October 23, 2017

Good Monday! Today, we have a short digest with several papers focused in pathogen research.


Human microbiome

Evaluation of inter-individual differences in gut bacterial isoflavone bioactivation in humans by PCR-based targeting of genes involved in equol formation – A. Braune – Journal of Applied Microbiology

Immune-modulatory genomic properties differentiate gut microbiota of infants with and without eczema – Seungdae Oh – PLoS One

Low-complexity microbiota in the duodenum of children with newly diagnosed ulcerative colitis – Fei Sjöberg – PLoS One

IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization – Neil D. Ritchie – BMC Genomics

Review: Sleeping with the enemy: Clostridium difficile infection in the intensive care unit – Florian Prechter – Critical Care

Hippurate as a metabolomic marker of gut microbiome diversity: Modulation by diet and relationship to metabolic syndrome – Tess Pallister – Scientific Reports


Environmental microbiomes

Mini-Review: Anaerobic Oxidation of Ethane, Propane, and Butane by Marine Microbes: A Mini Review – Rajesh Singh – Frontiers in Microbiology

Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert – Rakesh Mogul – Frontiers in Microbiology

Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean – Xiaomin Xia – Frontiers in Microbiology

Highly structured prokaryote communities exist within the skeleton of coral colonies – Vanessa R Marcelino – The ISME Journal


Animal Microbiomes

Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut – Yi Zhao Y – Science of The Total Environment


Pathogen Research

Genomic Comparison among Lethal Invasive Strains of Streptococcus pyogenes Serotype M1 – Gabriel R. Fernandes – Frontiers in Microbiology

Differential Identification of Mycobacterial Species Using High-Resolution Melting Analysis – Azar D. Khosravi –  Frontiers in Microbiology

Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies – Joon L. Tan – Frontiers in Microbiology

Exploring the Genome and Phenotype of Multi-Drug Resistant Klebsiella pneumoniae of Clinical Origin – João Anes – Frontiers in Microbiology

Contributions of MyD88-dependent receptors and CD11c-positive cells to corneal epithelial barrier function against Pseudomonas aeruginosa – Matteo M. E. Metruccio – Scientific Reports

Preprint: KKL-35 Exhibits Potent Antibiotic Activity Against Legionella Species Independently Of Trans-Translation Inhibition – Romain Brunel – BioRxiv

Antibiotics ameliorate lupus-like symptoms in mice – Qinghui Mu – Scientific Reports


More microbes

Preprint: A historical legacy of antibiotic utilization on bacterial seed banks in sediments – Laura Madueño​ – PeerJ

Expression of Genes for a Flavin Adenine Dinucleotide-Binding Oxidoreductase and a Methyltransferase from Mycobacterium chlorophenolicum Is Necessary for Biosynthesis of 10-Methyl Stearic Acid from Oleic Acid in Escherichia coli – Shuntaro Machida – Frontiers in Microbiology

Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N2O emission – Fernando Torralbo – Scientific Reports



miPepBase: A Database of Experimentally Verified Peptides Involved in Molecular Mimicry – Anjali Garg – Frontiers in Microbiology



October 22, 2017

A wide range of interesting articles today on the mouth, respiratory and gut microbiomes: Airway microbiota and obstruction in asthma, the tongue microbiome and pneumonia in the elderly, gut microbiome interactions with host G-protein coupled receptors, the effects of prebiotics and milk oligosaccharides on the mouse gut metabolome and stressor induced immune alterations, the impact of social stress on the gut microbiome and the host gut transcriptome, the impact of a Bacteroides integrase in a mouse model of colitis, and evidence that oral bacteria can colonize the gut in genetically and dysbiotic susceptible mice, leading to increased gut inflammation. 

  • Events and jobs

Postdoctoral Researcher in Microbiome Bioinformatics – Karolinska Institutet


  • Human respiratory microbiome

Different Functional Genes of Upper Airway Microbiome Associated with Natural Course of Childhood Asthma – Bong-Soo Kim – European Journal of Allergy and Clinical Immunology

*Atopic asthmatic immune phenotypes associated with airway microbiota and airway obstruction – Benjamin A. Turturice – PLOSone

  • Human oral microbiome

*Relationships of variations in the tongue microbiota and pneumonia mortality in nursing home residents – Shinya Kageyama – Journal of Gerontology

  • Human gut microbiome

Review: Host-Microbe Interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology

Development of severe bronchopulmonary dysplasia is associated with alterations in fecal volatile organic compounds – Daniel J C Berkhout – Pediatric Research

Gut Fermentation of Dietary Fibres: Physico-Chemistry of Plant Cell Walls and Implications for Health – Barbara A. Williams – International Journal of Molecular Sciences

Review: Food allergy: The influence of breast-feeding and gut microbiota – S. Hazebrouck – Revue Française d’Allergologie

Review: Whole cereal grains and potential health effects: Involvement of the gut microbiota – Lingxiao Gong – Food Research International

Review: Probiotic strains and mechanistic insights for the treatment of type 2 diabetes – Christiane S. Hampe – Endocrine

Review: Early-Life Gut Dysbiosis: A Driver of Later-Life Fibrosis? – Karen J. Ho – Journal of Investigative Dermatology

Review: Nutritional programming by glucocorticoids in breast milk: targets, mechanisms and possible implications – Jonneke J. Hollanders – Best Practice & Research Clinical Endocrinology & Metabolism

Review: Less Invasive Screening for Colorectal Cancer by Microbiota Analysis: Is it a Reality or an Illusion? – Hisashi Onodera – EBioMedicine

  • Fecal Transplants

The taxonomic composition of the donor intestinal microbiota is a major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative colitis – P. Kump – Alimentary Pharamacology and Therapeutics


  • Animal experiments

* Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

*Stressor-induced immunomodulation is attenuated by prebiotics and milk oligosaccharides: Role of the colonic metabolome – M. Bailey – Brain, Behavior, and Immunity

*The colonic epithelial transcriptome and intestinal microbiome are significantly changed by social stressor exposure – A.R. Mackos – Brain, Behavior, and Immunity

*A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis – Roopa Hebbandi Nanjundappa – Cell

Metformin Alters Upper Small Intestinal Microbiota that Impact a Glucose-SGLT1-Sensing Glucoregulatory Pathway – Paige V. Bauer – Cell Metabolism

Distribution of species and antimicrobial resistance among enterococci isolated from the fecal microbiota – Andréa de Andrade Rangel de Freitas – Science of The Total Environment

Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice – Takuya Kuno – Molecular Pharmaceutics

Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population – P. Villette – Epidemiology & Infection

High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community – Debora Garzetti – Genome Announcements

  • Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance – Stephan P. Rosshart – Cell

Impact of Low and High Doses of Marbofloxacin on the Selection of Resistant Enterobacteriaceae in the Commensal Gut Flora of Young Cattle: Discussion of Data from 2 Study Populations – Lhermie Guillaume – Foodborne Pathogens and Disease

  • Forensic Microbiome

Successive bacterial colonisation of pork and its implications for forensic investigations – Jessica Handke – Forensic Science International

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification – Sarah E. Schmedes – Forensic Science International: Genetics

  • Plant, root, and soil microbiome

Characterization of fungal communities of developmental stages in table grape grown in the northern region of South Africa – P.C. Carmichael – Journal of Applied Microbiology

Mycorrhizae, invasions, and the temporal dynamics of mutualism disruption – Sara Grove – Journal of Ecology

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter – Quan YuanSoil Biology and Biochemistry

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota – Muhammad Yasir – Brazilian Journal of Microbiology

  • Waste and Pollution 

Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community – Evangelia S. Papadopoulou – Environmental Pollution

  • Built environment

Human health risks for Legionella and Mycobacterium avium complex (MAC) from potable and non-potable uses of roof-harvested rainwater – Kerry A.Hamilton – Water Research

  • Techniques

Optimization of GC/TOF MS analysis conditions for assessing host-gut microbiota metabolic interactions: Chinese rhubarb alters fecal aromatic Amino acids and phenol metabolism – Shan Yin – Analytica Chimica Acta


  • Microbes in the news

Stress may harm gut health as much as junk food – Honor Whiteman – Medical News Today

Different Microbial Communities Live Along Female Reproductive Tract – GenomeWeb

Gut Health May Begin in the Mouth – Lydialyle Gibson – Havard

October 21, 2017

Plant and soil microbiome focus today: Rhizospheric microbial communities of the frankincense producing Boswellia sacra tree, Coffea arabica, and the damask rose, as well as plant species in the Puerto Rico tropical forest, the Mediterranean mountains, and extreme Arctic and Alpine climates. 

Events and jobs

Post-doctoral Fellowship in Microbial Genomics – Brigham & Women’s Hospital – The Massachusetts Host-Microbiome Center

Microbiology Sales Executive – Ireland

Microbiology Lab Technician – Catalent – Brussels, Belgium


  • General microbiome

Special Meeting Sections for the ASM Conference on Mechanisms of Interbacterial Cooperation and Competition – George A. O’Toole – Journal of Bacteriology

  • Human oral microbiome

Nutrigenomics in periodontics – An overview – Singh Soundanya –
International Journal of Oral Health Dentistry

  • Human gut microbiome

Review: Health and environmental applications of gut microbiome: a review – Soumya Chatterjee – The Journal of Society of Ecological Chemistry and Engineering

The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux—A Prospective Longitudinal Interventional Study – Christoph Castellani – Frontiers in Cellular and Infection Microbiology

Review: Host–Microbiota Mutualism in Metabolic Diseases – Salvatore Fabbiano – Frontiers in Endocrinology

Review: Interactions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts – Verónica Urdaneta – Frontiers in Medicine

Review: Prebiotic–Probiotic Relationship: The Genetic Fundamentals of Polysaccharides Conversion by Bifidobacterium and Lactobacillus Genera – Penka Petrova – Food Bioconversion

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome – Tanja V. Maier – mBio

Review: Can the gastrointestinal microbiota be modulated by dietary fibre to treat obesity? – H. C. Davis – Irish Journal of Medical Science

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology


  • Animal experiments

Study on alterations of physiological functions in aged constipation rats with fluid-deficiency based on metabonomic and microbiology analysis – Deliang Liu – Royal Society of Chemistry

  • Animal microbiome

The Low-Diversity Fecal Microbiota of the Critically Endangered Kākāpō Is Robust to Anthropogenic Dietary and Geographic Influences – Elena K. Perry – Frontiers and Microbiology

Alternative growth promoters modulate broiler gut microbiome and enhance body weight gain – Serajus Salaheen – Frontiers in Microbiology

Microbial Communities in North American Ixodid Ticks of Veterinary and Medical Importance – Andrea S. Varela-Stokes – Frontiers in Veterinary Science

Assessing the impact of rumen microbial communities on methane emissions and production traits in Holstein cows in a tropical climate – Camila S. Cunha – Systematic and Applied Microbiology

  • Plant, root, and soil microbiome

Root and rhizosphere bacterial phosphatase activity varies with tree species and soil phosphorus availability in Puerto Rico tropical forest – Kristine Grace Cabugao – Frontiers in Plant Science

Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches – Ines Krohn-Molt – Frontiers in Microbiology

Inoculation with arbuscular mycorrhizal fungi alleviates harmful effects of drought stress on damask rose – EslamAbdel-Salam – Saudi Journal of Biological Sciences

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

Plant growth promoting rhizobacteria in amelioration of salinity stress: a systems biology perspective – Gayathri Ilangumaran – Frontiers in Plant Science

Review: Mycorrhizosphere Interactions to Improve a Sustainable Production of Legumes – José-Miguel Barea – Microbes for Legume Improvement

Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains – José F. Cobo-Díaz – Forests

Review: Response and interaction of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi in the soybean rhizosphere – Ram Swaroop Meena – Plant Growth Regulation

Review: Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? – Joelle Sasse – Trends in Plant Science

Microbial indicators for soil quality – Michael Schloter – Biology and Fertility of Soils

Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants – Xiao Xiao – Applied Microbiology and Biotechnology

Soil water content during and after plant growth influence nutrient availability and microbial biomass – Ran Xue – Journal of soil science and plant nutrition

Isolation, screening and biochemical characterization of Phosphate-solubilizing rhizobacteria associated with Coffea arabica L – Befekadu Teshome – Advanced Journal of Biodiversity

Temporal variations of soil microbial community under compost addition in black soil of Northeast China – Wei Yang – Applied Soil Ecology

Differential seasonal effects of water addition and nitrogen fertilization on microbial biomass and diversity in a temperate desert – Gang Huang – Catena

Assessment of microbial diversity in the rhizosphere of Pinus roxburghii (Sarg.) and bio-inoculant potential of selected pine bacterial isolates for wheat varieties based on culture independent and culture dependent techniques – I. Naz – Plant Biology

Rhizospheric microbial communities associated with wild and cultivated frankincense producing Boswellia sacra tree – Abdul Latif Khan – PLOSone

Taxonomic structure and functional association of foxtail millet root microbiome – Tao Jin – GigaScience

  • Biotechnology

Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction – Dhaneshwaree Asem – PLOSone

Impact of treated wastewater for irrigation on soil microbial communities – A.M. Ibekwe – Science of the Total Environment

Advancing the design and delivery of CRISPR antimicrobials – Jennie R.Fagen – Current Opinion in Biomedical Engineering


  • Phages and viruses

Pre-Print: Insights into viral community composition of the cnidarian model metaorganism Aiptasia using RNA-Seq data – Jan D Brüwer – PeerJ

How does parvovirus B19 DNA achieve lifelong persistence in human cells? – Gloria Bua – Future Virology

  • Bioinformatics

Annotation: A Computational Solution for Streamlining Metabolomics Analysis – Xavier Domingo-Almenara – Analytical Chemistry

  • Techniques

Review: Combined imaging and molecular techniques for evaluating microbial function and composition: A review – Christopher G. Weisener – Surface and Interface Analysis


  • Microbes in the news

Simple Bacteria Offer Clues to the Origins of Photosynthesis – Jordana Cepelewicz – Quanta Magazine

Bacteria Found in Women’s Upper Reproductive Tracts – Diana Kwon – The Scientist

New Research Shows Asymmetry in Bacteria Might Help Us Fight Antibiotic Resistance – Karla Lant – Futurism

Metal-eating bacteria could have left their “fingerprints” on Mars, proving it once hosted life – Matt Williams – Universe Today

How gut bacteria saved ‘dirty mice’ from death – Elizabeth Pennisi – Science


October 20, 2017

A wide variety of studies today from the digestive microbiota of carnivorous pitcher plants, to the skin microbiome of dogs, and the impacts of probiotics on male fertility in a mouse model of obesity. 

Events and jobs

Microbiome World Congress – November 7-8, 2017, Capital Hilton, Washington, DC – registration


  • General microbiome

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae – Zhaobin Huang – Frontiers in Microbiology

Review: Uncultivated microbes in need of their own taxonomy – Konstantinos T Konstantinidis – The ISME Journal

Review: The growing tree of Archaea: new perspectives on their diversity, evolution and ecology – Panagiotis S Adam – The ISME Journal

  • Human respiratory microbiome

Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition – Anton Y. Peleg – Journal of Cystic Fibrosis

  • Human gut microbiome

Carbapenem-resistant Enterobacteriaceae colonization (CRE) and subsequent risk of infection and 90-day mortality in critically ill patients, an observational study – Thomas Howe McConville – PLOSone

Review: Antibiotics, gut microbiome, and obesity – Karen S. W. Leong – Clinical Endocrinology

Review: Gut microbiota changes in the extreme decades of human life: a focus on centenarians – Aurelia Santoro – Cellular and Molecular Life Sciences

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology


  • Animal Experiments

Lactobacillus rhamnosus PB01 (DSM 14870) supplementation affects markers of sperm kinematic parameters in a diet-induced obesity mice model – Fereshteh Dardmeh – PLOSone

  • Animal microbiome

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization – Beate M Slaby – The ISME Journal

A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs – Andrew R. Williams – PLOSone

Individual signatures and environmental factors shape skin microbiota in healthy dogs – Anna Cuscó – Microbiome

Review: Metagenomic investigation of gastrointestinal microbiome in cattle – Minseok Kim – AJAS

  • Plant, root, and soil microbiome

Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community – David W Armitage – The ISME Journal

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities – Roland C Wilhelm – The ISME Journal

Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness – David R. Toole – Biological Invasions

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis – Margarida M. Santana – Frontiers in Microbiology

  • Water and extremophile microbiome

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

Mixotrophy drives niche expansion of verrucomicrobial methanotrophs – Carlo R Carere – The ISME Journal

High abundance and expression of transposases in bacteria from the Baltic Sea – Theoden Vigil-Stenman – The ISME Journal

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB contaminated marine sediments – B. Matturro – FEMS Microbiology Ecology

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities – Oliver Röhl – Environmental Microbiology

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept – Christina Pavloudi – PeerJ

The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites – Gerrit Wienhausen – Frontiers in Microbiology

  • Built environment

Indoor microbiota in severely moisture damaged homes and the impact of interventions – Balamuralikrishna Jayaprakash – Microbiome


  • Probiotics / prebiotics

Review: Probiotics in the Prevention of Gestational Diabetes Mellitus – Luisa F. Gomez Arango – Nutrition and Diet in Maternal Diabetes

  • Phages and viruses

Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release – Gurinder K. Vinner – PLOSone

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology – Rachel L Marine – The ISME Journal

  • Techniques

A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping – Wan-Xiang Xu – PLOSone


October 19, 2017

Today, we have a short Digest but with interesting remarks: Alzheimer’s disease associated microbiome, the bacterial tree of Life and more.


Human Microbiome

Gut microbiome alterations in Alzheimer’s disease – Nicholas M. Vogt – Scientific Reports

Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease – Veronika B. Dubinkina – Microbiome (BMC)

Male-specific Association Between Fat Free Mass Index and Faecal Microbiota in 2 to 3 Year Old Australian Children – Paula Smith-Brown – Journal of Pediatric Gastroenterology & Nutrition


General Microbiome

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing – Noelle R. Noyes – Microbiome (BMC)

Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food – Sally V. Irwin – PLoS ONE

Research Highlights: Host-microbe interactions: Aiming at GPCRs – Mirella Bucci – Nature Chemical Biology


Animal Microbiome

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents – Paul M. Ryan – Scientific Reports

Microbiota Diversification and Crash Induced by Dietary Oxalate in the Mammalian Herbivore Neotoma albigula – Aaron W. Miller – mSphere

Commentary: Microbes REV up Host Metabolism around the Clock – Geoffrey N. Pronovost – Immunity

Impact of age-related mitochondrial dysfunction and exercise on intestinal microbiota composition – David Houghton – The Journals of Gerontology Series A

Comparative Analysis of Gut Microbiota of Culex restuans (Diptera: Culicidae) Females From Different Parents – Ephantus J Muturi – Journal of Medical Entomology


Beneficial Microbes and Molecules

Maternal milk feedings reduce sepsis, necrotizing enterocolitis and improve outcomes of premature infants – J Cortez – Journal of Perinatology

Therapeutic potential of Bifidobacterium breve strain A1 for preventing cognitive impairment in Alzheimer’s disease – Yodai Kobayash – Scientific Reports

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents – Paul M. Ryan – Scientific Reports


Environmental Microbiome

The plant circadian clock influences rhizosphere community structure and function – Charley J Hubbard – The ISME Journal



Towards a balanced view of the bacterial tree of life – Frederik Schulz – Microbiome (BMC)



Primary and heterotrophic productivity relate to multi-kingdom diversity in a hypersaline mat – Hans C. Bernstein – FEMS Microbiology Ecology


Non-Microbiology picks

Sci-Hub provides access to nearly all scholarly literature – Daniel S Himmelstein – PeerJ Preprints

Nature index: On the biotech block – Alexandra Ossola – Nature


October 18, 2017

Today, several reviews, including a trio of reviews about connections between HIV and microbiome.

Gut microbiome

Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection – Dominik Schneider – Scientific Data (NPG)

News and Views: Gastric cancer: The gastric microbiota — bacterial diversity and implications – Manish A. Shah – Nature Reviews Gastroenterology & Hepatology

Review: The hygiene hypothesis in autoimmunity: the role of pathogens and commensals – Jean-François Bach – Nature Reviews Immunology

The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity – Alli Lynch – Scientific Reports

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus – Cristina Llorente – Nature Communications

High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut – Timothy Heisel – mSphere

Review: Gut Microbiota and Nonalcoholic Fatty Liver Disease: Insights on Mechanisms and Therapy – Junli Ma – Nutrients (MDPI)

Review article: The gut microbiome in inflammatory bowel disease-avenues for microbial management – J. McIlroy – Alimentary Pharmacology & Therapeutics

Commentary: Regulation of glucagon-like peptide-1 sensitivity by gut microbiota dysbiosis – Shunsuke Yamane – Journal Of Diabetes Investigation

Low-grade small intestinal bacterial overgrowth is common in patients with non-alcoholic steatohepatitis on quantitative jejunal aspirate culture – UC Ghoshal – Indian Journal of Gastroenterology


Reproductive tract microbiome

The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases – Chen Chen – Nature Communication


Microbiome in general

The microbiome beyond the horizon of ecological and evolutionary theory – Britt Koskella – Nature Ecology & Evolution

Trios—promising in silico biomarkers for differentiating the effect of disease on the human microbiome network – Zhanshan (Sam) Ma – Scientific Reports


Beneficial microbes and molecules

Prebiotic and Synbiotic Modifications of Beta Oxidation and Lipogenic Gene Expression after Experimental Hypercholesterolemia in Rat Liver – Claudia C. Alves – Frontiers in Microbiology

Vildagliptin increases butyrate-producing bacteria in the gut of diabetic rats – Qian Zhang – PLoS ONE

Caprylic and Polygalacturonic Acid Combinations for Eradication of Microbial Organisms Embedded in Biofilm – Joel Rosenblatt – Frontiers in Microbiology

PostScript: Faecal microbiota transplantation donor stools need screening for poliovirus – Peter Gerald Speck – Gut (BMJ)


Environmental research

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils – Craig Anderson – PeerJ

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI – Miranda H. Hengy – PeerJ

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing – Yanying Zhang – Frontiers in Microbiology


HIV and microbiome

Review: HIV and aging: role of the microbiome – Seema N. Desai – Current Opinion in HIV & AIDS

Review: The functional consequences of the microbiome in HIV: insights from metabolomic studies – Sergio Serrano-Villar – Current Opinion in HIV & AIDS

Review: Cross-reactivity of HIV vaccine responses and the microbiome – Wilton B Williams – Current Opinion in HIV & AIDS


Respiratory tract microbiome

Lung Microbiota is Related to Smoking Status and to Development of ARDS in Critically Ill Trauma Patients – Ariane R Panzer – American Journal of Respiratory and Critical Care Medicine


More microbes

Adjacent-possible ecological niche: growth of Lactobacillus species co-cultured with Escherichia coli in a synthetic minimal medium – Kouhei Mizuno – Scientific Reports


October 17, 2017

The effects of antimicrobials in household products on the maternal and infant microbiome, water quality of an urban stream network, and using adaptive evolution to improve lager yeast hybrids.

Pregnancy and early life

Household triclosan and triclocarban effects on the infant and maternal microbiome – Jessica V Ribado – EMBO Molecular Medicine

Water and extremophile microbiome

Microbial diversity and iron oxidation at Okuoku-hachikurou Onsen, a Japanese hot spring analog of Precambrian iron formations – L M Ward – Geobiology

Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole – T L Hamilton – Geobiology

Built environment

Urban infrastructure influences dissolved organic matter quality and bacterial metabolism in an urban stream network – Clay P Arango – Freshwater Biology

Food microbiology

Pre-print: Enhanced wort fermentation with de novo lager hybrids adapted to high ethanol environments – Kristoffer Krogerus – bioRxiv

More microbes

Pre-print: Phosphate starvation induces replacement of phospholipids with the betaine lipid diacylglycerol-N,N,N-trimethylhomoserine in the human fungal pathogen Candida albicans – Surabhi Naik – bioRxiv

Microbes in the news

Infections by C.diff bacteria are on the rise and can cause serious problems – Consumer Reports – The Washington Post

Engineered bacteria build microstructures on their own – Michael Torrice – Chemical & Engineering News

Gut fungi might be linked to obesity and inflammatory bowel disorders – Tina Hesman Saey – Science News

Rare bacteria in dead elephant sparks alarm – Siba Mohanty – The New Indian Express

Woman Contracts Rare Bacterial Infection on 12-Hour Flight – Rachael Rettner – Live Science

Microbial Drug Resistant Mutations Found via Novel Genome Screen – Genetic Engineering and Biotechnology News

One More Small Piece of the Puzzle on the Role of Gut Micro-organisms in MS – Ana Belo Van Wijk – Multiple Sclerosis News Today

Microbes on the market

New Clinical Data and Microbiome Research from Rebiotix’s Phase 2 Program for RBX2660 Highlighted at the World Congress of Gastroenterology at ACG2017 – PR Newswire