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