17 October,​ 2018

General Microbiome

ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling.Zhang C. Frontiers in Physiology

Skin Microbiome

The emerging role of skin microbiome in atopic dermatitis and its clinical implication.Stalder JF. Journal of Dermatological Treatment

Oral Microbiome

Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.Hardy K. Environmental Anthropology

Gut Microbiome

Gut Microbial Product Predicts Cardiovascular Risk in Chronic Kidney Disease Patients.Jadoon A. American Journal of Nephrology

Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes.Luis AS. Current Opinions in Chemical Biology

Vitamin D and the gut microbiome: a systematic review of in vivo studies.Waterhouse M. European Journal of Nutrition

A Review: The Fate of Bacteriocins in the Human Gastro-Intestinal Tract: Do They Cross the Gut-Blood Barrier?Dicks LMT. Frontier in Microbiology

Precision identification of diverse bloodstream pathogens in the gut microbiome.Tamburini FB. Nature Medicine

Animal Microbiome

Rickettsia diversity in southern Africa: A small mammal perspective.Essbauer S. Tick and Tick-Borne Disease

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets.Liu B. Frontier in Microbiology

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau.Bai X. Frontier in Microbiology

Microbiome-assisted carrion preservation aids larval development in a burying beetle.Shukla SP. PNAS

The gut microbiome: Relationships with disease and opportunities for therapy.Durack J. Journal of Experimental Medicine

Water Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater.Fan XY. Bioresource Technology

Fine-scale spatial homogenization of microbial habitats: a multivariate index of headwater wetland complex condition.Moon JB. Ecological Applications

Functional and taxonomic classification of a greenhouse water drain metagenome.López-Leal G. Standards in Genomic Sciences

Plant and Soil Microbiome

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels.Zhou H. Science of the Total Environment

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation.Beckmann S. ISME Journal

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October 11, 2018

The effects of chronic ethanol ingestion on the fruit fly microbiota, engineering the mosquito microbiota to produce an antiplasmodial effector, how temperature change affects an ecosystems biodiversity and function.

General microbiome

Changes in temperature alter the relationship between biodiversity and ecosystem functioning – Francisca C García – PNAS

Human respiratory microbiome

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes – Wing Ho Man – The Pediatric Infectious Disease Journal

Human oral microbiome

Carious status and supragingival plaque microbiota in hemodialysis patients – Qi Yue – PLOS ONE

Human gut microbiome

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Raghavendra Paknikar – Surgical Infections

Review: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients – Chih-Yu Yang – Nephrology

Animal experiments

Risks Related to High-Dosage Recombinant Antimicrobial Peptide Microcin J25 in Mice Model: Intestinal Microbiota, Intestinal Barrier Function and Immune Regulation – Haitao Yu – Journal of Agricultural and Food Chemistry

Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet – Sun Min Lee – Frontiers in Microbiology

Animal microbiome

Pre-print: Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner – James Angus Chandler – bioRxiv

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota – Jackie L Shane – Nature Communications

Plant, root, and soil microbiome

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization – Guillermo A Maroniche – FEMS Microbiology Ecology

Water and extremophile microbiome

Seasonal variation of extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water – Ingrid Ivančić – FEMS Microbiology Ecology

Food microbiology

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging – Ahmad Rois Mansur – Food Microbiology

Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl – Ilenys M Pérez-Díaz – Food Microbiology

Bioinformatics

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo – Katherine A Dunn – Microbiome Analysis (Book)

Metabolomics

Targeted Metabolic Profiling Indicates Apple Rootstock Genotype-Specific Differences in Primary and Secondary Metabolite Production and Validate Quantitative Contribution From Vegetative Growth – Rachel Leisso – Frontiers in Plant Science

Techniques

Analyzing Metabolic Pathways in Microbiomes – Mobolaji Adeolu – Microbiome Analysis (Book)

More microbes

Prevalence of Yersinia Species in the Ileum of Crohn’s Disease Patients and Controls – Guillaume Le Baut – Frontiers in Cellular and Infection Microbiology

October 9, 2018

 

Pregnancy and early life

Gut Microbiota and Body Weight in School‐Aged Children: The KOALA Birth Cohort Study – Catherine A. Mbakwa – Obesity

Multi-site human microbiome

Grow With the Challenge – Microbial Effects on Epithelial Proliferation, Carcinogenesis, and Cancer Therapy – Jakob von Frieling – Frontiers in Microbiology

Human respiratory microbiome

Microbiome dataset from the upper respiratory tract of patients living with HIV, HIV/TB and TB from Myanmar – Kyaw SoeHtuna – Data in Brief

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda‐Kuroki – Experimental Dermatology

Human vaginal microbiome

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M. Wylie – BMC Research Notes

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Animal experiments

Protective effects of a triple-fermented barley extract (FBe) against HCl/EtOH-induced gastric mucosa damage in mice – Jong‐Min Lim – Food Science & Nutrition

Guarana (Paullinia cupana Mart.) alters gut microbiota and modulates redox status, partially via caffeine in Wistar rats – Alexandre Kleber Silveira – Phytotherapy Research

Gut microbiota–dependent modulation of innate immunity and lymph node remodeling affects cardiac allograft outcomes – Jonathan S. Bromberg – JCI Insight

Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny – T Swierts – FEMS Microbiology Ecology

In vitro experiments

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Animal microbiome

Tissue-specific immune responses to Vibrio sp. infection in mussels (Perna canaliculus): A metabolomics approach – Thao V. Nguyen – Aquaculture

Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – Peer J

Microbial community composition of nest-carton and adjoining soil of the ant Lasius fuliginosus and the role of host secretions in structuring microbial communities – Pina Brinker – Fungal Ecology

Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea) – Wen Wang – Microbiology Open

Microbiome and Blood Analyte Differences Point to Community and Metabolic Signatures in Lean and Obese Horses – Amy S. Biddle – Frontiers in Veterinary Science

Plant, root, and soil microbiome

Determinants of Deadwood-Inhabiting Fungal Communities in Temperate Forests: Molecular Evidence From a Large Scale Deadwood Decomposition Experiment – Witoon Purahong –

Induction of defense mechanisms involved in disease resistance of onion blight disease caused by Botrytis allii – Mohamed M A Hussein – Egyptian Journal of Biological Pest Control

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island – E.V. Pershina – Antarctic Science

Fungal, Bacterial, and Archaeal Diversity in Soils Beneath Native and Introduced Plants in Fiji, South Pacific – Gian Maria Niccolò Benucci – Microbial Ecology

Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China – Xiaolan Lin – Microbial Ecology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Draft Genome Sequence of Burkholderia reimsis BE51, a Plant-Associated Bacterium Isolated from Agricultural Rhizosphere – Qassim Esmaeel – Microbiology Resource Announcements

Rhizosphere microbial response to multiple metal(loid)s in different contaminated arable soils indicates crop-specific metal-microbe interactions – Weimin Sun – Applied and Environmental Microbiology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Draft Genome Sequence of Pseudomonas sp. Strain MWU13-2860, Isolated from a Wild Cranberry Bog in Truro, Massachusetts – Ghazal Ebadzadsahrai – Microbiology Resource Announcements

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil – Érica Barbosa Felestrino – World Journal of Microbiology and Biotechnology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Spatial variability of microbial communities in a fractured sedimentary rock matrix impacted by a mixed organics plume – Gláucia da P. Lima – Journal of Contaminant Hydrology

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions – Xihui Xu – The ISME Journal

Root growth, function and rhizosphere microbiome analyses show local rather than systemic effects in apple plant response to replant disease soil – Maik Lucas – PLOS One

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4 years – X.Jia – Science of the Total Environment

Water and extremophile microbiome

Desiccation- and Saline-Tolerant Bacteria and Archaea in Kalahari Pan Sediments – Steffi Genderjahn – Frontiers in Microbiology

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecký – Extremophiles

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – N. V. Pimenov – Microbiology

Characterization of a novel bacteriophage specific to Exiguobacterium indicum isolated from a plateau eutrophic lake – Shiying Zhang – Journal of Basic Biology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Podell – The ISME Journal

The impact of iron nanoparticles on technetium-contaminated groundwater and sediment microbial communities – Laura Newsome – Journal of Hazardous Materials

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk – Science of the Total Environment

Reduced chlorine in drinking water distribution systems impacts bacterial biodiversity in biofilms – Claire Bertelli – Frontiers in Microbiology

Microbial Ecology

A Microbial Saga: How to Study an Unexpected Hot Spot of Microbial Biodiversity from Scratch? – Valeria Souza – Cuatro Ciénegas Ecology, Natural History and Microbiology

How Divergent Is the Cuatro Ciénegas Oasis? Genomic Studies of Microbial Populations and Niche Differentiation – Zulema Gomez-Lunar – Cuatro Ciénegas Ecology, Natural History and Microbiology

Trace metals supplementation enhanced microbiota and biohythane production by two-stage thermophilic fermentation – Chonticha Mamimin – International Journal of Hydrogen Energy

Microcosms and Mesocosms: A Way to Test the Resilience of Microbial Communities in Cuatro Ciénegas – Nguyen E. López-Lozano – Cuatro Ciénegas Ecology, Natural History and Microbiology

Resistome

Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis – Robert Zarnowski – PLOS One

Microbes in space

Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments – Vincenzo Zammuto – Mary Ann Liebert Publishers

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Probiotics / prebiotics

Understanding mode of action can drive the translational pipeline towards more reliable health benefits for probiotics – Michiel Kleerebezem – Current Opinion in Biotechnology

Systematic review with meta‐analysis: the efficacy of prebiotics, probiotics, synbiotics and antibiotics in irritable bowel syndrome – Alexander C. Ford – Alimentary Pharmacology and Therapeutics

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – M.N.Weber – Virology

Hyperdiverse Viral Communities in an Oligotrophic Oasis (Cuatro Ciénegas): Marine Affinities and Microgeographic Differentiation – P. Isa – Cuatro Ciénegas Ecology, Natural History and Microbiology

Bioinformatics

IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes – I-Min A Chen – Nucleic Acids Research

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

Strain-GeMS: Optimized subspecies identification from microbiome data based on accurate variant modeling – Chongyang Tan – Bioinformatics

 

 

September 25, 2018

Events and jobs

4th Annual European Microbiome Congress – London UK – November 14-15 2018

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General microbiome

Review: “Under the Skin” and into the Gut: Social Epidemiology of the Microbiome – Jennifer Beam Dowd – Current Epidemiology Reports

Review: Concurrent cross‐reactivity of microbiota‐derived epitopes to both self and pathogens may underlie the “Hygiene hypothesis” – David Usharauli – Scandinavian Journal of Immunology

Pregnancy and early life

Influence of non-polio enteroviruses and the bacterial gut microbiota on oral poliovirus vaccine response: a study from south India – Ira Praharaj – The Journal of Infectious Diseases

A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space – Samanta Michelini – Microbiome

Human respiratory microbiome

Review: Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma – Elliot Mathieu – Frontiers in Physiology

Different Upper Airway Microbiome and Their Functional Genes Associated with Asthma in Young Adults and Elderly Individuals – Jin‐Jae Lee – Allergy

Human oral microbiome

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption – Annette Carola Anderson – Scientific Reports

Human gut microbiome

Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects – Mireia Lopez-Siles – Frontiers in Cellular and Infection Microbiology

Influence of gender and menopausal status on gut microbiota – Jose A.Santos-Marcos – Maturitas

Review: High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group – François Blachier – Clinical Nutrition

Review: Review of the effects of sliver nanoparticle exposure on gut bacteria – Jiangyan Li – Journal of Applied Toxicology

Review: Interactions between Bitter Taste, Diet and Dysbiosis: Consequences for Appetite and Obesity – Alexandria Turner – Nutrients

Review: Progress in characterizing the linkage between Fusobacterium nucleatum and gastrointestinal cancer – Yang Liu – Journal of Gastroenterology

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome – Keisuke Kosumi – The American Journal of Pathology

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Animal experiments

Commensal microbiota induces colonic barrier structure and functions that contribute to homeostasis – Christina L. Hayes – Scientific Reports

Palmatine ameliorated murine colitis by suppressing tryptophan metabolism and regulating gut microbiota – Xiao-Jun Zhang – Pharmacological Research

Behavioral response to fiber feedingis cohort-dependent and associated with gut microbiota composition in mice – Lucy J.Mailing – Behavioural Brain Research

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Goji Berry Modulates Gut Microbiota and Alleviates Colitis in IL‐10‐Deficient Mice – Yifei Kang – Molecular Nutrition and Food Research

Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota – Yongbo Kang – International Journal of Obesity

Polysaccharide from fermented Momordica charantia L. with Lactobacillus plantarum NCU116 ameliorates type 2 diabetes in rats – He Gao – Carbohydrate Polymers

Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy – Andreassen M – Allergy and Immunology

In vitro experiments

Dietary fatty acids sustain growth of human gut microbiota – Richard Agans – Applied and Environmental Microbiology

Animal microbiome

Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri) – Xiao-Ling Wan – Scientific Reports

Differences in the Gut Microbiota Establishment and Metabolome Characteristics Between Low- and Normal-Birth-Weight Piglets During Early-Life – Na Li – Frontiers in Microbiology

Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves – Bridget E. Fomenky – Scientific Reports

Evaluation of microbial communities associated with the liquid and solid phases of the rumen of cattle offered a diet of perennial ryegrass or white clover – Jenna M. Bowen – Frontiers in Microbiology

Possibilities of early life programming in broiler chickens via intestinal microbiota modulation – Luis A Rubio – Poultry Science

A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms – Alejandra Hernandez-Agreda – Frontiers in Microbiology

Plant, root, and soil microbiome

Interactions of mycorrhiza and protists in the rhizosphere systemically alter microbial community composition, plant shoot-to-root ratio and within-root system nitrogen allocation – Gunnar J. Henkes – Frontiers in Environmental Science

Combined effects of biochar addition and nitrogen fertilizer reduction on the rhizosphere metabolomics of maize (Zea mays L.) seedlings – Nan Cheng – Plant and Soil

Does sulfur fertilizer influence Cu migration and transformation in colloids of soil pore water from the rice (Oryza sativa L.) rhizosphere? – Lijuan Sun – Environmental Pollution

The Alleopathic Compound Luteolin from Peanut Litter Affects Peanut Nodule Formation and the Rhizosphere Microbial Community – Hong-Wei Wang – Agronomy Journal

Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains – Shuai Chang – Plant Diversity

The effect of a medic-wheat rotational system and contrasting degrees of soil disturbance on nematode functional groups and soil microbial communities – Johan Habig – Agriculture, Ecosystems & Environment

Soil-microbial communities indexing from mangroves rhizophere and barren sandy habitats – Kandasamy Saravanakumar – Physiological and Molecular Plant Pathology

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil – Boxi Wang – PLOS One

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – FEMS Microbiology Ecology

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest – Merlin Sheldrake – The ISME Journal

Genetic correlation network prediction of forest soil microbial functional organization
Bin Ma – The ISME Journal

Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach – M. H. Hemmat-Jou – Ecotoxicology

Water and extremophile microbiome

Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs – Nathaniel W. Fortney – Frontiers in Microbiology

Methanogens and iron-reducing bacteria: the overlooked members of mercury methylating microbial communities in boreal lakes – Andrea G. Bravo – Applied and Environmental Microbiology

Metagenomics reveals microbial diversity and metabolic potentials of seawater and surface sediment from a hadal biosphere at the Yap Trench – Xinxu Zhang – Frontiers in Microbiology

Dynamics and determinants of amoeba community, occurrence and abundance in subtropical reservoirs and rivers – Kexin Ren – Water Research

Microbial Ecology

Review: A coexistence theory in microbial communities – Marina Dohi – Royal Society Open Science

Inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier – Data in Brief

Resistome

Selection for increased quorum-sensing cooperation in Pseudomonas aeruginosa through the shut-down of a drug resistance pump – Ron D. Oshri – The ISME Journal

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Fecal Transplants

A Systematic Review of the Efficacy and Safety of Fecal Microbiota Transplant for Clostridium difficile Infection in Immunocompromised Patients – Oluwaseun Shogbesan – Canadian Journal of Gastroenterology and Hepatology

Faecal microbiota transplantation as a treatment for inflammatory bowel disease: a national survey of adult and paediatric gastroenterologists in the UK – James Roger Mcilroy – Frontline Gastroenterology

Introduction to the joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) faecal microbiota transplant guidelines – Benjamin H. Mullish – The Journal of Hospital Infection

Phages and viruses

Detection of Viruses in Clinical Samples Using Metagenomic Sequencing and Targeted Sequence Capture – Kristine M. Wylie – Journal of Clinical Microbiology

Waste and Pollution

Pathogens, faecal indicators and human‐specific microbial source‐tracking markers in sewage – Cristina García‐Aljaro – Journal of Applied Microbiology

September 24, 2018

General microbiology

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt, PHYSICAL REVIEW LETTERS

Small at Size, Big at Impact: Microorganisms for Sustainable Development – Nasib Singh, Microbial Bioprospecting for Sustainable Development

Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations – David J. Krause, Population Genomics

Pregnancy and early life

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum – Aina Gotoh, Scientific Reports

Multi-site human microbiome

Gut–Liver Axis: How Do Gut Bacteria Influence the Liver? – Peter Christopher Konturek, Medical Sciences

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer, Plos One

Optimal immunosuppressor induces stable gut microbiota after liver transplantation – Jian-Wen Jiang, World Journal of Gastroenterology

Human respiratory microbiome

The Microbiome and Tuberculosis: Early Evidence for Cross Talk – Sivaranjani Namasivayam, mBio

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells – Andreas Kyburz, Journal of Allergy and Clinical Immunology

Human oral microbiome

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situbiofilm model – Stefan Rupf, Scientific Reports

Human gut microbiome

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota – A. S. Kovtun, Russian Journal of Genetics

Gut microbiota modulates drug pharmacokinetics – Juanhong Zhang, Drug Metabolism Reviews

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β‐Glucuronidase from the Human Gut Microbiome – Michael S. Little, Protein Science

Structural and Functional Analysis of the Gut Microbiome for Toxicologists – Robert G. Nichols, Current Protocols in Toxicology

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

Animal experiments

Response of goose intestinal microflora to the source and level of dietary fiber – Haizhu Zhou, Poultry Science

Microbiota modulation by eating patterns, dietary and macronutrient composition; impact on food intake – Elizabeth A. Klingbeil, American Journal of Physiology

Water and extremophile microbiome

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking – Moa Hägglund, Frontiers in Microbiology

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N – Beatriz Fernández-Gómez, ISME

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean – Francisco Martinez-Hernandez, ISME

Microbial Community Function in Electroactive Biofilm-based Constructed Wetlands – Ramírez Vargas, Biogeosciences

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation – Emily R. Wolfe, Synthesising Ecology

Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill – Corianne Tatariw, Environmental Pollution

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination – Blaise P. Bougnom, Environmental Research

Plant, root, and soil microbiome

Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat – Muhammad Suleman, Plos One

Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests – Pengyu Zhao, PeerJ

Aphid Colonization Affects Potato Root Exudate Composition and the Hatching of a Soil Borne Pathogen – Grace A. Hoysted, Frontiers in Plant Sciences

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions – Michael James Van Oosten, BMC Plant Biology

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France) – Jorge R. Osman, Antonie van Leeuwenhoek

Plant roots alter microbial functional genes supporting root litter decomposition – Shengjing Shi, Soil Biology and Biochemistry

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil‐specific in Texas Prairie grassland – Swastika Raut, Global Change Biology

Built environment

Houseplants as home health monitors – C. Neal Stewart Jr., SYNTHETIC BIOLOGY

Characterization of Aspergillus niger Isolated from the International Space Station – Jillian Romsdahl, mSystems

Food microbiology

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations – Cristina Sánchez-Gamboa, Foods

Supplementation in mushroom crops and its impact on yield and quality – Jaime Carrasco, AMB Express

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro‐Inflammatory Markers in a Caco‐2/endothelial Cell Co‐Culture Model – Ting Wu, Molecular Nutrition and Food Research

Techniques

A critical evaluation of the use of gas chromatography- and high performance liquid chromatography-mass spectrometry techniques for the analysis of microbial metabolites in human urine after consumption of orange juice – José Luis Ordóñez, Journal of Chromatography A

Recovering cellular biomass from fluids using chemical flocculation – Paul A. Kenward, Environmental Microbiology Reports

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier, Data in Brief

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC – Dhavalkumar Patel, Biotech

Bioinformatics

Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development – Dipannita Hazra, Microbial Bioprospecting for Sustainable Development

Metabolomics

Paradoxes in leaky microbial trade – Yoav Kallus, Nature Communications

Antibiotics

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen – Gleb Pishchany, PNAS

Microbes in the news

Subculture show converts Storefront for Art and Architecture into living lab – The Architects Newspaper, Ali Oriaku

19 September, 2018

Today’s midweek digest includes a brilliant review on the occurrence of HGT within human holobiont and a new approach to analysing microbiome data

General Microbiome

REVIEW: Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.Sitaraman R. Microbiome

Epidemiological aspects of healthcare-associated infections and microbial genomics.Mirande C. Europeans Journal of Clinical Microbiology and Infectious Diseases

Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study. Lee SH. Journal of Clinical Medicine

REVIEW: Proteomics and the microbiome: pitfalls and potential.Lin H. Expert Review of Proteomics

Biological films adhering to the oral soft tissues: structure, composition and potential impact on taste perception.Neyraud E. Journal of Texture Studies

Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. Flaherty BR. Microbiome

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.Jarett JK. Microbiome

The Extended Genotype: Microbially Mediated Olfactory Communication.Carthey AJR. Trends in Ecology and Evolution

Ceftriaxone administration disrupts intestinal homeostasis, mediating non-inflammatory proliferation and dissemination of commensal enterococci.Chakraborty R. Infection and Immunity

Gut Microbiome

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.Martínez I. eLIFE

Human gut <i>Bacteroides</i> capture vitamin B<sub>12</sub> via cell surface-exposed lipoproteins.Wexler AG. eLIFE

Structural basis for the role of serine-rich repeat proteins from <i>Lactobacillus reuteri</i> in gut microbe-host interactions.Sequeira S. PNAS

Rapid and complete dehalogenation of halonitromethanes in simulated gastrointestinal tract and its influence on toxicity. Yin J. Chemosphere.

Diet: Cause or Consequence of the Microbial Profile of Cholelithiasis Disease?Gutiérrez-Díaz I. Nutrients

Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-κB activation through gut microbiota disturbance. Jang HM. Scientific Reports

Salmonella stimulates pro-inflammatory signalling through p21-activated kinases bypassing innate immune receptors.Sun H. Nature Microbiology

Lung Microbiome

Deciphering the Lung Microbiome: Implications for Lung Health and Disease.Johnson MM. Respiration

Plant and Soil Microbiome

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. Sánchez-Soto Jiménez MF. PeerJ.

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing. Li Z. Current Microbiology

Molecular characterization and detection of 16SrIII group phytoplasma associated with Huanglongbing symptoms.Wulff NAA. Phytopathology

Water Microbiome

Analysis of Bacterial Community Structure of Activated Sludge from Wastewater Treatment Plants in Winter. Xu S. BioMed Research International

Biological As(III) oxidation in biofilters by using native groundwater microorganisms.Crognale S. Science of the Total Environment

Animal Experiments and Microbiome

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. Bredon M. Microbiome

The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome.Dranse HJ. PeerJ

Techniques

KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA.Randolph TW. The Annals of Applied Statistics

September 18, 2018

Quite a few articles of interest today:

  1. Foods that are protective of the gut microbiome: Specific oligosaccharides in breast milk can compensate for the effects of C-section births, and cranberries can compensate for the effects of dietary changes in mice.
  2. A possible bi-directional relationship between the gut microbiome and high altitudes: Specific differences in the gut microbiome are associated with differences in tolerance to high altitudes in males, and exposure to high altitudes can alter the gut microbiome in mice.
  3. Microbes in Space: Nitrogen cycle nicroorganisms that may be able to produce food, water and O2 in space, and exposing desert extremophiles to Martian conditions to learn about the kinds of bacteria on other planets

Also: How smoking impacts the lung virome, the association between fecal microbiome profile and phylogeny in deer genera, and the development of the dust microbiome over time in a classroom

Pregnancy and early life

*Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota – Katri Korpela – Scientific Reports

The influence of maternal vaginal flora on the intestinal colonization in newborns and 3-month-old infants – Iwona Gabriel – The Journal of Maternal-Fetal & Neonatal Medicine

Fecal Volatile Organic Compounds in Preterm Infants Are Influenced by Enteral Feeding Composition – Sofia el Manouni el Hassani – Sensors

Multi-site human microbiome

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

Human respiratory microbiome

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

Human anal microbiome

Anal microbial patterns and oncogenic HPV in a pilot study of Nigerian men who have sex with men at risk for or living with HIV – Rebecca G Nowak – AIDS Research and Human Retroviruses

Human gut microbiome

*Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – American Journal of Physiology

Intestinal barrier integrity in patients with plaque psoriasis – Mariusz Sikora – The Journal of Dermatology

Review: Mechanisms by which gut microorganisms influence food sensitivities
– Alberto Caminero – Nature Reviews Gastroenterology & Hepatology

Review: Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis – Kayle Dickson – Medical Hypotheses

Review: ADHD-originating in the gut? The emergence of a new explanatory model – Anna M. Sandgren – Medical Hypotheses

Review: Guideline for the Management of Clostridium Difficile Infection in Children and Adolescents With Cancer and Pediatric Hematopoietic Stem-Cell Transplantation Recipients – Caroline Diorio – Journal of Clinical Oncology

Review: Altered Gut Microbiota in Type 2 Diabetes: Just a Coincidence? – Antonio Sircana – Current Diabetes Reports

Review: Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? – Hanne L.P. Tytgat – Trends in Microbiology

Review: Fecal microbiota transplant – a new frontier in inflammatory bowel disease – Sunkara T – Dove Press

Review: Gut microbiota, cognitive frailty and dementia in older individuals: a systematic review –  Ticinesi A – Dove Press

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Animal experiments

Deletion of poly(ADP‑ribose) polymerase-1 changes the composition of the microbiome in the gut – András Vida – Molecular Medicine Reports

Lactobacillus reuteri F‐9‐35 Prevents DSS‐Induced Colitis by Inhibiting Proinflammatory Gene Expression and Restoring the Gut Microbiota in Mice – Mao‐cheng Sun – Journal of Food Science

*Cranberries attenuate animal-based diet-induced changes in microbiota composition and functionality: A randomized crossover controlled feeding trial – Jose Rodríguez-Morató – The Journal of Nutritional Biochemistry

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

The Effects of Berberine on the Gut Microbiota in Apc min/+ Mice Fed with a High Fat Diet – Huan Wang – Molecules

The influence of gut microbiota dysbiosis to the efficacy of 5-Fluorouracil treatment on colorectal cancer – Lu Yuan – Biomedicine & Pharmacotherapy

Protein deficiency reduces efficacy of oral attenuated human rotavirus vaccine in a human infant fecal microbiota transplanted gnotobiotic pig model – Ayako Miyazaki – Vaccine

In vitro experiments

Butyrate upregulates the TLR4 expression and the phosphorylation of MAPKs and NK‑κB in colon cancer cell in vitro – Tengfei Xiao – Oncology Letters

Animal microbiome

Comparison of the gut microbiota of captive common bottlenose dolphins, Tursiops truncatus in three aquaria – Akihiko Suzuki – Journal of Applied Microbiology

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil – Vinícius C. Cláudio – PLOS ONE

*Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae – Jiaying Li – Frontiers in Microbiology

Probiotics modify body weight together with anxiety states via pro-inflammatory factors in HFD-treated Syrian golden hamster – Ennio Avolio – Behavioural Brain Research

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

The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency – Chloe Matthews – Gut

MicrobesEvaluation of conjunctival microbiota in clinically normal persian squirrels (Sciurus Anomalus) – Houman Faghihi – Journal of Zoo and Wildlife Medicine

Plant, root, and soil microbiome

Trichoderma gamsii affected herbivore feeding behaviour on Arabidopsis thaliana by modifying the leaf metabolome and phytohormones – Dongmei Zhou – Microbial Biotechnology

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Soil microbial response to Rhododendron understory removal in southern Appalachian forests: Effects on extracellular enzymes – Ernest D. Osburn – Soil Biology and Biochemistry

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Bacterial diversity in rhizosphere of Paspalum scrobiculatum L. (kodo millet) is revealed with shotgun metagenome sequencing and data analysis – Ratna Prabha – Data in Brief

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types – Hailing Yu – Soil and Tillage Research

Microbial Ecology

Effects of Cd, Cu, Zn and their combined action on microbial biomass and bacterial community structure – Jiuwei Song – Environmental Pollution

Effects of graphene oxides and silver-graphene oxides on aquatic microbial activity – Kwanyoung Ko – Science of The Total Environment

Built environment

*Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten – Anders B. Nygaard – Microbiome

Microbiological analysis of contact lens cases: impact of the hospital environment – Vinicius Targa Villas Bôas – Arquivos Brasileiros de Oftalmologia

Microbes in space

*Nitrogen cycle microorganisms can be reactivated after Space exposure – Ralph E. F. Lindeboom – Scientific Reports

*Desert cyanobacteria under space and planetary simulations: a tool for searching for life beyond Earth and supporting human space exploration – Daniela Billi – International Journal of Astrobiology

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Bioinformatics

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis – Gherman V. Uritskiy – Microbiome

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations  – Alex N Salazar – Bioinformatics

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Microbes in the news

The electrifying energy of gut microbes – Laty A. Cahoon – Nature News and Views

Bacteria and Art

How Anicka Yi’s Science Experiments Are Expanding the Boundaries of Art – Andrew Russeth – W