Meta-analysis of the lung microbiota in pulmonary tuberculosis – Bo-young Hong – Tuberculosis

Human skin microbiome

Longitudinal study of the psoriasis-associated skin microbiome during therapy with ustekinumab in a randomized Phase 3b clinical trial – Michael Loesche – Journal of Investigative Dermatology

Human oral microbiome

The subgingival microbiome in patients with established rheumatoid arthritis – Ted R Mikuls – Rheumatology

Self-reported bovine milk intake is associated with oral microbiota composition – Ingegerd Johansson – PLOSone

Human uro-genital microbiome

A Distinctive Urinary Metabolomic Fingerprint Is Linked With Endoscopic Postoperative Disease Recurrence in Crohn’s Disease Patients – Ammar Hassanzadeh Keshteli – Inflammatory Bowel Diseases

Human gut microbiome

Review: Interrelation of Diet, Gut Microbiome, and Autoantibody Production – Ioanna Petta – Frontiers in Immunology

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Animal experiments

Microbiome-metabolome signatures in mice genetically prone to develop dementia, fed a normal or fatty diet – Elena Sanguinetti – Scientific Reports

Influence of dietary protein and fructooligosaccharides on fecal fermentative end-products, fecal bacterial populations and apparent total tract digestibility in dogs – Carlo Pinna – BMC Veterinary Research

Animal microbiome

Review: The tripartite interactions between the mosquito, its microbiota and Plasmodium – Ottavia Romoli – BMC Parasites & Vectors

Nutrient-Dependent Impact of Microbes on Drosophila suzukii Development – XiaoLi Bing – mBio

Lower dietary concentrate level increases bacterial diversity in the rumen of Cervus elaphus yarkandensis – Wenxi Qian- Canadian Journal of Microbiology

Evaluation of milk sample fractions for characterization of milk microbiota from healthy and clinical mastitis cows – Svetlana Ferreira Lima – PLOSone

Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ

Effects of high ambient temperature on the community structure and composition of ileal microbiome of broilers – X J Wang – Poultry Science

Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv

Plant, root, and soil microbiome

High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits – Marta Maciejewska – Antibiotics

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly – Kateryna Zhalnina – Nature Microbiology

Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms – Ma del Carmen Orozco-Mosqueda – Microbiological Research

Specificity in Arabidopsis thaliana recruitment of root fungal communities from soil and rhizosphere – Hector Urbina – Fungal Biology

Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth – Terry J. McGenity – The ISME Journal

Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system – Ilonka C. Engelhardt – The ISME Journal

Water and extremophile microbiome

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition – Geoff A. Christensen – PLOSone

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

Microbial parasites make cyanobacteria blooms less of a trophic dead end than commonly assumed – Matilda Haraldsson – The ISME Journal

Air Microbiome

Deposition rates of viruses and bacteria above the atmospheric boundary layer
– Isabel Reche – The ISME Journal

Microbial Ecology

Review: Understanding Microbiome Stability in a Changing World – Ashley Shade – mSystems

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Probiotics / prebiotics

*Effect of Probiotic Supplementation on Cognitive Function and Metabolic Status in Alzheimer’s Disease: A Randomized, Double-Blind and Controlled Trial – Elmira Akbari – Frontiers in Aging Neuroscience

Bioinformatics

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes – Joel A Boyd – Nucleic Acids Research

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing – Hiroshi Mori – BMC Systems Biology

Machine learning for tackling microbiota data and infection complications in immunocompromised patients with cancer – J. Luis Espinoza – Journal of Internal Medicine

A highly adaptive microbiome-based association test for survival traits – Hyunwook Koh – BMC Genomics

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Microbes in the news

Making intricate images with bacterial communities – Psy.Org

Many Non-Antibiotic Drugs Affect Gut Bacteria. A new study finds that more than 200 human-targeted, non-antibiotic drugs inhibit the growth of bacterial species that make up part of the human microbiome – Catherine Offord

‘New life form’ answers question about evolution of cells – Science Daily

Bacteria and Art

This watercolour painting was created by artistic bacteria – Sarah Roberts had a germ of an idea: let bacteria take creative control – Anna Marks – Wired

Crocheted and Embroidered Bacteria Grow in Elin Thomas’s Fiber Art Petri Dishes – Laura Staugaitis – Colossal

 

March 1, 2018

Quite a few articles on viruses today: The identification of human-like hormones in viral genomes that can bind to human and murine receptors; identification of multiple Antarctic sea-ice bacteriophages that are only active in the cold; bacterial immunity loss explains bacteria/phage co-existence; and the plans for a global virome project.

Pregnancy and early life

The microbiome and metabolome of pre-term infant stool is personalized, and not driven by health outcomes including necrotizing enterocolitis and late-onset sepsis -Stephen Wandro – bioRxiv

Review: Relationships Between Perinatal Interventions, Maternal-Infant Microbiomes, and Neonatal Outcomes – Gregory Valentine – Clinics in Perinatology

Human respiratory microbiome

Review: The Respiratory Microbiome in COPD – Orla O’Carroll – COPD – An Update in Pathogenesis and Clinical Management

Human vaginal microbiome

Bacterial identification of the vaginal microbiota in Ecuadorian pregnant teenagers: an exploratory analysis – Ana María Salinas – PeerJ

Human gut microbiome

Dissertation: Multi-Omic Analysis of Complex Microbial Communities in Gastrointestinal Lavage Fluid and their Association with Pancreatic Ductal Adenocarcinoma – Brittany Ferguson-Williams – University of South Alabama

Gut microbiota diversity according to dietary habits and geographical provenance – Bruno Senghor – Human Microbiome Journal

Intestinal microbiota, metabolome and gender dimorphism in autism spectrum disorders – Rafail I.Kushak – Research in Autism Spectrum Disorders

Review: A gut feeling: Microbiome-brain-immune interactions modulate social and affective behaviors – Kristyn E.Sylvia – Hormones and Behavior

Gorillibacterium timonense sp. nov. and Vitreoscilla massiliensis sp. nov., two new bacterial species isolated from stool specimens of obese Amazonian patients – Sokhna Ndongo – New Microbes and New Infections

«Collinsella provencensis» sp. nov., «Parabacteroides bouchesdurhonensis» sp. nov., and «Sutterella seckii» sp. nov., three new bacterial species identified from human gut microbiota – Niokhor Dione – New Microbes and New Infections

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Animal experiments

Gastrointestinal colonisation and systemic spread of Candida albicans in mice treated with antibiotics and prednisolone – Michiyo Kobayashi-Sakamoto – Microbial Pathogenesis

Effects of non-purified and semi-purified commercial diets on behaviors, plasma corticosterone levels, and cecum microbiome in C57BL/6J mice – Atsushi Toyoda – Neuroscience Letters

Brain-derived neurotrophic factor preserves intestinal mucosal barrier function and alters gut microbiota in mice – Chen Li – The Kaohsiung Journal of Medical Sciences

Immunization with intestinal microbiota-derived Staphylococcus aureus and Escherichia coli reduces bacteria-specific recolonization of the intestinal tract – Julio Adrián Garfias-López – Immunology Letters

Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis – Joel R.Wilmore – Cell Host & Microbe

Animal microbiome

Effects of glyphosate herbicide on the gastrointestinal microflora of Hawaiian green turtles (Chelonia mydas) Linnaeus – Ronald P.Kittle – Marine Pollution Bulletin

Identification of Uncultured Bacterial Species from Firmicutes, Bacteroidetes and CANDIDATUS Saccharibacteria as Candidate Cellulose Utilizers from the Rumen of Beef Cows – Lee James Opdahl – Microorganisms

Microbial community dynamics during rearing of black soldier fly larvae (Hermetia illucens) and its impact on exploitation potential – Jeroen De Smet – Applied and Environmental Microbiology

Urea nitrogen induces changes in rumen microbial and host metabolic profiles in dairy cows – D.Jin – Livestock Science

Air Microbiome

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states – Tina Šantl-Temkiv – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Shrub encroachment is associated with changes in soil bacterial community composition in a temperate grassland ecosystem – Xingjia Xiang – Plant and Soil

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau – Peng Dang – Science of The Total Environment

Characterization of halotolerant, pigmented, plant growth promoting bacteria of groundnut rhizosphere and its in-vitro evaluation of plant-microbe protocooperation to withstand salinity and metal stress – Avishek Banik – Science of The Total Environment

Arbuscular mycorrhizal fungal and soil microbial communities in African Dark Earths – Tessa Camenzind – FEMS Microbiology Ecology

Effects of thinning intensity on understory vegetation and soil microbial communities of a mature Chinese pine plantation in the Loess Plateau – Peng Dang – Science of The Total Environment

Plant growth-promoting rhizobacteria inoculation and nitrogen fertilization increase maize (Zea mays L.) grain yield and modified rhizosphere microbial communities – Luciana P. Di Salvo – Applied Soil Ecology

Review: Understanding the impact of soil sodicity on mycorrhizal symbiosis: Some facts and gaps identified from cotton systems – Samieh Eskandari – Applied Soil Ecology

Morphological, biochemical and molecular characterization of culturable epilithic and endolithic bacteria from rocks of Ayubia (Murree), lower Himalaya, Pakistan – I. Khan –
Applied Ecology and Environmental Research

Impact of sugarcane bagasse-derived biochar on heavy metal availability and microbial activity: A field study – Chengrong Nie – Chemosphere

Water and extremophile microbiome

Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors – Kai-Hui Liu – Extremophiles

Marine microbes in 4D — using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health – Pier Luigi Buttigieg – Current Opinion in Microbiology

The future of genomics in polar and alpine cyanobacteria – Nathan A M Chrismas – FEMS Microbiology Ecology

Unexpected fungal communities in the Rehai thermal springs of Tengchong influenced by abiotic factors – Kai-Hui Liu – Extremophiles

Actinobacterial community structure in the Polar Frontal waters of the Southern Ocean of the Antarctica using Geographic Information System (GIS): A novel approach to study Ocean Microbiome – P. Sivasankar – Data in Brief

Review: Actinobacterial community structure in the Polar Frontal waters of the Southern Ocean of the Antarctica using Geographic Information System (GIS): A novel approach to study Ocean Microbiome – P. Sivasankar – Data in Brief

Microbial Ecology

Symbiosis in the microbial world: from ecology to genome evolution – Jean-Baptiste Raina – Biology Open

Dissertation: Understanding Microbial Community Dynamics in High-Solids Lignocellulolytic Systems Using Bioinformatics Tools – Joshua Thomas Claypool – University of California, Davis

Review: Uncultivated microbes—in need of their own nomenclature? – Aharon Oren – The ISME Journal

Resistome

Diverse and abundant antibiotic resistance genes from mariculture sites of China’s coastline – Quanxin Gao – Science of The Total Environment

Evaluation of resistance gene transfer from heat-treated Escherichia coli – Laëtitia Le Devendec – International Journal of Food Microbiology

Phages and viruses

*The Global Virome Project – Dennis Carroll – Science

*Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions – Emrah Altindis – PNAS

*The first known virus isolates from Antarctic sea ice have complex infection patterns – Anne-Mari Luhtanen – FEMS Microbiology Ecology

*Immune loss as a driver of coexistence during host-phage coevolution
Jake L Weissman – The ISME Journal

PuLSE: Quality control and quantification of peptide sequences explored by phage display libraries – Steven Shave – PLOSone

Metabolomics

A quantitative metabolomics study of bacterial metabolites in different domains – Fanyi Zhong – Analytica Chimica Acta

Waste and Pollution

Ferric sulfate and proline enhance heavy-metal tolerance of halophilic/ halotolerant soil microorganisms and their bioremediation potential for spilled-oil under multiple stresses – Dina M. Al-Mailem – Frontiers in Microbiology

The divergence between fungal and bacterial communities in seasonal and spatial variations of wastewater treatment plants – Ziyan Wei – Science of The Total Environment

Techniques

Genome-scale metabolic models as platforms for identification of novel genes as antimicrobial drug targets – Bashir Sajo Mienda – Future Medicine

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Microbes in the news

Microbiota-gut-brain axis is at epicenter of new approach to mental health – Mary Ann Leibert – EurekAlert

Dietary Advice Based on the Bacteria in Your Gut – Charles Wallace – The Wall Street Journal

The silent microbiome crisis – Tobias Rees – The Washington Post

C-sections and gut bacteria increase risk of childhood obesity – Medical Press

Researchers film bacteria using melee combat to steal antibiotic resistance genes – Phys.org

February 7, 2018

Today we have many “gut microbiota” and “water microbiome” articles, as well as quite a few reviews in “Food microbiology” sector. One article (among many interesting today) I would like to highlight is the one from Guillaume Bernard and how unraveling the microbial dark matter should be identified as a central priority for biologists.

Jobs

Microbiology Technician -R&D, Lille, France

Consultant Medical Microbiologist, Birmingham, UK

Events

1st International Conference on Microbial Food and Feed Ingredients (MiFFI2018): 2-4 May 2018, Denmark

12th Vaccine Congress, Budapest, Hungary

General microbiome

Synergistic gold–copper detoxification at the core of gold biomineralisation in Cupriavidus metallidurans  – L. Bütof – Metallomics

The role of the type VI secretion system vgrG gene in the virulence and antimicrobial resistance of Acinetobacter baumannii ATCC 19606 – Jianfeng Wang – PLOS One

Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria – Marike Palmer – Frontiers in Microbiology

Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery – Guillaume Bernard – Genome Biology and Evolution

Draft genome sequence of Paenibacillus strain LK1, a phytohormone producing bacterium – Kun Liu – 3 Biotech

Pregnancy and early life

Review: Urinary tract infection during pregnancy: current concepts on a common multifaceted problem – Kallirhoe Kalinderi – Journal of Obstetrics and Gynaecology

Human respiratory microbiome

In children, the microbiota of the nasopharynx and brochoalveolar lavage fluid are both similar and different – Kirsten M. Kloepfer – Pediatric Pulmonology

At the Root: Defining and Halting Progression of Early Chronic Obstructive Pulmonary Disease – Fernando J. Martinez – American Journal of Respiratory and Critical Care Medicine

Oral microbiome

Transcriptome of healthy gingival tissue from edentulous sites in patients with a history of generalized aggressive periodontitis – Tiago Taiete – Journal of Periodontology

Evaluation of oxidative status in patients with chronic periodontitis and polycystic ovary syndrome: A cross-sectional study – Ebru Saglam – Journal of Periodontology

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research – Irina Marie Velsko – bioRxiv

Presence of the esp gene in Enterococcus faecium derived from oropharyngeal microbiota of haematology patients – Milica Jovanović – Archives of Oral Biology

Short-term microbiological effects of photodynamic therapy in non-surgical periodontal treatment of residual pockets: A split-mouth RCT – Mônica Grazieli Corrêa – Lasers in Surgery and Medicine

Human skin microbiome

Platelet activation and aggregation by the opportunistic pathogen Cutibacterium (Propionibacterium) acnes – Frida Petersson – PLOS One

Human vaginal microbiome

Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections – Noa Ziklo – Frontiers in Celular & Infection Microbiology

Human gut microbiome

Report: Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria – Christine M. Deje – Science

Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells – Liam Chung – Cell Host & Microbe

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis – Michael Mintz – PLOS One

Infectious bursal disease virus infection leads to changes in the gut associated-lymphoid tissue and the microbiota composition – Li Li – PLOS One

Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades – Shinichiro Hirai – PLOS One

Gut microbiome and depression: what we know and what we need to know – Gal Winter – Reviews in the Neurosciences

Connection between BMI related plasma metabolite profile and gut microbiota – Filip Ottosson – The Journal of Clinical Endocrinology & Metabolism

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – Tanya T. Nguyen – Journal of Psychiatric Research

Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Anaerobic 4-hydroxyproline utilization: discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity – Yolanda Y. Huang – Gut Microbes

Micro Integral Membrane Protein (MIMP), a Newly Discovered Anti-Inflammatory Protein of Lactobacillus Plantarum, Enhances the Gut Barrier and Modulates Microbiota and Inflammatory Cytokines – Yin M. – Cellular Physiology and Biochemistry

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations – Matthew A. Jackson – PeerJ

Animal experiments 

Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin – Lance W. Noll – PLOS One

Shift of uterine microbiota associated with antibiotic treatment and cure of metritis in dairy cows – Soo Jin Jeon – Veterinary Microbiology

Microbiota-derived Metabolic Factors Reduce Campylobacteriosis in Mice  – Xiaolun Sun – Gastroenterology

Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis – Bi-Feng Yuan – Analitical Chemistry

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS One

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance – Devin B.Holman – Veterinary Microbiology

IL-6-mediated signaling pathways limit Chlamydia muridarum infection and exacerbate its pathogenicity in the mouse genital tract  – Xin Sun – Microbes and Infection

Gut microbial composition can differentially regulate bile acid synthesis in humanized mice – Dae Joong Kang – Hepatology Communications

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction – Youlian Zhou – mSystems

Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents – Leore T. Geller – Molecular & Cellular Oncology

Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Scientific Reports

Dietary supplementation with a nucleotide-rich yeast extract modulates gut immune response and microflora in weaned pigs in response to a sanitary challenge – S. M. Waititu – Animal

Animal microbiome 

Cellulose-dependent expression and antibacterial characteristics of surfactin from Bacillus subtilis HH2 isolated from the giant panda – Ziyao Zhou – PLOS One

Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection – Mirela D’arc – BMC Retrovirology

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

Plant, root, and soil microbiome

Effects of an EPSPS-transgenic soybean line ZUTS31 on root-associated bacterial communities during field growth – Gui-Hua Lu – PLOS One

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities – Eric R. Hester – mSystems

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome – Collin M. Timm – mSystems

Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits – Thangasamy Saminathan – Frontiers in Plant Science

Links between nanoscale and macroscale surface properties of natural root mucilage studied by atomic force microscopy and contact angle – Robin Kaltenbach – Journal of Colloid and Interface Science

Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron – Ao-Lei He – International Journal of Molecular Science

Water and extremophile microbiome 

High growth potential and nitrogen removal performance of marine anammox bacteria in shrimp-aquaculture sediment – LuongVan Duc – Chemosphere

Establishment and convergence of photosynthetic microbial biomats in shallow unit process open-water wetlands – Zackary L.Jones – Water Research

Review: Bioactive compounds from marine macroalgae and their hypoglycemic benefits – ChaoZhao – Trends in Food Science & Technology

A Short Comparison of Two Marine Planktonic Diazotrophic Symbioses Highlights an Un-quantified Disparity – Andrea Caputo – Frontiers in Marine Science

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O. Roger Anderson – Frontiers in Marine Science

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes – Thea Van Rossum  – bioRxiv

Trace Metal Requirements and Interactions in Symbiodinium kawagutii – Irene B. Rodriguez – Frontiers in Microbiology

Depth-Resolved Variations of Cultivable Bacteria and Their Extracellular Enzymes in the Water Column of the New Britain Trench – Qianfeng Liu – Frontiers in Microbiology

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function – Sheila Roitman – The ISME Journal

Picoplankton distribution influenced by thermohaline circulation in the southern Adriatic – Tina Šilović – Continental Shelf Research

Evaluation of the relationship of picoplankton and viruses to environmental variables in a lagoon system (Çakalburnu Lagoon, Turkey) – Yucel-Gier – Chemistry and Ecology

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea – Shu-Xian Yu – PeerJ

Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics – Sonja Oberbeckmann – Frontiers in Microbiology

Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic – Oriol Grau – Molecular Ecology

Built environment 

Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting – Yanan Yin – Canadian Journal of Microbiology

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Josh – Journal of Environmental Sciences

Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics – Ryan P. Bartelme – Frontiers in Microbiology

Food microbiology

Review: Recent advances in understanding the anti-obesity activity of anthocyanins and their biosynthesis in microorganisms – Lianghua Xie – Trends in Food Science & Technology

Review: Combining reformulation, active packaging and non-thermal post-packaging decontamination technologies to increase the microbiological quality and safety of cooked ready-to-eat meat products – Claudia N.Horita – Trends in Food Science & Technology

Review: Impact of curcumin nanoformulation on its antimicrobial activity – Anderson Clayton da Silva – Trends in Food Science & Technology

Review: Antimicrobial potential of legume extracts against foodborne pathogens: A review – M.C.Pina-Pérez – Trends in Food Science & Technology

Long-term kinetics of Salmonella Typhimurium ATCC 14028 survival on peanuts and peanut confectionery products – Maristela S. Nascimento – PLOS One

Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages – Marina Giello – Food Microbiology

Effects of microbial diversity on nitrite concentration in pao cai, a naturally fermented cabbage product from China – Zhaoxia Wang – Food Microbiology

Bacterial and fungal microbiota of spontaneously fermented Chinese products, Rubing milk cake and Yan-cai vegetable pickles – Xin Liu – Food Microbiology

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese – A. S. Bertuzzi – mSytems

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions – Nan Li – Scientific Reports

Phages and viruses

The Human Virome – Selene Zárate – Archives of Medical Research

Microreview: Contractile injection systems of bacteriophages and related systems – Nicholas M.I. Taylor – Molecular Microbiology

In vitro models for deciphering the mechanisms underlying the sexual transmission of viruses at the mucosal level – Julie Frouard – Virology

Bioinformatics

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria – Eliot C. Bush – BMC Bioinformatics

Microbes in the news

Scientists say Earth’s atmosphere is raining viruses and bacteria down on the entire planet

Medicines from engineered bacteria offer promise — and pitfalls

Microbes on the market 

uBiome, the Leader in Microbial Genomics, Launches New Research Study Allowing SmartGut™ Patients to Assess the Impact of Diet and Lifestyle on Gut Conditions

January 15, 2018

Today’s digest is full of great papers, including new methods of detection and quantificaion of HGT in anoxic conditions, and a brilliant paper on root-rhizosphere interactome.

General Microbiome

Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis. Mateos, R. Bioelectrochemistry.

Gut Microbiome

Dietary Factors Modulate Colonic Tumorigenesis Through the Interaction of Gut Microbiota and Host Chloride Channels. Zhang Y. Molecular Nutrition Food Research

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients. Cui, X. Scientific Reports

Nasal Microbiome

An insight into intestinal mucosal microbiota disruption after stroke.Stanley,D. Scientific Reports

Influence of pig farming on the human’s nasal microbiota: The key role of the airborne microbial communities. Kraemer, JG. Applied and Environmental Microbiology

Fecal Microbiome

Letters to Editor: Sucrase-isomaltase 15Phe IBS risk variant in relation to dietary carbohydrates and faecal microbiota composition. Thingholm L. Gut

Plant, Soil, and Water Microbiome

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. Yergeau, E. The ISME Journal

Indoor Microbiome

Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities.Raghupathi, PK. Applied and Environmental Microbiology

Resitome

Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration. Shi, Y. Applied Microbioloby and Biotechnology

Animan Experiments and Microbiome

Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel. He, J. Scientific Reports

Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats. Khan, TJ. Scientific Reports

Protocol/Techniques

Fluorescence recovery allows the implementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments. Pinilla, R. Applied and Environmental Microbiology

Microbiome Jobs

Part-Time Microbiology Laboratory Technician

-Inside Higher Ed Careers