September 17, 2018

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

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June 25, 2018

Today’s Microbiome Digest features the sea turtle microbiome, the bacteria responsible for degrading bioplastics, a new clinical center for phage therapy, the gut-microbiome-brain axis in an Alzheimer’s Disease model, and a preprint about image duplication in scientific publishing.

Pregnancy and early life

Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study. – Daniel J C Berkhout- Clinical Infectious Diseases

Human vaginal microbiome

Abnormal vaginal microbioma is associated with severity of localized provoked vulvodynia. Role of aerobic vaginitis and Candida in the pathogenesis of vulvodynia. – Gilbert G. G. Donders- European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

* Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – Filipe De Vadder – PNAS

Linking the Gut Microbiota to a Brain Neurotransmitter – Kelly G. Jameson – Trends in Neurosciences

Can epilepsy be treated by antibiotics? – Hilde M. H. Braakman – Journal of Neurology

* Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count – Yongjia Ji – Emerging Microbes & Infections

Review: Human gut microbiome: hopes, threats and promises – Patrice D Cani – Gut

Review: New treatments and therapeutic targets for IBS and other functional bowel disorders – Magnus Simrén – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease – Bo Cui – Journal of Neuroinflammation

Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance – Alec M. Judd – Applied and Environmental Microbiology

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system – Kateřina Jirků Pomajbíková – Parasitology

Protective role of commensal bacteria in Sjögren Syndrome – Mahira Zaheer – Journal of Autoimmunity

Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. – Mubina Isani – PLOS One

Animal microbiome

Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas – D. X. Vega-Manriquez – Veterinary Research Communications

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates – Padmini Ramachandran – Genome Announcements

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals – S. Quercia – Equine Veterinary Journal

Plant, root, and soil microbiome

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests – Lenka Jeszeová – World Journal of Microbiology and Biotechnology

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China – Yuan Gong – Systematic and Applied Microbiology

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. – Hongkai Liao – Science of The Total Environment

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. – Margarita Lopez-Fernandez – FEMS Microbial Ecology

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. – Jun Zhao – Applied Microbiology and Biotechnology

* Dispersal-competition tradeoff in microbiomes in the quest for land colonization – Francisco Dini-Andreote – Scientific Reports

Water and extremophile microbiome

Linking patterns of net community production and marine microbial community structure in the western North Atlantic. – Seaver Wang – The ISME Journal

Probiotics/Prebiotics

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. – Kaarel Adamberg – Anaerobe

Review: Nutraceuticals in Colorectal Cancer: A Mechanistic Approach – Marco Rossi – European Journal of Pharmacology

Science, publishing, and career

* Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience – Arturo Casadevall – bioRxiv

Microbes in the news

U.S. center will fight infections with viruses – Kelly Servick – Science

Alyson’s non-microbiology pick

Neanderthal brain organoids come to life – Jon Cohen – Science

February 24, 2018

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

ReviewHuman 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

August 3, 2017

The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature

April 13, 2017

Profiles of ulcerative colitis patients’ microbiota after fecal microbiota transplantation, a bioinformatics software package for rarefaction analysis, an artist who uses sweat and bacteria to create scents and sculptures.

General microbiome

Review: Microbial metabolites in nutrition, healthcare and agriculture – Rajendra Singh – 3 Biotech

Review: Modified Mediterranean Diet for Enrichment of Short Chain Fatty Acids: Potential Adjunctive Therapeutic to Target Immune and Metabolic Dysfunction in Schizophrenia? – Jamie Joseph – Frontiers in Neuroscience

Human respiratory microbiome

The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana – Matthew S Kelly – Pediatric Infectious Disease Journal

Human gut microbiome

* Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation – Susana Fuentes – ISME Journal

Intestinal microbiome in children with severe and complicated acute viral gastroenteritis – Shih-Yen Chen – Scientific Reports

Unusual active site location and catalytic apparatus in a glycoside hydrolase family – Jose Munoz-Munoz – PNAS

Animal experiments

Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans – Carrie E Graham – PNAS

The therapeutic protection of a living and dead Lactobacillus strain against aluminum-induced brain and liver injuries in C57BL/6 mice – Fengwei Tian & Leilei Yu – PLOS One

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria – Yusuke Nagara – PLOS One

Review: Caspase recruitment domain 9, microbiota, and tryptophan metabolism: dangerous liaisons in inflammatory bowel diseases – Bruno Lamas – Current Opinion in Clinical Nutrition and Metabolic Care

Individual variation of natural D. melanogaster associated bacterial communities – Yun Wang – bioRxiv

Plant, root, and soil microbiome

A new polyketide glycoside from the rhizospheric Clonostachys rogersoniana associated with Panax notoginseng – Tian-Peng Yin – Journal of Asian Natural Products Research

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter – Ember M Morrissey – ISME Journal

Population and function analysis of cultivable bacteria associated with spores of arbuscular mycorrhizal fungus Gigaspora margarita – Liangkun Long – 3 Biotech

Water and extremophile microbiome

Exploring the ecological coherence between the spatial and temporal patterns of bacterioplankton in boreal lakes – Juan P. Niño García – Frontiers in Microbiology

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems – Sean P Jungbluth – PeerJ

Bacterial community composition and dynamics spanning five years in freshwater bog lakes – Alexandra M Linz – bioRxiv

Occurrence of high-diversity metazoan- to microbial-dominated bioconstructions in a shallow Kimmeridgian carbonate ramp (Jabaloyas, Spain) – G San Miguel – Facies

Expression patterns of elemental cycling genes in the Amazon River Plume – Brandon M Satinsky – ISME Journal

Built environment

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes – Jiajiong Xu – Applied Microbiology and Biotechnology

Probiotics/prebiotics

Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models – In Young Hwang – Nature Communications

Review: Unraveling the Differences between Gram-Positive and Gram-Negative Probiotics in Modulating Protective Immunity to Enteric Infections – Sukumar Kandasamy – Frontiers in Immunology

Bioinformatics

* RTK: efficient rarefaction analysis of large datasets – Paul Saary – Bioinformatics

A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S Hahn – Scientific Data

Metabolomics

Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study – Vanessa D de Mello – Scientific Reports

More microbes

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells – Laura Rago – Bioelectrochemistry

Microbes in the news

Waste-munching bacteria could make nuclear stores safer – Sam Wong – New Scientist

‘Young poo’ makes aged fish live longer – Ewen Callaway – Nature

Microbiology: Gut microbes augment neurodegeneration – Daniel Erny – Nature

* This Artist Turns Sweat and Bacteria Into Art – Annie Tittiger – Wired

Science, publishing, and career

Why do scientists fabricate and falsify data? A matched-control analysis of papers containing problematic image duplications – Daniele Fanelli – bioRxiv

Amy’s non-microbiology picks

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity – Danish Saleheen – Nature

March 8th, 2017

Today is the International Women’s Day! This is a day for awareness about the importance of support equality in rights and opportunities for women.

About International Women’s Day

Gender at Nature Ecology & Evolution

Helping women progress in traditionally male dominated fields

Rosalind Franklin: Navigating workplace politics to gain recognition in science

International Women’s Day 2017: pursuing a career in science

BMC Series Blog: International Women’s Day

Events and Webinars

3rd Annual Translational Microbiome Conference, April 12-13, 2017 in Boston, MA

Webinar: Nomadic nanopore sequencing of metagenomes with the MinION

Microbiome research

Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients – Na Tian – Applied and Environmental Microbiology

Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island – Jiro Nakayama – Frontiers in Microbiology

Comparison of culture-dependent and culture-independent molecular methods for characterization of vaginal microflora – Shirali Pandya – Journal of Medical Microbiology

Effect of predatory bacteria on the gut bacterial microbiota in rats – Kenneth Shatzkes – Scientific Reports

Methods article: Critical Issues in Mycobiota Analysis – Bettina Halwachs – Frontiers in Microbiology

Microbiota alteration is associated with the development of stress-induced despair behavior – Ioana A. Marin – Scientific Reports

Review: Beyond Hygiene: Commensal Microbiota and Allergic Diseases – Sung-Wook Hong – Immune Network

Fecal Bacterial Communities in treated HIV infected individuals on two antiretroviral regimens – Sandra Pinto-Cardoso – Scientific Reports

Editorial: How can the gut microbiota affect immune recovery in HIV-infected individuals? – Sergio Serrano-Villar – Future Microbiology

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Probiotics

Lactobacillus rhamnosus GG supernatant enhance neonatal resistance to systemic Escherichia coli K1 infection by accelerating development of intestinal defense – Xiaolong He – Scientific Reports

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat  – Elaine Patterson – Scientific Reports

Timely use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: a Systematic Review with Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Metagenomics

Review: Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience – Raquel S. Peixoto – Frontiers in Microbiology

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples – Feiqiao Yu – bioRxiv

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning – John Vollmers – Frontiers in Microbiology

Environmental Viral Genomes Shed New Light on Virus-Host Interactions in the Ocean – Yosuke Nishimura – mSphere

Pathogens

Metabolic activity, urease production, antibiotic resistance and virulence in dual species biofilms of Staphylococcus epidermidis and Staphylococcus aureus – Ilse Vandecandelaere – PLoS ONE

Review: Mollicutes in vaginal microbiology: Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum and Mycoplasma genitalium – David Taylor-Robinson – Research in Microbiology

Case report: Contribution of Ultra Deep Sequencing in the Clinical Diagnosis of a New Fungal Pathogen Species: Basidiobolus meristosporus – Emilie Sitterlé – Frontiers in Microbiology

The Chlamydia suis genome exhibits high levels of diversity, plasticity and mobile antibiotic resistance: comparative genomics of a recent livestock cohort shows influence of treatment regimes – Helena M.B. Seth-Smith – Genome Biology and Evolution

Extremophiles

Reducing salinity by flooding an extremely alkaline and saline soil changes the bacterial community but its effect on the archaeal community is limited – Arit S de León-Lorenzana – Frontiers in Microbiology

Early life

Paleoproterozoic sterol biosynthesis and the rise of oxygen – David A. Gold – Nature

January 5, 2017

Microbiome of Inuit, centenarians, microbes showing differential expression when they are grown with sound, taxonomy of prokaryotic viruses.

Human gut microbiome

Gut Microbiome of the Canadian Arctic Inuit – Catherine Girard – mSphere

The gut microbiota of centenarians: Signatures of longevity in the gut microbiota profile – Biagi Elena – Mechanisms of Ageing and Development

Review: Understanding the Molecular Mechanisms of the Interplay Between Herbal Medicines and Gut Microbiota – Jun Xu – Medicinal Research Reviews

Editorial: The microbiome as a source of new enterprises and job creation: Considering clinical faecal and synthetic microbiome transplants and therapeutic regulation – Daniel van der Lelie – Microbial Biotechnology

Animal experiments

Effect of dietary kefir on the growth performance, feed utilization and fatty acid profile of juvenile rainbow trout, Oncorhynchus mykiss – E. Gümüş – Aquaculture Nutrition

Plant, root, and soil microbiome

The Pseudomonas putida T6SS is a plant warden against phytopathogens – Patricia Bernal – The ISME Journal

Mycorrhizal Colonization Status and Rhizosphere Soil Properties of BCSIR Reserve Forest Rajshahi, Bangladesh – M. Halder – Current World Environment

Waste and pollution microbiology

Batch and continuous removal of heavy metals from industrial effluents using microbial consortia – F. Migahed – International Journal of Environmental Science and Technology

Musical microbes

Frequency-dependent response of Chromobacterium violaceum to sonic stimulation, and altered gene expression associated with enhanced violacein production at 300 Hz – Chinmayi Joshi – bioRxiv

Bioinformatics

Book: Molecular Data Analysis Using R – Csaba Ortutay

Viruses and phages

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee – Evelien M. Adriaenssens – Archives of Virology

Metabolomics

Optimal allocation of metabolic functions among organisms in a microbial ecosystem – Qi Zhao – Decision and Control (CDC), 2016 IEEE 55th Conference on

Microbes in the news

CDC keeps secret its mishaps with deadly germs: CDC blacked-out information from lab incident reports – Alison Young – USA Today

Single fecal transplant no more effective than standard of care in treating C. diff – MedicalXpress

Alaska gulls are picking up antibiotic-resistant bacteria that could infect humans – Yereth Rosen – ADN

Man-made lake near Linganore drained to kill toxic pink bacteria: pink-colored cyanobacterium releases a toxin – Samantha Hogan – The Frederick News Post

Bacteria Hysteria

Dirty Money. The public health case for a cashless society – Dina Fine Maron – Scientific American
The Money in Your Wallet Might Be Covered With Poop, Mold, and Cocaine – Brad
– Money
The 5 Dirtiest Things You Touch Every Day – Markham Heid – Time

Microbes in the market

Israeli Gut Microbiome Startup Lands Mayo Clinic Venture Backing – TwinCities Business

Ritter Pharmaceuticals Phase 2a Lactose Intolerance Clinical Trial Microbiome Data, Published in Proceedings of the National Academy of Sciences – Yahoo

Cambridge BioMarketing Announces Five Predictions for 2017 – Yahoo

Bruker Announces Acquisition of CMO InVivo Biotech to Expand Molecular Biology, Microbiology and Pathology Consumables and Assay Business – PR Newswire

Science integrity

Bavarian court sentences me to prison if I dare repeat unwelcome facts of Walles’ trachea transplants – Leonid Schneider – For Better Science