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

 

 

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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 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

 

 

April 12, 2018

Of note today: non-exclusive breastfeeding increases the risk of HIV transmission via the alteration of gut microbiome/T-cell activation; Fasting altered the gut microbiome in beneficial ways but only in mice previously fed a high fat diet; An investigation into new species of the honey and bumblebee gut commensal genus Gilliamella; Catfish development shapes gut microbial community structure independent of diet; A metagenomic analysis of the skin microbiome of the frog, Craugastor fitzingeri; The microbiome is altered during the bioremediation of herbicide contaminated soil; The impact of urban density on the soil microbiome; A randomized placebo controlled clinical trial of a microbiota based drug for the prevention of Clostridium difficile Infection; and the virome of the Cuatro Ciénegas Basin of Mexico

 
Pregnancy and early life

*Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants – Lianna F Wood – Clinical Infectious Diseases

Comparative Analysis of Gut Microbial Communities in Children under 5 Years Old with Diarrhea – Hongyu Wen – Journal of Microbiology and Biotechnology

Review: Microbiome in Embryonic Implantation and Implantation Failure – Jason M. Franasiak – Recurrent Transplant Failure

Human oral microbiome

The cultivable bacterial flora of the esophagus in subjects with esophagitis – Elisabeth Norder Grusell – Scandinavian Journal of Gastroenterology

Human urogenital microbiome

The upper and lower tract urinary microbiomes of stone formers are similar: a pilot study – Heiko Yang – The Journal of Urology

Human gut microbiome

Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy – Evgenii I – bioRxiv

The microbial metabolite TMAO in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages – Catharina Missailidis – AIDS

Review: Microbiome-Mediated Upregulation of MicroRNA-146a in Sporadic Alzheimer’s Disease – Yuhai Zhao – Frontiers in Neurology

Review: Interplay Between the Gut-Brain Axis, Obesity and Cognitive Function – Ana Agustí – Frontiers in Neuroscience

Review: The Brain–Intestinal Mucosa–Appendix– Microbiome–Brain Loop – Luis Vitetta – Diseases

Review: New Therapeutic Drugs from Bioactive Natural Molecules: the Role of Gut Microbiota Metabolism in Neurodegenerative Diseases – Francesco Di Meo – Current Drug Metabolism

Review: Microbial Effects on Immunity in HIV: Virus, Gender or Sexual Preference Induced? – Nichole R. Klatt – EBioMedicine

Review: Microbiome and Gut Dysbiosis – José E. Belizário – Metabolic Interaction in Infection

Review: Clostridium Bacteria and Autism Spectrum Conditions: A Systematic Review and Hypothetical Contribution of Environmental Glyphosate Levels – Isadora Argou-Cardozo  – Medical Science

Review: Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions – Edmund B. Chen – Journal of Gastrointestinal Surgery

Review: Maintenance of intestinal homeostasis by mucosal barriers – Ryu Okumura – Inflammation and Regeneration

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Animal experiments

*Food withdrawal alters the gut microbiota and metabolome in mice – Xiaojiao Zheng – The FASEB Journal

Animal microbiome

*Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera) – Jane Ludvigsen – International Journal of Systematic and Evolutionary Microbiology

*Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water – Zhimin Zhang – Frontiers in Microbiology

*The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data – Eria A. Rebollar – Frontiers in Microbiology

Gut Microbiota-Regulated Pharmacokinetics of Berberine and Active Metabolites in Beagle Dogs After Oral Administration – Ru Feng – Frontiers in Pharmacology

Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season – Allison Clark – Frontiers in Physiology

Review: Opinion: Pesticides Could Alter Amphibian Skin Microbiomes and the Effects of Batrachochytrium dendrobatidis – Krista A. Mccoy – Frontiers in Microbiology

Preprint: Earthworms and Cadmium – heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils? – Maja Šrut – bioRxiv

Effect of Dietary Non-phytate Phosphorus Levels on the Diversity and Structure of Cecal Microbiota in Meat Duck from 1 to 21 d of age – S J Dai – Poultry Science

Rumen bacterial community structure impacts feed efficiency in beef cattle – Henry A Paz – Journal of Animal Science

Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein  – E A Latham – Journal of Animal Science

Plant, root, and soil microbiome

*Dynamic changes in microbial communities during the bioremediation of herbicide (chlorimuron-ethyl and atrazine) contaminated soils by combined degrading bacteria – Jian Wang – PLOSone

Comparison of Microbial Community Structure in Kiwifruit Pollens – Min-Jung Kim – The Plant Pathology Journal

*Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces – Haitao Wang – Environmental Science and Technology

Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China – Baihui Ren – Scientific Reports

Preprint: Social Motility: Interaction between two sessile soil bacteria leads to emergence of surface motility – Lucy M McCully – bioRxiv

Water and extremophile microbiome

Sulphate-reducing bacteria (SRB) in the Yangtze Estuary sediments: Abundance, distribution and implications for the bioavailibility of metals – Zuo-shun Niu – Science of The Total Environment

Bacterial community succession and degradation patterns of hydrocarbons in seawater at low temperature – Leendert Vergeynst – Journal of Hazardous Materials

Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition – Emily B. Graham – PeerJ

Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries – Kai Wang – Science of The Total Environment

Nitrate amendment reduces biofilm biomass and shifts microbial communities in remote, oligotrophic ponds – Carmella Vizza – Freshwater Science

Microbial Ecology

Bacterial interspecies quorum sensing in the mammalian gut microbiota – Karina Bivar Xavier – Comptes Rendus Biologies

Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass – Aoife Joyce – Frontiers in Microbiology

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Probiotics / prebiotics

*Results from a Randomized Placebo-Controlled Clinical Trial of a RBX2660—a Microbiota-based Drug for the Prevention of Recurrent Clostridium difficile Infection – Erik R Dubberke – Clinical Infectious Dieases

Outer Membrane Vesicles From Probiotic and Commensal Escherichia coli Activate NOD1-Mediated Immune Responses in Intestinal Epithelial Cells – María-Alexandra Cañas – Frontiers in Microbiology

Fecal Transplants

Recruitment of feces donors among blood donors: Results from an observational cohort study – Simon Mark Dahl Jørgensen – Gut Microbes

Fecal microbiota transplantation associated with 10 years of stability in a patient with SPMS – Seraj Makkawi – Neurology, Neuroimmunology & Neuroinflammation

Phages and viruses

Metagenomic analysis of ssDNA viruses in surface seawater of Yangshan Deep-Water Harbor, Shanghai, China – Hongming Wang – Marine Genomics

*The viral structure of the Cuatro Ciénegas Basin, a unique oasis in Northern Mexico, reveals a highly diverse population at a small geographic scale – B. Taboada – Applied and Environmental Microbiology

Waste and Pollution

Metataxonomy and functionality of wood-tar degrading microbial consortia – Lorenzo Brusetti – Journal of Hazardous Materials

Variations in the denitrifying microbial community and functional genes during mesophilic and thermophilic anaerobic digestion of cattle manure – Kaiyu Zhang – Science of The Total Environment

Techniques

Electrochemical detection of viable bacteria in urine and antibiotic selection – Noriyuki Nakamura – Biosensors and Bioelectronics

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Microbes in the news

Nova-like explosion of spinning live bacteria explained – A’ndrea Elyse Messer – Phys.org

New ‘NanoZymes’ use light to kill bacteria – Science Daily

The Germs That Love Diet Soda – Moises Velasquez-Manoff

Bacteria can pass on memory to descendants, researchers discover – Melody Pupols – Phys.org

Charting an underexplored landscape: The genitourinary microbiome – Medical Press

April 5, 2018

Of note today: An evaluation of multi-site human microbiome temporal stability over six months; The impacts of 1,000 non-antibiotic drugs on the in vitro gut microbiome; Caspase-1 might modulate the relationship between stress, the gut microbiome, inflammation and depressive-like behaviour in mice; And the impact of warming on the Antarctic soil microbiome

Events and jobs

Community Sequencing Scientists, Indigo, Boston MA

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General microbiome

Review: No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases – Douglas B. Kell – Biological Review

Review: Environmental microbiology to the rescue of planet Earth – Víctor de Lorenzo – Environmental Microbiology

Multi-site human microbiome

*Quantification of Human Microbiome Stability over Six Months: Implications for Epidemiologic Studies – Rashmi Sinha – American Journal of Epidemiology

Review: Of genes and microbes: solving the intricacies in host genomes – Jun Wang – Protein & Cell

Human gut microbiome

Review: Serotonin as a Link Between the Gut-Brain-Microbiome Axis in Autism Spectrum Disorders – Narek Israelyan – Pharmacological Research

The Intestinal Microbiome Influences the Response of Cancers to PD-1–Based Immunotherapy: Might Fecal Transplantation Become Part of Cancer Therapy? – Paolo Biancheri – Gastroenterology

*Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi – Thomas A. Auchtung – mSphere

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

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Animal experiments

*The inflammasome and the microbiota-gut-brain axis – Ma-Li Wong – Neurology, Psychiatry and Brain Research

Exposure to Formaldehyde Perturbs the Mouse Gut Microbiome – Junhui Guo – Genes

Effect of prenatal administration of low dose antibiotics on gut microbiota and body fat composition of newborn mice – Ayumi Yoshimoto – Journal of Clinical Biochemistry and Nutrition

The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts – Savannah L. Logan – PNAS

Microbes vs. chemistry in the origin of the anaerobic gut lumen – Elliot S. Friedman – PNAS

Animal microbiome

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil – Andrea Bagi – BMC Microbiology

Review: Host-microbe interactions in octocoral holobionts – recent advances and perspectives – Jeroen A. J. M. van de Water – BMC Microbiome

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure – Inês Barros – AIMS Microbiology

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary – Zana Brigitta –  Acta Veterinaria Hungarica

Plant, root, and soil microbiome

Microbial community responses to modern environmental and past climatic conditions in Omongwa pan, western Kalahari: A paired 16S rRNA gene profiling and lipid biomarker approach – S. Genderjahn – Biogeosciences

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

*Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region – Dockyu Kim – Journal of Basic Microbiology

Effect of temperature on bacterial community in petroleum hydrocarbon-contaminated and uncontaminated Antarctic soil – C. W. Chong – Polar Biology

Variations of bacterial community diversity within the rhizosphere of three phylogenetically related perennial shrub plant species across environmental gradients – Xiaofan Na – Frontiers in Microbiology

Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove – Moriyuki Hamada – Archives of Microbiology

Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam – C.N. Le – Biological Control

Microbial Decomposer Dynamics: Diversity and Functionality Investigated through a Transplantation Experiment in Boreal Forests – Alessia Bani – Microbial Ecology

Investigation of the core microbiome in main soil types from the East European plain – Elizaveta V. Pershina – Science of The Total Environment

Water and extremophile microbiome

Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia) – Andrea Y. Calvo – Canadian Journal of Microbiology

Review: Extremophilic yeasts: the toughest yeasts around? – Pietro Buzzini – Yeast

Neptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea – Yan-Jiao Zhang – International Journal of Systematic and Evolutionary Microbiology

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K. Nuy – Science of The Total Environment

*Evidence for selective bacterial community structuring on microplastics – Martin Ogonowski – Environmental Microbiology

Microbial Ecology

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis – Promi Das – PLOSone

Review: What will it take to understand the ecology of symbiotic microorganisms? – Angela E Douglas – Environmental Microbiology

Built environment

Fungi-induced paint deterioration and air contamination in the Assiut University hospital, Egypt – Ismail R. Abdel-Rahim – Indoor and Buility Environment

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Probiotics / prebiotics

Lactobacilli and lactoferrin: Biotherapeutic effects for vaginal health – Lucia Bertuccini – Journal of Functional Foods

The viability of probiotics in water, breast milk, and infant formula – Claire Watkins – European Journal of Pediatrics

Bioinformatics

Constructing Lightweight And Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA) – Trevor Cickovski – Bioinformatics

Numerical analyses of intestinal microbiota by data mining – Toshio Kobayashi – Journal of Clinical Biochemistry and Nutrition

Waste and Pollution

Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community – S. W. How – Water Science and Technology

Techniques

Visualization of Microbiota in Tick Guts by Whole-Mount In Situ Hybridization – Caitlin E. Moss – Jove

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Microbes in the news

Phage-host interactions are more complicated than most laboratory studies suggest – Phys.org

 

March 29, 2018

Of special note today: gut microbiota species expressing orthologs of human Ro60 might be involved in triggering and sustaining chronic autoimmunity in lupus; The portal vein blood microbiome in patients with liver cirrhosis; A randomized clinical study suggests dietary promotion of short chain fatty acid producing gut microbes as an effective treatment for type 2 diabetes; and the sexual dimorphism of root, flower and leaf microbiomes in the wild strawberry plant

Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University – NY

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General microbiome

Review: Discovering antibiotics from the global microbiome – Yick Chong Lam – Nature Microbiology

Pregnancy and early life

Review: Milk Glycans and Their Interaction with the Infant-Gut Microbiota – Nina Kirmiz – Annual Review of Food Science and Technology

Multi-site human microbiome

*Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus – Teri M. Greiling – Science Translational Medicine

Human nearly-sterile sites

*Circulating microbiome in blood of different circulatory compartments – Robert Schierwagen – BMJ Blood

Human gut microbiome

*Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes – Liping Zhao – Science

Review: Impact of dietary compounds on cancer-related gut microbiota and microRNA – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Review: Influence of Altered Gut Microbiota Composition on Aging and Aging-Related Diseases – Jeonghyun Choi – Journal of Lifestyle Medicine

Review: Gut microbiome modulates efficacy of immune checkpoint inhibitors
Ming Yi – Journal of Hematology & Oncology

Protocol: Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods  – Shoshannah Eggers – BMJ Journal

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Animal experiments

MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota – Chong-Tao Du – International Journal of Molecular Sciences

Loss of microRNA-21 Influences the Gut Microbiota Causing Reduced Susceptibility in a Murine Model of Colitis – Daniel G W Johnston – Journal of Crohn’s and Colitis

Towards an Integrative Understanding of tRNA Aminoacylation–Diet–Host–Gut Microbiome Interactions in Neurodegeneration – Elena L. Paley – Nutrients

Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – eLife

Animal microbiome

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle – Mi Zhou – BMC Microbiology

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore – Angélique Gobet – BMC Microbiology

Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome – Laura B. Dickson – BMC Parasites & Vectors

Plant, root, and soil microbiome

*The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – Scientific Reports

The potential of plant microbiota in reducing postharvest food loss – Franziska Buchholz – Microbial Biotechnology

Root microbiota shift in rice correlates with resident time in the field and developmental – Jingying Zhang – Science China Life Sciences

Microbial Ecology

Allometry and Ecology of the Bilaterian Gut Microbiome – Scott Sherrill-Mix – mBio

Preprint: Changes in the genetic requirements for microbial interactions with increasing community complexity – Manon Morin – bioRxiv

Built environment

Drinking water microbiome assembly induced by water stagnation – Fangqiong Ling – The ISME Journal

Food microbiology

Constraint-based modeling in microbial food biotechnology – Martin H. Rau – Biochemical Society Transactions

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing – Zhichang Qiu – Food Research International

Guidance on the characterisation of microorganisms used as feed additives or as production organisms – EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) – EFSA Journal

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Probiotics / prebiotics

Probiotic treatment reduces the autistic-like excitation/inhibition imbalance in juvenile hamsters induced by orally administered propionic acid and clindamycin – Afaf El-Ansary – Metabolic Brain Disease

Review: A review of probiotic supplementation in healthy adults: helpful or hype? – Saman Khalesi – European Journal of Clinical Nutrition

Fecal Transplants

Effect of Vegan Fecal Microbiota Transplantation on Carnitine‐ and Choline‐Derived Trimethylamine‐N‐Oxide Production and Vascular Inflammation in Patients With Metabolic Syndrome – Loek P. Smits – Journal of the American Heart Association

Bioinformatics

Review: Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome – Morgan G. I. Langille – mSystems

Techniques

Hybridization capture reveals microbial diversity missed using current profiling methods – Cyrielle Gasc – BMC Microbiology

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Microbes in the news

Just passing through: fungi not part of the gut – Fungus species don’t play a role in healthy human microbiomes – Andrew Masterson – Cosmos

Plants, fungi and bacteria work together to clean polluted land – Genetic analysis shows microbial interactions help fast-growing trees break down petrochemical pollutants in soil – Science Daily

Bacteria and Art

Art and biology students participate in creative collaboration – Sierra Guardiola – The Ithacan

 

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