Category Archives: Human reproductive or urinary

March 3, 2017

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Antiphage defense systems in microbial genomes, oral pathogen inhibition by wine polyphenols and an oral probiotic, and analysis of E. coli gene expression in simulated spaceflight.

Events and jobs

Call for Expressions of Interest: Microbiology Twitter Teachers for New MOOC – Spanish Society for Microbiology

Endowed Chair in Molecular Genetics Waksman Institute of Microbiology – Rutgers University

General microbiome

Creating a 3D microbial and chemical snapshot of a human habitat – Clifford A Kapono – Scientific Reports

Human oral microbiome

Inhibition of Oral Pathogens Adhesion to Human Gingival Fibroblasts by Wine Polyphenols Alone and in Combination with an Oral Probiotic – Adelaida Esteban-Fernández – Journal of Agricultural and Food Chemistry

Human vaginal microbiome

Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Zhi-Luo Deng – bioRxiv

Human gut microbiome

Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia – Bruce A Rosa – Microbiome

Animal experiments

Pre-print: Orthogonal dietary niche enables reversible engraftment of a gut bacterial commensal – Sean M Kearney – bioRxiv

Pre-print: Clearing the FoG: Antifungal tolerance is a subpopulation effect that is distinct from resistance and is associated with persistent candidemia – Alexander Rosenberg – bioRxiv

Blueberry Supplementation Influences the Gut Microbiota, Inflammation, and Insulin Resistance in High-Fat-Diet–Fed Rats – Sunhye Lee – Journal of Nutrition

Animal microbiome

Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus – Biao Chen – AMB Express

Water and extremophile microbiome

Pre-print: Microzooplankton distribution in the Amundsen Sea Polynya (Antarctica) during an extensive Phaeocystis antarctica bloom – Rasmus Swalethorp – bioRxiv

Microbes in space

Pre-print: Analysis of Escherichia coli Flagellin Gene Expression in Simulated Spaceflight Growth Conditions – Kyle M Hetrick – bioRxiv

Phages and viruses

Systematic discovery of antiphage defense systems in the microbial pangenome – Shany Doron – Science

Bioinformatics

Pre-print: VirTect: a computational method for detecting virus species from RNA-Seq and its application in head and neck squamous cell carcinoma – Atlas Khan – bioRxiv

Techniques

Pre-print: Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets – Edouard A Hay – bioRxiv

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem – Stilianos Louca – Microbiome

Improving saliva shotgun metagenomics by chemical host DNA depletion – Clarisse A Marotz – Microbiome

Microbes in the news

Your skin is crawling with bacteria, and some of them might help fight cancer – Claire Maldarelli – Popular Science

Most Viruses And Bacteria Fall From The Sky – Astrobiology Web

Microbes on the market

Six Leading Pharma Firms to Participate at Pharmaceutical Microbiology Event in San Diego – Technology Networks

Science, career, and publishing

Pre-print: Persistent Underrepresentation of Women’s Science in High Profile Journals – Yiqin Alicia Shen – bioRxiv

Pre-print: Female grant applicants are equally successful when peer reviewers assess the science, but not when they assess the scientist – Holly O Witteman – bioRxiv

March 2, 2018

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Events and jobs

Enter our ‘scientist at work’ photo contest – Nature

General microbiome

Review: To respond or not to respond — a personal perspective of intestinal tolerance – AM Mowat – Nature Reviews

“Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system – AE Naas – BMC Microbiome

Human vaginal microbiome

Fractional CO2 laser for genitourinary syndrome of menopause in breast cancer survivors: clinical, immunological, and microbiological aspects – A Becorpi – Lasers in Medical Science

Human gut microbiome

Environment dominates over host genetics in shaping human gut microbiota – D Rothschild – Nature

The gut microbiota and immune checkpoint inhibitors – A Humphries – Human Vaccines and Immunotherapeutics

Probiotic supplementation increases obesity with no detectable effects on liver fat or gut microbiota in obese Hispanic adolescents: a 16-week, randomized, placebo-controlled trial. – RB Jones – Pediatric Obesity

Adaptation of adherent-invasive E. coli to gut environment: Impact on flagellum expression and bacterial colonization ability. – G Sevrin – Gut Microbes

Editorial: Gut microbiomes and their metabolites shape human and animal health – W Park –  Journal of Microbiology

Review: Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease – T Eom – Journal of Microbiology

Review: Targeting friend and foe: Emerging therapeutics in the age of gut microbiome and disease – JA Cho – Journal of Microbiology

Review: Mind-altering with the gut: Modulation of the gut-brain axis with probiotics – N Kim – Journal of Microbiology

Gut microbial composition in patients with psoriasis – FM Codoñer – Scientific Reports

Clostridium scindens is present in the gut microbiota during Clostridium difficile infection. A metagenomic and culturomic analysis. – S Amrane – Journal of Clinical Microbiology

Letter to Editor: Microbiome and Esophageal Adenocarcinoma—Letter – NO Kaakoush – Cancer Research

Animal experiments 

Altered gut microbiome promotes proteinuria in mice induced by Adriamycin – Q Jiang – AMB Express

Functional Anthocyanin-Rich Sausages Diminish Colorectal Cancer in an Animal Model and Reduce Pro-Inflammatory Bacteria in the Intestinal Microbiota. – G Fernández – Genes (Basel)

Animal microbiome 

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen – RD Stewart – Nature Communications

The Ruminococci: key symbionts of the gut ecosystem – AJL Reau – Journal of Microbiology

Plant, root, and soil microbiome

Concepts & Synthesis: Toward more robust plant-soil feedback research – MJ Rinella – Ecology

Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. – FP Cid – Extremophiles

Competition–colonization tradeoffs structure fungal diversity – GR Smith – The ISME Journal

Water microbiome and extremophile 

Environmental factors driving fungal distribution in freshwater lake sediments across the Headwater Region of the Yellow River, China – J Tian – Scientific Reports

Community assembly processes underlying phytoplankton and bacterioplankton across a hydrologic change in a human-impacted river. – A Isabwe – The Science of the Total Environment

Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation – R Omrani – Biodegradation

Built environment 

‘Cyclical Bias’ in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation – A Rodriguez-Palacios – Scientific Reports

Phages and viruses

Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics – JA Grasis – Viral Metagenomics

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere – J Abrahão – Nature Communications

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages – L Cheng – BMC Microbiology

Techniques

Highly sensitive detection and quantification of the secreted bacterial benevolence factor RoxP using a capacitive biosensor: A possible early detection system for oxidative skin diseases. – G Ertürk – PLoS One

Review: Emerging Technologies for Molecular Diagnosis of Sepsis – M Sinha – Clinical Microbiology Reviews

Microbes in the news

Biofilm Replaces Plastic Packaging in this Dutch Supermarket Aisle – Futurism

For the Microbiome, the Nature vs. Nurture Debate Comes into Focus – GEN

With $36M series B, Finch goes full speed ahead in microbiome therapy – Fierce Biotech

Genetics or lifestyle: What is it that shapes our microbiome? – Science Daily

More than soap scum: Learning about biofilms – Silive

7 Startups Treating Disease Using the Microbiome – Nanalyze

ATM keypads, restaurant menus full of bacteria – News3Channel

Non-microbiology picks

Intellectual Synthesis in Mentorship Determines Success in Academic Careers – JF Lienard – bioRxiv

 

March 1, 2018

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

Pregnancy and early life

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

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

Human respiratory microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

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

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

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Animal experiments

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

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

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

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

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

Animal microbiome

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

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

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

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

Air Microbiome

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

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

Microbial Ecology

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

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

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

Resistome

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

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

Phages and viruses

*The Global Virome Project – Dennis Carroll – Science

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

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

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

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

Metabolomics

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

Waste and Pollution

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

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

Techniques

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

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Microbes in the news

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

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

The silent microbiome crisis – Tobias Rees – The Washington Post

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

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

February 24, 2018

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100+ alerts today with interesting papers across every category. Some highlights include choosing FMT donors, viral insulin-like peptides, and 2 papers on detecting duplicated figures.

General microbiome
Review: The microbiome in precision medicine: the way forward. – Joseph F Petrosino – Genome Medicine

Motivations of participants in the citizen science of microbiomics: data from the British Gut Project. – Lorenzo Del Savio – Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Pregnancy and early life
The Role of the Genitourinary Microbiome in Pediatric Urology: a Review. – Daniel Gerber – Current Urology Reports

Review: Reproductive outcome of patients undergoing in vitro fertilization treatment and diagnosed with bacterial vaginosis or abnormal vaginal microbiota: a systematic PRISMA review and meta-analysis. – Thor Haahr – Bjog : An International Journal Of Obstetrics And Gynaecology

Multi-site human microbiome
Review: The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. – Bruno Bonaz – Frontiers In Neuroscience

Human vaginal microbiome
Protein Content of Cervicovaginal Fluid Is Altered During Bacterial Vaginosis. – Carolina Sanitá Tafner Ferreira – Journal Of Lower Genital Tract Disease

Human nearly-sterile sites
Microbiome-Host Interactions in Hematopoietic Stem-Cell Transplant Recipients. – Tessa Andermann – Biology Of Blood And Marrow Transplantation : Journal Of The American Society For Blood And Marrow Transplantation

Human gut microbiome
** Competitively Selected Donor Fecal Microbiota Transplantation: Butyrate Concentration and Diversity as Measures of Donor Quality. – Danielle Barnes – Journal Of Pediatric Gastroenterology And Nutrition

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. – Federica Gigliucci – Frontiers In Cellular And Infection Microbiology

Review: Human Gut Microbiota and Gastrointestinal Cancer. – Changting Meng – Genomics, Proteomics & Bioinformatics

Review: Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism. – Jing Gao – Frontiers In Cellular And Infection Microbiology

Microbial interactions
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia. – Ross P Carlson – Biochemical Society Transactions

Worlds Apart – Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions. – Zhi-Luo Deng – Frontiers In Microbiology

Using niche breadth theory to explain generalization in mutualisms – Rebecca T. Batstone – Ecology

Metabolic division of labor in microbial systems – Ryan Tsoi – PNAS

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle – Karthik Anantharaman – ISME

Review: Bacterial – Fungal Interactions: ecology, mechanisms and challenges. – A Deveau – Fems Microbiology Reviews

Role of extracellular polymeric substances in polymicrobial biofilm infections of Staphylococcus epidermidis and Candida albicans modelled in the nematode Caenorhabditis elegans. – Jillian E Holt – Pathogens And Disease (older, from July 2017)

Animal experiments
Acute and repeated exposure to social stress reduces gut microbiota diversity in Syrian hamsters. – Katherine A Partrick – Behavioural Brain Research

1H NMR based identification of intestinally-absorbed metabolites by Ussing chamber analysis of the rat cecum. – Meredith Dinges – Analytical Chemistry

Influence of gemcitabine chemotherapy on the microbiota of pancreatic cancer xenografted mice. – Concetta Panebianco – Cancer Chemotherapy And Pharmacology

Grape seed proanthocyanidins influence gut microbiota and enteroendocrine secretions in female rats. – Àngela Casanova-Martí – Food & Function

Combined Dietary Anthocyanins, Flavonols, and Stilbenoids Alleviate Inflammatory Bowel Disease Symptoms in Mice. – Aurelia Scarano – Frontiers In Nutrition

Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion. – Jörn Karhausen – Laboratory Investigation; A Journal Of Technical Methods And Pathology

Glucocorticosteroids and ciclosporin do not significantly impact canine cutaneous microbiota. – Giovanni Widmer – Bmc Veterinary Research

The effects of high dose of two manganese supplements (organic and inorganic) on the rumen microbial ecosystem. – Svetlana Kišidayová – Plos One

Hydrogen peroxide production by lactobacilli promotes epithelial restitution during colitis. – Ashish K Singh – Redox Biology

Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. – Meng-Fei Sun – Brain, Behavior, And Immunity

Rotenone induces gastrointestinal pathology and microbiota alterations in a rat model of Parkinson’s disease. – Michaela E Johnson – Neurotoxicology

Prenatal Androgen Exposure Causes Hypertension and Gut Microbiota Dysbiosis. – Shermel Sherman – Gut Microbes

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome – Claudia Pogoreutz – Ecology And Evolution

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. – Mireia Uribe-Herranz – Jci Insight

Animal microbiome
Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract. – Li Zhang – Frontiers In Microbiology

Characterization of gut bacterial flora of Apis mellifera from north-west Pakistan – Syed Ishtiaq Anjum – Saudi Journal Of Biological Sciences

A Member of the Roseobacter Clade, Octadecabacter sp., is the Dominant Symbiont in the Brittle Star Amphipholis squamata. – Kathleen M Morrow – Fems Microbiology Ecology

Alimentary microbes of winter-form Drosophila suzukii. – M T Fountain – Insect Molecular Biology

The development of gut microbiota in ostriches and its association with juvenile growth – Elin Videvall – bioRxiv

Review: Regulation of intestinal health by branched-chain amino acids. – Hua Zhou – Animal Science Journal = Nihon Chikusan Gakkaiho

Book chapter: Termite Gut Microbiome – Navodita Maurice – Sustainability in Plant and Crop Protection

Plant, root, and soil microbiome
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. – Joseph A Edwards – Plos Biology

Quantitative Genetic Analysis of the Maize Leaf Microbiome – Jason G. Wallace – bioRxiv

 

Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation. – Miriam B Herold – Fems Microbiology Letters

Landscape topography structures the soil microbiome in arctic polygonal tundra. – Neslihan Taş – Nature Communications

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China. – Xiaodong Yao – The Science Of The Total Environment

Seasonal dynamics in the community structure and trophic structure of testate amoebae inhabiting the Sanjiang peatlands, Northeast China. – Lihong Song – European Journal Of Protistology

Investigation of rhizospheric microbial communities in wheat, barley and two rice varieties at the seedling stage. – Tao Lu – Journal Of Agricultural And Food Chemistry

Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy warrants ecosystem function. – Witoon Purahong – Environmental Microbiology

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems. – Qisong Li – International Journal Of Molecular Sciences

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. – Liesje Mommer – The New Phytologist

Isolation and characterization of N2 -fixing bacteria from giant reed and switchgrass for plant growth promotion and nutrient uptake – Jia Xu – Journal of Basic Microbiology

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks – Hirokazu Toju – bioRxiv

Water and extremophile microbiome
Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation. – Ian Salter – Plos One

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. – Jeremiah J Minich – Plos One

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge. – Blake D Ramsby – Molecular Ecology

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems – Navdeep K Dhami – Frontiers In Microbiology

Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River. – Yaxin Pei – Frontiers In Microbiology

Assessing the microbial communities inhabiting drinking water networks and nitrifying enrichments with special respect on nitrifying microorganisms. – Zsuzsanna Nagymáté – Acta Microbiologica Et Immunologica Hungarica

Microbial community composition along a 50,000 year lacustrine sediment sequence. – Aurèle Vuillemin – Fems Microbiology Ecology

Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. – Eléonore Frouin – Frontiers In Microbiology

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition – Alescia A. Roberto – Water Research

Built environment
Dog introduction alters the home dust microbiota. – Alexandra Sitarik – Indoor Air

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors. – Anirudra Parajuli – Frontiers In Microbiology

Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors. – Shaoli Li – Scientific Reports

Microbes in space
Soil microbial habitats in an extreme desert Mars-analogue environment – Kimberley Warren-Rhodes – bioRxiv

Food microbiology
** Editorial: Microbiome Yarns: human milk oligosaccharides, Bifidobacterium and immunopowergames. – Kenneth Timmis – Microbial Biotechnology

Detection of Bacterial DNA During the Process of Sake Production Using Sokujo-Moto. – Momoka Terasaki – Current Microbiology

A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial. – Charlotte Bamberger – Nutrients

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity. – Rocío Escribano-Viana – Frontiers In Microbiology

Review: The Promising Pharmacological Effects and Therapeutic/Medicinal applications of Punica Granatum L. (Pomegranate) as a Functional Food in Humans and Animals. – Kuldeep Dhama – Recent Patents On Inflammation & Allergy Drug Discovery

Probiotics / prebiotics / antibiotics
Bile-Salt-Hydrolases from the Probiotic Strain – Thibault Allain – Frontiers In Microbiology

** A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. – Marc W Van Goethem – Microbiome

PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community. – Jing Wang – Environmental Pollution (Barking, Essex : 1987)

Short-term Oral Antibiotics Treatment Promotes Inflammatory Activation of Colonic Invariant Natural Killer T and Conventional CD4 – Claudia Burrello – Frontiers In Medicine

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3 – François P. Douillard – Plos One

A probiotic complex, rosavin, zinc, and prebiotics ameliorate intestinal inflammation in an acute colitis mouse model. – Jin-Sil Park – Journal Of Translational Medicine

Phages and viruses
** Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host-microbe interactions. – Emrah Altindis – Proceedings Of The National Academy Of Sciences Of The United States Of America

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. – Mitsuhiro Yoshida – Frontiers In Microbiology

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. – Jacob H Munson-McGee – The Isme Journal

Bioinformatics
MUGAN: Multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment. – Byunghan Lee – Bioinformatics (Oxford, England)

Techniques
Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next-Generation Sequencing – Alyssa J. Badgley – Forensic Sciences

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data – Jonathan M Palmer – bioRxiv

Genomes
Complete Genome Sequence and Genomic Characterization of – Won-Hyong Chung – Frontiers In Pharmacology

Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L. –  Guo-Yan Zhao – International Journal of Systematic and Evolutionary Microbiology

Science, publishing, and career
Testing Hypotheses on Risk Factors for Scientific Misconduct via Matched-Control Analysis of Papers Containing Problematic Image Duplications – Daniele Fanelli – Scientific and Engineering Ethics

Bioscience-scale automated detection of figure element reuse – Daniel E Acuna – bioRxiv

February 21, 2018

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Events and jobs

BioData World West 2018 – March 13-14 – Hotel Kabuki, San Francisco, CA

General microbiome

[editorial] Systems biology of the human microbiome – BP Bernabé, L Cralle, JA Gilbert – Current Opinion in Biotechnology, 2018

[pre-print] Growth tradeoffs produce complex microbial communities without direct interactions – Michael Manhart – bioRxiv

Exploring the Multifaceted Role of Microbes in Pharmacology – Mitali Mishra – Microbial Biotechnology

Human reproductive or urinary microbiome

Seminal bacterial composition in patients with obstructive and non-obstructive azoospermia – Houyang Chen – Experimental and Therapeutic Medicine

Human respiratory microbiome

Virome and bacteriome characterization of children with pneumonia and asthma in Mexico City during winter seasons 2014 and 2015 – Jose A. Romero-Espinoza – PLOS One

Human gut microbiome

[pdf[ Phytochemicals that influence gut microbiota as prophylactics and for the treatment of obesity and inflammatory diseases – Lucrecia Carrera-Quintanar – Hindawi

Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis – F Bishehsari – Genes

A Cross-Talk Between Microbiota-Derived Short-Chain Fatty Acids and the Host Mucosal Immune System Regulates Intestinal Homeostasis and Inflammatory Bowel Disease – Pedro Gonçalves – Inflammatory Bowel Diseases

Animal microbiome

Differential microbial communities of omnivorous and herbivorous cattle in Southern China – Susanna K.P. Lau – Computational and Structural Biotechnology Journal

The gills of reef fish support a distinct microbiome influenced by host-specific factors – Zoe A. Pratte – Applied and Environmental Microbiology

Metagenomic analysis of orange colored protrusions from the muscle of Queen Conch Lobatus gigas (Linnaeus, 1758) – Jaison H. Cuartas – PeerJ

Plant, root, and soil microbiome

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Structural and metabolic diversity of rhizosphere microbial communities of Phragmites karka in a tropical coastal lagoon – Pratiksha Behera – Applied Soil Ecology

Responses of soil microbial communities to a short-term application of seaweed fertilizer revealed by deep amplicon sequencing – Mingpeng Wang – Applied Soil Ecology

[pdf] The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery – Roberta Fulthorpe – Frontiers in Ecology and Evolution

Microbes and Their Role in Drought Tolerance of Agricultural Food Crops – Rout George Kerry – Microbial Biotechnology

Microscopic and Metagenomic Analyses of Peltigera ponojensis (Peltigerales, Ascomycota) – Linda E. Graham – International Journal of Plant Sciences

Frankia Diversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity of Frankia Populations in Corresponding Rhizosphere Soils – Seifeddine Ben Tekaya – Applied and Environmental Microbiology

High frequency cropping of pulses modifies soil nitrogen level and the rhizosphere bacterial microbiome in 4-year rotation systems of the semiarid prairie – Chantal Hamel – Applied Soil Ecology

Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization – Birgit Wolters – FEMS Microbiology Ecology

Water and extremophile microbiome

Variability in metagenomic samples from the Puget Sound: Relationship to temporal and anthropogenic impacts – James C. Wallace – PLOS One

Linking the effect of antibiotics on partial-nitritation biofilters: performance, microbial communities and microbial activities – Alejandro Gonzalez-Martinez – Frontiers in Microbiology

The effect of epiphytic macroinvertebrates on microbial communities in different types of macrophyte-dominated shallow lakes – Tomasz Mieczan –  Knowl. Manag. Aquat. Ecosyst

Watershed-induced limnological and microbial status in two oligotrophic Andean lakes exposed to the same climatic scenario – Alex Echeverría-Vega – Frontiers in Microbiology

** A novel β-glucosidase isolated from the microbial metagenome of Lake Poraquê (Amazon, Brazil) – Danyelle Toyama – Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics

Variations in culturable bacterial communities and biochemical properties in the foreland of the retreating Tianshan No. 1 glacier – Xiukun Wu – Brazilian Journal of Microbiology

Food microbiology

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation – Haizhou Li – PLOS One

Metagenomic Insights into Environmental Microbiome and Their Application in Food/Pharmaceutical Industry – Ramya Sree Boddu – Microbial Biotechnology

Phages and viruses

[pre-print] THEA: A novel approach to gene identification in phage genomes – Katelyn McNair – bioRxiv

Bioinformatics

* [pdf] Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models – Aeriel Belk – Genes

COREMIC: a web-tool to search for a niche associated CORE MICrobiome – Richard R. Rodrigues – PeerJ

Techniques

Isotope fractionation in biogas allows direct microbial community stability monitoring in anaerobic digestion – Jo De Vrieze – Environmental Science & Technology

Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples – Rishi Mahajan – Molecular Biology Reports

Microbes in the news

These Bacteria Eat Toxic Metal, ‘Poop’ Gold Nuggets – Live Science

Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)

Earthquakes follow wastewater disposal patterns in southern Kansas

Ultra-processed foods ‘linked to cancer’

Promising cancer vaccine would use patient’s own cells to train the immune system

Does GMO corn increase crop yields? 21 years of data confirm it does—and provides substantial health benefits

Poor fitness linked to weaker brain fiber, higher dementia risk

Low cigarette consumption and risk of coronary heart disease and stroke: meta-analysis of 141 cohort studies in 55 study reports

Fewer Infants Died In States That Allowed Affordable Care Act

February 20, 2018

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In today’s digest you can read: about advantages of Atomic Force Microscopy in studying of oral microbiota in the paper by S. S. Salavadhi; about gut microbiome association with Type 1 diabetes in the paper by J.A. Mullaney; about influence of steroids on the gut microbiota in the review by M.J Tetel and about the ability of Synechococcus cyanobacteria to dynamically change their pigment content to match the ambient light color, in the paper by T. Grébert. These are of course just a few of many interesting articles today. Enjoy!

Events and jobs

MS graduate position: Amoeba microbiome, Conway, Arkansas, US

Research Fellow in Cell Biology – Microscopy, Warwick, UK

PhD Student, ROYAL NIOZ-TEXEL, Texel, the Netherlands

General microbiome

Review: A new piece in the microbiome puzzle – Lindsay J. Pike – Nature Reviews Microbiology

The importance of resolving biogeographic patterns of microbial microdiversity – Alexander B Chase – Microbiology Australia

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession – Rüdiger Ortiz-Álvarez – the ISME Journal

Pregnancy and early life

Infant formulae supplemented with prebiotics: Are they better than unsupplemented formulae? An updated systematic review – Agata Skórka – British Journal of Nutrition

Early Dietary Patterns and Microbiota Development: Still a Way to Go from Descriptive Interactions to Health-Relevant Solutions – Patricia Iozzo – Frontiers in Nutrition

Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring – Hein M. Tun – JAMA Pediatrics

Multi-site human microbiome

A blinded observational cohort study of the microbiological ecology associated with pyuria and overactive bladder symptoms – Kiren Gill – International Urogynecology Journal

Oral microbiome

Atomic force microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis – Shyam Sunder Salavadhi – Journal of Indian Society of Periodontology

Human gut microbiome

Review: Steroids, stress and the gut microbiome-brain axis – M. J. Tetel – Journal of Neuroendocrinology

Alterations of the Gut Microbiota in Hashimoto’s Thyroiditis Patients – Zhao Fuya – Thyroid

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean Michael Kearney – bioRxiv

Alterations in Intestinal Microbiota Lead to Production of Interleukin 17 by Intrahepatic γδ T-cell Receptor-positive Cells and Pathogenesis of Cholestatic Liver Disease – Dana Tedesco – Gastroenterology

Type 1 diabetes susceptibility alleles are associated with distinct alterations in the gut microbiota – Jane A. Mullaney – BMC Microbiome

Animal experiments

Effect of Dietary Chestnut or Quebracho Tannin Supplementation on Microbial Community and Fatty Acid Profile in the Rumen of Dairy Ewes – Arianna Buccioni – BioMed Research International

Long-Term Treatment with Green Tea Polyphenols Modifies the Gut Microbiome of Female Sprague-Dawley Rats – Jincheng Wang – The Journal of Nutritional Biochemistry

Microbiota-Derived Indole Metabolites Promote Human and Murine Intestinal Homeostasis through Regulation of Interleukin-10 Receptor – Erica E. Alexeev – The Americn Journal of Pathology

Interrelations between the rumen microbiota and production, behavioral, rumen-fermentation, metabolic, and immunological attributes of dairy cows – M. Schären – Journal of Diary Science

Animal microbiome

Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kešnerová – PLOS One

Plant, root, and soil microbiome

Soil mixture composition alters Arabidopsis susceptibility to Pseudomonas syringae infection – Jana A. Hassan – Plant Direct

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.) – Ting Gao – Archives of Microbiology

The soil microbiome — from metagenomics to metaphenomics – Janet K Jansson – Current Opinion in Microbiology

Exometabolomic profiling of bacterial strains cultivated using Arabidopsis root extract as the sole carbon source – Richard Paul Jacoby – Molecular Plant-Microbiome Interactions

A strain of Streptomyces sp. isolated from rhizospheric soil of Crataegus oxycantha producing Nalidixic acid, a synthetic antibiotic – Nidhi Arora – Journal of Applied Microbiology

High microbial diversity promotes soil ecosystem functioning – Pierre-Alain Maron – Applied and Environmental Microbiology

Water and extremophile microbiome 

Apportioning bacterial carbon source utilization in soil using 14C isotope analysis of FISH-targeted bacterial populations sorted by Fluorescence Activated Cell Sorting (FACS): 14C-FISH-FACS – Christos Gougoulias – Environmental Microbiology Reports

Insights into the fundamental physiology of the uncultured Fe-oxidizing bacterium Leptothrix ochracea – E. J. Fleming – Applied and Environmental Microbiology

Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria – Théophile Grébert – PNAS

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning – Zhili He – mBio

Iron and phosphorus deprivation induce sociality in the marine bloom-forming cyanobacterium Trichodesmium – Yael Tzubari – the ISME Journal

Cryptophyta as major bacterivores in freshwater summer plankton – Vesna Grujcic – the ISME Journal

Phages and viruses

The impact of bacteriophages on phyllosphere bacterial abundance and composition – Norma M. Morella – Molecular Ecology

Microbes in the news 

Guts and gory: vampire bats need bacteria to digest blood

Using mutant bacteria to study how changes in membrane proteins affect cell functions

February 19, 2018

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Events and jobs

Research Technician I – University at Buffalo

General microbiome

Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation – Ji Lu, bioRxiv

Oncologists tap the microbiome in bid to improve immunotherapy outcomes – Asher Mullard, Nature Reviews Drug Discovery

Nasal microbiome

Establishment of the Nasal Microbiota in the first 18 Months of Life – Correlation with Early Onset Rhinitis and Wheezing – Le Duc Huy Ta, Journal of Allergy and Clinical Immunology

The nasal microbiome in chronic rhinosinusitis: analyzing the effects of atopy and bacterial functional pathways in 111 patients – Mahboobeh Mahdavinia, Journal of Allergy and Clinical Immunology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela S. A. Goltsman, bioRxiv

Human vaginal microbiome

Microbiota changes impact on sexually transmitted infections and the development of pelvic inflammatory disease – Nathalie Loeper, Microbes and Infection

Human gut microbiome

Efficacy of Bifidobacterium breve Fermented Milk in Maintaining Remission of Ulcerative Colitis – Katsuyoshi Matsuoka, Digestive Diseases and Sciences

Comparison of Different Strategies for Providing Fecal Microbiota Transplantation to Treat Patients with Recurrent Clostridium difficile Infection in Two English Hospitals: A Review – Simon D. Goldenberg, Infectious Diseases and Therapy

Fecal Microbiota Transplant for Refractory Clostridium difficile Infection Interrupts 25-Year History of Recurrent Urinary Tract Infections – Tiffany Wang, Open Forum Infectious Diseases

Fecal microbiota transplantation for severe complicated C. difficile colitis in a patient with acquired immunodeficiency syndrome – P. Martínez-Ayala, Revista de Gastroenterología de México

Microbial Engraftment and Efficacy of Fecal Microbiota Transplant for Clostridium difficile Patients With and Without IBD – Robert P Hirten, bioRxiv

The impact of a helminth-modified microbiome on host immunity – Tara P. Brosschot &
Lisa A. Reynolds, Mucosal Immunology

Depression and obesity: evidence of shared biological mechanisms – Yuri Milaneschi, Molecular Psychiatry

Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation – Juliana Durack, Nature Communications

Roux-en-Y Gastric-Bypass and sleeve gastrectomy induces specific shifts of the gut microbiota without altering the metabolism of bile acids in the intestinal lumen – Henri Duboc, International Journal of Obesity

Effects of ewe’s milk yogurt (whole and semi-skimmed) and cow’s milk yogurt on inflammation markers and gut microbiota of subjects with borderline-high plasma cholesterol levels: a crossover study – Noemí Redondo, European Journal of Nutrition

Impact of food additives on the gut-brain axis – Mary K. Holder, Physiology & Behavior

Gut microbiota injury in allogeneic haematopoietic stem cell transplantation – Yusuke Shono, Nature Reviews Cancer

Microbiota: Pathobiont peacekeepers – Kirsty Minton, Nature Reviews Immunology

Gut Microbiomics—A Solution to Unloose the Gordian Knot of Biological Effects of Ionizing Radiation – Amy Zhang, Journal of Heredity

Oral microbiome

Host defense against oral microbiota by bone-damaging T cells – Masayuki Tsukasaki, Nature Communications

Beyond Streptococcus mutans: clinical implications of the evolving dental caries aetiological paradigms and its associated microbiome – N. Philip, BDJ

Animal experiments

The Divergence in Bacterial Components Associated with Bactrocera dorsalis across Developmental Stages – Xiaofeng Zhao, Frontiers in Microbiology

Microbiota in fermented feed and swine gut – Cheng Wang, Applied Microbiology and Biotechnology

Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract – Carl J. Yeoman, Scientific Reports

Animal microbiome

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure – Kieran A. Bates, Nature Communications

The effect of cadmium exposure on diversity of intestinal microbial community of Rana chensinensis tadpoles – Danyang Mu, Ecotoxicology and Environmental Safety

A new cell extraction method reveals hemolymph microbiome of three aquatic invertebrates – Xinxu Zhang, Applied Microbiology and Biotechnology

The gastrointestinal tract microbiota of northern white-cheeked gibbons (Nomascus leucogenys) varies with age and captive condition – Ting Jia, Scientific Reports

Plant, root, and soil microbiome

Manipulation of the rhizosphere microbial community through application of a new bio-organic fertilizer improves watermelon quality and health – Jia Zhao, PLOS One

Water and extremophile microbiome

Seasonal dynamics of tetracycline resistance gene transport in the Sumas River agricultural watershed of British Columbia, Canada – Patricia L. Keen, Science of The Total Environment

Microbial diversity and toxin risk in tropical freshwater reservoirs of Cape Verde – Ana Paula Semedo-Aguiar, bioRxiv

Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities – Adam C. Mumford, Applied and Environmental Microbiology

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in A Bioreduced Uranium Contaminated Site after Reoxidation – Bing Li, Applied and Environmental Microbiology

Properties of bacterial communities attached to artificial substrates in a hypereutrophic urban river – Xianlei Cai, AMB Express

Food microbiology

Nitrogen removal enhancement using lactic acid fermentation products from food waste as external carbon sources: performance and microbial communities – Jialing Tang, Bioresource Technology

Probiotics/Prebiotics

Advances in Probiotic Regulation of Bone and Mineral Metabolism – Laura R. McCabe, Calcified Tissue International

Prebiotics as functional food ingredients preventing diet-related diseases – A. Florowska, Food and Function

A prebiotic mixture improved Lactobacillus acidophilus and Bifidobacterium animalisgastrointestinal in vitro resistance in petit-suisse – Marina Padilha, Food and Function

Bioinformatics

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses – Tomáš Větrovský, Bioinformatics

Techniques

Use of Rectal Swab Samples for Analysis of the Intestinal Microbiome in Children – Nan Zhang, Chinese Medical Journal

February 14, 2018

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The role of saliva in structuring human oral bacterial communities, effects of permafrost thaw on methanogenic communities, and articles on the microbiomes of termites, burying beetles, honey bees, and mosquitoes.

Human oral microbiome

A spatial gradient of bacterial diversity in the human oral cavity shaped by salivary flow – Diana M Proctor – Nature Communications

Human vaginal microbiome

To ‘douche’ or not to ‘douche’: hygiene habits may have detrimental effects on vaginal microbiota – Erdogan Aslan – Journal of Obstetrics and Gynaecology

Human gut microbiome

Elevated circulating levels of succinate in human obesity are linked to specific gut microbiota – Carolina Serena – The ISME Journal

Infection and Microbiome: Impact of Tuberculosis on Human Gut Microbiome of Indian Cohort – Utkarsh Sood – Indian Journal of Microbiology

Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder – Zhi Chen – NeuroReport

Animal experiments

Protective effect of Group B Streptococcus type-III polysaccharide conjugates against maternal colonization, ascending infection and neonatal transmission in rodent models – Emiliano Chiarot – Scientific Reports

Animal microbiome

Pre-print: Axenic Aedes aegypti develop without live bacteria, but exhibit delayed development and reduced oviposition – Maria A Correa – bioRxiv

Two novel strains of Torulaspora delbrueckii isolated from the honey bee gut microbiome and their use in honey fermentation – Joseph P Barry – bioRxiv

Gut microbiota in the burying beetle, Nicrophorus vespilloides, provide colonization resistance against larval bacterial pathogens – Yin Wang – Ecology and Evolution

Rampant Host Switching Shaped the Termite Gut Microbiome – Thomas Bourguignon – Current Biology

Plant, root, and soil microbiome

Melanization of mycorrhizal fungal necromass structures microbial decomposer communities – Christopher W Fernandez – Journal of Ecology

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence – Andreas Hagenbo – Journal of Ecology

Mycorrhizal symbioses influence the trophic structure of the Serengeti – Bo Maxwell Stevens – Journal of Ecology

The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome – M A Cregger – Microbiome

Water and extremophile microbiome

Pre-print: Transgenerational inheritance of shuffled symbiont communities in the coral Montipora digitata – Kate Quigley – bioRxiv

Shifts of methanogenic communities in response to permafrost thaw results in rising methane emissions and soil property changes – Shiping Wei – Extremophiles

Food microbiology

Dynamic correlations between microbiota succession and flavor development involved in the ripening of Kazak artisanal cheese – Xiaoji Zheng – Food Research International

Application of high-throughput pyrosequencing in the analysis of microbiota of food commodities procured from small and large retail outlets in a U.S. metropolitan area – A pilot study – Daleniece Higgins – Food Research International

Phages and viruses

The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain) – Vicente Pérez-Brocal – PLOS ONE

More microbes

Lactobacillus plantarum lipoteichoic acid inhibits biofilm formation of Streptococcus mutans – Ki Bum Ahn – PLOS ONE

Microbes in the news

In soil-dwelling bacteria, scientists find a new weapon to fight drug-resistant superbugs – Melissa Healy – Los Angeles Times

Interdisciplinary approach yields new insights into human evolution – Liz Entman – Vanderbilt University News

Viruses and Bacteria Travel Along a High-Altitude Superhighway – Dave Roos – Seeker

Science, career, and publishing

Pre-print: The impact on authors and editors of introducing Data Availability Statements at Nature journals – Rebecca Grant – bioRxiv

February 12, 2018

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A rich Digest to start your work week. Highlights include a review in Lancet cautionary about precision nutrition, an NIH metagenome FTP site, and a sampling of songbirds that reveals high prevalence of antibiotic resistant bacteria.

Events

Intellectual Property x The Microbiome – SF Bay Area Microbiome Meetup

General microbiology

Expanding our Understanding of the Role of the Microbiome in Health and Disease – Rob Knight – Archives of Medical Research

* NIH Metagnome FTP site

* The Ecosystem Services of Animal Microbiomes – E.A. McKenney et al. – Molecular Ecology

Preprint: Experimental Evolution of Cell Shape in Bacteria – Paul Richard Yulo et al. – bioRxiv

Human skin microbiome

In vitro: Yeasts from skin colonization are able to cross the acellular dermal matrix – Isabele Carrilho Jarros et al. – Microbial Pathogenesis

Human vaginal microbiome

Review: Immunology of the Uterine and Vaginal Mucosae – Jordan Z. Zhou et al. – Trends in Immunology

Human gut microbiome

The Role of Diet in the Treatment of Irritable Bowel Syndrome : A Systematic Review – Rajdeep Singh et al. – Gastroenterology Clinics of North America

Review: Metabolic Surgery : Weight Loss, Diabetes, and Beyond – Manan Pareek et al. – Journal of the American College of Cardiology

Review: Environmental Noise and the Cardiovascular System – Thomas Münzel et al. – Journal of the American College of Cardiology

The effects of synbiotic supplementation on insulin resistance/sensitivity, lipid profile and total antioxidant capacity in women with gestational diabetes mellitus: a randomized double blind placebo controlled clinical trial – Zohoor Nabhani et al. – Diabetes Research and Clinical Practice

* Precision nutrition for prevention and management of type 2 diabetes – Dong D Wang and Frank B Hu – The Lancet Diabetes & Endocrinology

The Small Intestine Converts Dietary Fructose into Glucose and Organic Acids – Cholsoon Jang et al. – Cell Metabolism

Review: Therapeutic implications of the gastrointestinal microbiome – Purna C Kayshap and Eamonn MM Quigley – Current Opinion in Pharmacology

Risk factors for Clostridium difficile infection in intestinal transplant recipients during the first year post transplant – Luis Guzman et al. – Transplant Infectious Disease

Metabolomics

Review: Advances in computational metabolomics and databases deepen the understanding of metabolisms – Hiroshi Tsugawa – Current Opinion in Biotechnology

Animal experiments

Rat: Onion quercetin monoglycosides alter microbial activity and increase antioxidant capacity – Katarzyna Grzelak-Błaszczyk et al. – The Journal of Nutritional Biochemistry

Preview: Cultivating a Relationship with Gut Bacteria – Catherine E. Schretter and Sarkis K. Mazmanian – Cell Metabolism

Effect of two seaweed polysaccharides on intestinal microbiota in mice evaluated by illumina PE250 sequencing – Zhongshan Zhang et al. – International Journal of Biological Macromolecules

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice – Li Wang et al. – Journal of Food Science

Animal microbiome

* Antibiotic resistant bacteria are widespread in songbirds across rural and urban environments – Diana L. Carter et al. – Science of The Total Environment

Effects of chlorogenic acids-enriched extract from Eucommia ulmoides leaves on growth performance, stress response, antioxidant status and meat quality of lambs subjected or not to transport stress – H.W. Liu et al. – Animal Feed Science and Technology

Characterisation of Bergeyella spp. isolated from the nasal cavities of piglets – M. Lorenzo de Arriba et al. – The Veterinary Journal

Horse: The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins – L.E. Peachey et al. – International Journal for Parasitology

The effects singular or combined administration of fermentable fiber and probiotic on mucosal immune parameters, digestive enzyme activity, gut microbiota and growth performance of Caspian white fish (Rutilus frisii kutum) fingerlings – Ali Taheri Mirghaed et al. – Fish & Shellfish Immunology

Diagnostics and Treatments in Chronic Diarrhea and Weight Loss in Horses – Olimpo Oliver-Espinosa – Veterinary Clinics: Equine Practice

Plant, root and soil microbiome

Diversifying crop rotation increased metabolic soil diversity and activity of the microbial community – Luciana D’Acunto et al. – Agriculture, Ecosystems & Environment

The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome – Franck Stefani et al. – Scientific Reports

Water and extremophile microbiome

Antibiotic resistome in landfill leachate from different cities of China deciphered by metagenomic analysis – Renxin Zhao et al. – Water Research

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH – Raquel Quatrini and D Barrie Johnson – Current Opinion in Microbiology

Effect of heat shock on hot water plumbing microbiota and Legionella pneumophila control – Pan Ji et al. – Microbiome

Food microbiology

Variability within the dominant microbiota of sliced cooked poultry products at expiration date in the Belgian retail – Wim Geeraerts et al. – Food Microbiology

Modelling the growth of Listeria monocytogenes in Mediterranean fish species from aquaculture production – Araceli Bolívar et al. – International Journal of Food Microbiology

Prebiotic in fruit juice: processing challenges, advances, and perspectives – Thatyane Vidal Fonteles and Sueli Rodrigues – Current Opinion in Food Science

Technology

Multi-omics approach to elucidate the gut microbiota activity. Metaproteomics and metagenomics connection – Maria Guirro et al. – Electrophoresis

Microbes in the news

Can Your Gut Protect You Against Cancer? – Michelle Schoffro Cook – Care2

Millions of Mosquitoes to Be Released in Florida for Good Cause – Inside Edition

Using Special UV Light in Public Spaces Could Kill Flu Viruses, Bacteria – Jakob Nielson – Apex Tribune

 

February 8, 2018

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Many interesting articles today: the geographical location of habitat has a stronger impact on the fecal microbiome of lemurs than sex, age, or species;  the mechanism for pathobiont-dependent inflammatory bowel disease involves microbiota reactive T cells; highly active antiretroviral therapy can restore gut microbiome diversity in AIDS patients; host immunity can interact with skin microbiota composition as shown in two species of giant salamander; the development of the small intestine microbiome in silka deer; and the gut microbiome of preterm infants that are breastfed develops normally.

Events and jobs

FEMS Project: Volunteer for the Opportunities Board Taskforce

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General microbiome

Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists – A. B. F. Ivens – Molecular Ecology

Pregnancy and early life

Maternal antibiotic exposure during pregnancy and hospitalization with infection in offspring: a population-based cohort study – Jessica Eden Miller – International Journal of Epidemiology

*Intestinal microbiota development and gestational age in preterm neonates – Katri Korpela – Scientific Reports

Human oral microbiome

Diversity analysis of subgingival microbial bacteria in peri-implantitis in Uygur population – Gao, Xiaowei MM – Medicine

Human vaginal microbiome

Commentary: The implausible “in vivo” role of hydrogen peroxide as an antimicrobial factor produced by vaginal microbiota – Gilda Tachedjian – Microbiome

Human gut microbiome

Microbiome–host systems interactions: Protective effects of propionate upon the blood–brain barrier – Lesley Hoyles – bioRxiv

*Alterations in the gut microbiota of patients with acquired immune deficiency syndrome – Youlian Zhou – Journal of Cellular and Molecular Medicine

Open-label pilot for treatment targeting gut dysbiosis in myalgic encephalomyelitis/chronic fatigue syndrome: neuropsychological symptoms and sex comparisons – Amy Wallis – Microbiome

Review: Diet and microbiota linked in health and disease  – T. Requena – Food And Function

Review: The role of gut microbiota and IL-23/IL-17 pathway in ankylosing spondylitis immunopathogenesis: New insights and updates – Farhad Babaie – Immunology Letters

Dissertation: Interaction of Cocoa Powder with Intestinal Microbiota – Zuyin Li – Louisiana State University


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Animal experiments

*c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont – Mo Xu – Nature

Dysregulated bile acid synthesis and dysbiosis are implicated in Western diet–induced systemic inflammation, microglial activation, and reduced neuroplasticity – Prasant Kumar Jena – The FASEB Journal

High-fat diet stimulates the gut pathogenic microbiota and maintains hepatic injury in antibiotic-treated rats – Sooad Al-Daihan – Cellular and Molecular Biology

Review: Searching for the gut microbial contributing factors to social behavior in rodent models – Brittany D. Needham – Developmental Neurobiology

Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria – Evelyne Mann – Frontiers in Microbiology


Animal microbiome

*Occupancy strongly influences faecal microbial composition of wild lemurs – Alexander Umanets – FEMS Microbiology Ecology

*Influence of immunogenetics, sex, and body condition on the cutaneous microbial communities of two giant salamanders – Obed Hernández-Gómez – Molecular Ecology

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities – Christine P. Zolnik – Tick and Tick-borne Diseases

The Development of Microbiota and Metabolome in Small Intestine of Sika Deer (Cervus nippon) from Birth to Weaning – Zhipeng Li – Frontiers in Microbiology

Exploring coral microbiome assemblages in the South China Sea – Lin Cai – Scientific Reports

Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea – Esther Rubio-Portillo – Frontiers in Microbiology

Survival and growth of Stenotrophomonas maltophilia in free-living amoebae (FLA) and bacterial virulence properties – Elodie Denet – PLOSone

Gut Microbiota Mediate Insecticide Resistance in the Diamondback Moth, Plutella xylostella (L.) – Xiaofeng Xia – Frontiers in Microbiology

Effects of predation stress and food ration on perch gut microbiota – Yinghua Zha – Microbiome

Longitudinal Effects of Supplemental Forage on the Honey Bee (Apis mellifera) Microbiota and Inter- and Intra-Colony Variability – Jason A. Rothman – Microbial Ecology


Plant, root, and soil microbiome

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain – Yu Shi – Microbiome

Soil incubation studies with Cry1Ac protein indicate no adverse effect of Bt crops on soil microbial communities – Li Zhaolei – Ecotoxicology and Environmental Safety

The influence of cattle grazing on methane fluxes and engaged microbial communities in alpine forest soils – Mira Mutschlechner – FEMS Microbiology Ecology

Diversity and metabolic potential of the microbiota associated with a soil arthropod – Simon Bahrndorff – Scientific Reports

Soil pH rather than nutrients drive changes in microbial community following long-term fertilization in acidic Ultisols of southern China – Jia Liu – Journal of Soils and Sediments

Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate – Larisa Cortes-Tolalpa – Applied Microbiology and Biotechnology

Commentary: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection

Review: Does genotypic and species diversity of mycorrhizal plants and fungi affect ecosystem function? – Christina Hazard – New Phytologist

Review: Putting concerns for caution into perspective: microbial plant protection products are safe to use in agriculture – Ben Lugtenberg – Journal of Plant Diseases and Protection


Water and extremophile microbiome

Ultra-rare marine microbes contribute to key sulfur related ecosystem functions – Dimitri Kalenitchenko – Molecular Ecology

Review: The microbial contribution to reactive oxygen species dynamics in marine ecosystems – Erik R. Zinser – Environmental Microbiology Reports

Application of metagenome analysis to characterize the molecular diversity and saxitoxin-producing potentials of a cyanobacterial community: a case study in the North Han River, Korea – Keon Hee Kim – Applied Biological Chemistry

Built environment

Airborne microbial communities in the atmospheric environment of urban hospitals in China – Xin-Lei Gao – Journal of Hazardous Materials


Food microbiology

Effects of chitosan oligosaccharides on microbiota composition of silver carp (Hypophthalmichthys molitrix) determined by culture-dependent and independent methods during chilled storage – Shiliang Jia – International Journal of Food Microbiology

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Probiotics / prebiotics

Lactobacillus plantarum AN1 cells increase caecal L. reuteri in an ICR mouse model of dextran sodium sulphate-induced inflammatory bowel disease – Yasushi Yokota – International Immunopharmacology

Lactobacillus salivarius LA307 and Lactobacillus rhamnosus LA305 attenuate skin inflammation in mice – S. Holowacz – Beneficial Microbes

Bifidobacteria and its rice fermented products on diet induced obese mice: analysis of physical status, serum profile and gene expressions – M. Ray – Beneficial Microbes

Lactobacillus rhamnosus GG Affects Microbiota and Suppresses Autophagy in the Intestines of Pigs Challenged with Salmonella Infantis – Wei Zhang – Frontiers in Microbiology

Probiotic Use in Equine Gastrointestinal Disease – Angelika Schoster – Veterinary Clinics: Equine Practice

Review: The Role of Prebiotics and Probiotics in Gastrointestinal Disease – Martin H. Floch – Gastroenterology Clinics

Effects of Bentonite Bgp35b-p on the Gut Microbiota of Mice Fed a High-Fat Diet – Eun-Sook Lee – Journal of the Science of Food and Agriculture

Feeding the developing brain: Juvenile rats fed diet rich in prebiotics and bioactive milk fractions exhibit reduced anxiety-related behavior and modified gene expression in emotion circuits – Agnieszka Mika – Neuroscience Letters

Biotechnology

Effects of voltage on sulfadiazine degradation and the response of sul genes and microbial communities in biofilm-electrode reactors – Xiao-Li Yang – Ecotoxicology and Environmental Safety

Waste and Pollution

Biodegradation of n-alkanes on oil–seawater interfaces at different temperatures and microbial communities associated with the degradation – Synnøve Lofthus – Biodegradation

Techniques

The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens – Stefanie U. Wetzels – PLOSone

More bang for the buck? Can arbuscular mycorrhizal fungal communities be characterized adequately alongside other fungi using general fungal primers? – Ylva Lekberg – New Phytologist


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Microbes in the news

These Bacteria Digest Toxic Metals And Poop Out Tiny Gold Nuggets – Signe Dean – Science Alert

The discovery of a third form of flagella-mediated motility in symbiotic bacteria – Phys.org

Phage or foe? – In light of new evidence, we have to reassess the role of bacteriophages in microbial communities: are they always the enemy? – Lucía Fernández – npj Biofilms and Microbiomes

The effect of gut bacteria on bone health cannot be generalized – Randi Lundberg – Taconic

Here’s What You Need To Know About The Bacteria In Your Vagina
A microbiome doesn’t just exist in your gut – Sarah DiGiulio – Huffington Post

Understanding Microbial Communities Living On Amphibian Skin – Sofia Prado-Irwin – Science Trends

In the battle against cancer, microbes could be the answer – Nicola Davison – Wired