The Verge had a fun article by Rachel Becker on Thursday about funny science stock photos called “Stock photos of scientists reveal that science is mostly about staring –
Sometimes at chickens“.
In case you did not know, I made a whole collection of these on this blog – brought together on this page: Lab Stock Photo Fails.
And it made me realize that it was time for a new installment of this series. Today, let’s focus on some great ways to pipet sideways. Because gravity is so over-rated.
Today we have a few day’s worth of microbiome science to chew on… some interesting skin microbiome studies, bioinformatics publications, and our typical servings of gut /plant-root-soil/animal/water-extremophiles/general microbiome studies. Dig in!
Events and jobs
Manager, QC Microbiology – Celgene – Phoenix, AZ
Pathology and Microbiology & IPID Graduate Student Research Seminar – UNMC
General microbiome
Cost-benefit analysis of introducing next-generation sequencing (metagenomic) pathogen testing in the setting of pyrexia of unknown origin – Jia Hui Chai – PLOS ONE
* [pre-print] Phylogenetically novel uncultured microbial cells dominate Earth microbiomes – Karen G. Lloyd – bioRxiv
Hologenomics: Systems-Level Host Biology – Kevin R. Theis – mSystems
Antibiotics as Instigators of Microbial Dysbiosis: Implications for Asthma and Allergy – Tomasz P. Wypych – Trends in Immunology
[perspective] Function and functional redundancy in microbial systems – Stilianos Louca – Nature Ecology & Evolution
Human oral microbiome
Comparison of the oral microbiome in mouthwash and whole saliva samples – Xiaozhou Fan – PLOS ONE
Oral Dysbiotic Communities and Their Implications in Systemic Diseases – Preethi Sudhakara – Dentistry Journal
Human skin microbiome
[pre-print] Umbilical Microbiome and Laparoscopic Surgery: A Descriptive Clinical Study – Aiolfi Alberto – Journal of Laparoendoscopic & Advanced Surgical Techniques
The skin microbiome of wound scars and unaffected skin in patients with moderate to severe burns in the subacute phase – Su‐Hsun Liu – Wound Repair and Regeneration
Human gut microbiome
Microbiome-Mediated Bile Acid Modification: Role in Intestinal Drug Absorption and Metabolism – Elaine F. Enright – Pharmacological Research
Non-microbicidal small molecule inhibition of polysaccharide metabolism in human gut microbes: a potential therapeutic avenue – Anthony D. Santilli – ACS Chemical Biology
The Use of Antimicrobials as Adjuvant Therapy for the Treatment of Obesity and Insulin Resistance: Effects and Associated Mechanisms – Sandra Aparecida dos Reis – Diabetes / Metabolism Research and Reviews
* Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection – Firas S Midani – The Journal of Infectious Disease
Interactions of Dihydromyricetin, a Flavonoid from Vine Tea (Ampelopsis grossedentata) with Gut Microbiota – Li Fan – Journal of Food Science
Characteristics of the gut microbiota in adult patients with type 1 and 2 diabetes based on the analysis of a fragment of 16S rRNA gene using next-generation sequencing – Dominika Salamon – Polish Archives of Internal Medicine
The Intestinal Microbiota in Colorectal Cancer -Herbert Tilg – Cancer Cell
The Endotoxemia Marker Lipopolysaccharide‐Binding Protein is Reduced in Overweight‐Obese Subjects Consuming Pomegranate Extract by Modulating the Gut Microbiota: A Randomized Clinical Trial – Antonio González‐Sarrías – Molecular Nutrition
Hepatocellular Carcinoma is Associated with Gut Microbiota Profile and Inflammation in Non-Alcoholic Fatty Liver Disease – Francesca Romana Ponziani – Hepatology
Antibiotic‐Associated Disruption of Microbiota Composition and Function in Cirrhosis is Restored by Fecal Transplant – Jasmohan S Bajaj – Hepatology
Does the gastrointestinal microbiome contribute to the “obesity paradox” in melanoma survival? – E A Langan – British Journal of Dermatology
Animal experiments
Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota – Laura J den Hartigh – JN The Journal of Nutrition
Tuna oil alleviate D-galactose induced aging in mice accompanied by modulating gut microbiota and brain protein expression – Dijun Zhang – Journal of Agricultural and Food Chemistry
Dietary Mannan Oligosaccharides Modulate Gut Microbiota, Increase Fecal Bile Acid Excretion, and Decrease Plasma Cholesterol and Atherosclerosis Development – Lisa R. Hoving – Molecular Nutrition
[Review] The Role of the Gut Microbiota in the Metabolism of Polyphenols as Characterized by Gnotobiotic Mice – Pasinetti, Giulio Mari – Journal of Alzheimer’s Disease
Animal microbiome
Shared larval rearing environment, sex, female size and genetic diversity shape Ae. albopictus bacterial microbiota – Guillaume Minard – PLOS ONE
Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut – Floor Hugenholtz – PLOS ONE
Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE
* Bacterial communities associated with honeybee food stores are correlated with land use – Philip Donkersley – Ecology and Evolution
Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC) – Tara G McDaneld – Journal of Animal Science
Controlling ticks and tick-borne diseases…looking forward – José de la Fuente – Ticks and Tick-borne Diseases
The inside tract: The appendicular, cecal, and colonic microbiome of captive aye‐ayes – Lydia K. Greene – American Journal of Physical Anthropology
Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE
Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production – Lan Mi – Frontiers in Microbiology
Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment – Geon Goo Han – Nature Scientific Reports
Development of the tonsillar microbiome in pigs from newborn through weaning – Luis Carlos Pena Cortes – BMC Microbiology
Plant, root, and soil microbiome
Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field – Arne Weinhold – eLife
Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach – Gui-Hua Lu – Genes
Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation – Narjes Dashti – MicrobiologyOpen
Embracing Community Ecology in Plant Microbiome Research – Francisco Dini-Andreote – Trends in Plant Science
Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil – Felipe Rezende Lima – Brazilian Journal of Microbiology
Soil microbial communities and glyphosate decay in soils with different herbicide application history – Keren Hernández Guijarro – Science of the Total Environment
Shining a light on the dark world of plant root-microbe interactions – Philip Poole – PNAS
Water and extremophile microbiome
Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico – D. B. Johnson – gebiology
Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia) – Zorigto Namsarae – Extremophiles
The ecology and diversity of microbial eukaryotes in geothermal springs – Angela M. Oliverio – The ISME Journal
Built environment
Deposition of Bacteria and Bacterial Spores by Bathroom Hot Air Hand Dryers – Luz del Carmen Huesca-Espitia – American Society for Microbiology
Food microbiology
Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis – Maria Teresa P. Gonçalves – Journal of Food Science
Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR – Andrea Osimani – International Journal of Food Microbiology
Bioinformatics
Computer-guided design of optimal microbial consortia for immune system modulation – Richard R Stein – eLife
[uncorrected proof] Using pseudoalignment and base quality to accurately quantify microbial community composition – Mark Reppell – PLOS Computational Biology
Fast Metagenomic Binning via Hashing and Bayesian Clustering – Popic Victoria – Journal of Computational Biology
* Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity – Luis M. Rodriguez-R – mSystems
Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities – Robert S. Harbert – Applications in Plant Science
Microbes in the news
Scientists Accidentally Make Plastic-Eating Bacteria Even More Efficient
New York City Mice: Here Are The Bacteria And Viruses That They Carry
Fecal microbiota transplant improves brain function in hepatic encephalopathy
Microbes on the market
Science, publishing, and career
Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses – K. Scott Weber – PLOS ONE
Ed’s non-microbiology picks
News articles below have actual study links inside.
Since 2016, Half of All Coral in the Great Barrier Reef Has Died
Marijuana’s effects on young brains diminish 72 hours after use, research says
Cannabinoids are easier on the brain than booze, study finds
Stem cell treatment drastically reduces drinking in alcoholic rats
How your next meal could help fight depression, stress
Study: People with less political knowledge think they know a lot about politics
Today’s digest is packed with exciting research on links between gut microbiome and bone generation/development, also an interesting approach to fecal metabolome sampling
Gut Microbiome
Gut Microbiome and Bone.Ibáñez L. Joint Bone Spine
The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.Rezazadeh A. International Immonopharmacology
Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.Pan WH. Genome Medicine
Fecal Microbiome
Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Seekatz AM. Anaerobe
Clostridium difficile stool shedding in infants hospitalized in two neonatal intensive care units is lower than previous point prevalence estimates using molecular diagnostic methods.Hines AG. BMC Pediatrics
Plant, Soil, and Water Microbiome
Metataxonomy and functionality of wood-tar degrading microbial consortia.Brusetti L. Journal of Hazardous Materials
In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.Xie Y. Environmental Pollution
Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures.Liu C. Bioresource Technology
Cadmium exposure and <i>Sedum alfredii</i> planting interactions shape the bacterial community in rhizosphere of the hyperaccumulator plant. Hou D. Applied Environmental Microbiology
Animal Experiments and Microbiome
The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria. Jung DH. Applied Microbiology and Biotechnology
Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs.Xiao Y. Scientific Reports
Changes in the Rumen Epithelial Microbiota and Host Gene Expression of Cattle in Response to Alterations in Dietary Carbohydrate Composition.Petri RM. Applied Environmental Microbiology
Preprint
Mercury methylating microbial communities of boreal forest soils
Jingying Xu. bioRxiv
Techniques
Rat Fecal Metabolomics-Based Analysis.Deda O. Methods in Molecular Biology: Metabolic Profiling
Correction
Correction: <i>’Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance</i>.British Journal of Sports Medicine
Today’s digest features an interesting article on microbial resevoirs in an urban setting, and influence of sequencing depth in chareterising the resistome .
General Microbiome
Diversity of the midstream urine microbiome in adults with chronic kidney disease.Kramer H. International Urology and Nephrology
Oral/Gut Microbiome
Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.Laudadio I. OMICS
The role of the gut microbiota in the pathology and prevention of liver disease.Altamirano-Barrera A. Journal of Nutritional Biochemistry
Effects of green tea on miRNA and microbiome of oral epithelium.Adami GR. Scientific Reports
Plant, Soils, and Water Microbiome
High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens.Xu H. Science of Total Environment
Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.Charlop-Powers Z. PNAS
Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.Mandakovic D. Scientific Reports
Multivariate relationships between microbial communities and environmental variables during co-composting of sewage sludge and agricultural waste in the presence of PVP-AgNPs.Zhang L. Bioresources Technology
Animal Experiments and Microbiome
Gut microbiota recovery and immune response in ampicillin-treated mice.Castro-Mejía JL. Research in Veterinary Sciences
When the Nose Doesn’t Know: Canine Olfactory Function Associated With Health, Management, and Potential Links to Microbiota.Jenkins EK. Frontiers in Veterinary Sciences
Resistome
Microbiota transplantation and/or CRISPR-Cas in the battle against antimicrobial resistance.Vila J. Clinical Microbiology and Infection
Impact of sequencing depth on the characterization of the microbiome and resistome.Zaheer R. Scientific Reports
Today’s digest is short and sweet, but includes exciting science that explores how a vegan diet modulates the gut microbiome and new techniques for detection of DNA SNIPs.
General Microbiome
Effect of nisin on microbiome-brain-gut axis neurochemicals by Escherichia coli-induced diarrhea in mice.Jia Z. Microbial Pathogenesis
Food for Gut: Microbiota Fuels Immune Reconstitution after BMT.Simms-Waldrip TR. Cell Host and Microbe
Oral/Gut Microbiome
Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids.Martinez-Guryn K. Cell Host and Microbe
Impact of a vegan diet on the human salivary microbiota. Hansen TH. Scientific Reports
Plant, Soils, and Water Microbiome
Bacterial communities of four adjacent fresh lakes at different trophic status. Ji B. Ecotoxicology and Environmental Safety
Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.Wille L. Plant, Cell and Environment
Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.Daleo P. Ecology
Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.Ye F. Microbial Ecology
d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere.Hener C, Hummel S. International Journal of Molecular Sciences
Animal Microbiome and Experiments
Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.Salami SA. FEMS Microbiology Ecology
Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.Thies S. Scientific Reports
Pasture Feeding Changes the Bovine Rumen and Milk Metabolome.O’Callaghan TF. Metabolites
Microbial metabolites, short-chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice.Kim M. European Journal of Immunology
Molecular diversity of the faecal microbiota of Toy Poodles in Japan.Omatsu T. Journal of Veterinary Medicine
Techniques
SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.Youngblut ND. Frontiers in Microbiology
Of note today: non-exclusive breastfeeding increases the risk of HIV transmission via the alteration of gut microbiome/T-cell activation; Fasting altered the gut microbiome in beneficial ways but only in mice previously fed a high fat diet; An investigation into new species of the honey and bumblebee gut commensal genus Gilliamella; Catfish development shapes gut microbial community structure independent of diet; A metagenomic analysis of the skin microbiome of the frog, Craugastor fitzingeri; The microbiome is altered during the bioremediation of herbicide contaminated soil; The impact of urban density on the soil microbiome; A randomized placebo controlled clinical trial of a microbiota based drug for the prevention of Clostridium difficile Infection; and the virome of the Cuatro Ciénegas Basin of Mexico
Pregnancy and early life
*Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants – Lianna F Wood – Clinical Infectious Diseases
Comparative Analysis of Gut Microbial Communities in Children under 5 Years Old with Diarrhea – Hongyu Wen – Journal of Microbiology and Biotechnology
Review: Microbiome in Embryonic Implantation and Implantation Failure – Jason M. Franasiak – Recurrent Transplant Failure
Human oral microbiome
The cultivable bacterial flora of the esophagus in subjects with esophagitis – Elisabeth Norder Grusell – Scandinavian Journal of Gastroenterology
Human urogenital microbiome
The upper and lower tract urinary microbiomes of stone formers are similar: a pilot study – Heiko Yang – The Journal of Urology
Human gut microbiome
Shifts in the gut microbiota structure caused by Helicobacter pylori eradication therapy – Evgenii I – bioRxiv
The microbial metabolite TMAO in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages – Catharina Missailidis – AIDS
Review: Microbiome-Mediated Upregulation of MicroRNA-146a in Sporadic Alzheimer’s Disease – Yuhai Zhao – Frontiers in Neurology
Review: Interplay Between the Gut-Brain Axis, Obesity and Cognitive Function – Ana Agustí – Frontiers in Neuroscience
Review: The Brain–Intestinal Mucosa–Appendix– Microbiome–Brain Loop – Luis Vitetta – Diseases
Review: New Therapeutic Drugs from Bioactive Natural Molecules: the Role of Gut Microbiota Metabolism in Neurodegenerative Diseases – Francesco Di Meo – Current Drug Metabolism
Review: Microbial Effects on Immunity in HIV: Virus, Gender or Sexual Preference Induced? – Nichole R. Klatt – EBioMedicine
Review: Microbiome and Gut Dysbiosis – José E. Belizário – Metabolic Interaction in Infection
Review: Clostridium Bacteria and Autism Spectrum Conditions: A Systematic Review and Hypothetical Contribution of Environmental Glyphosate Levels – Isadora Argou-Cardozo – Medical Science
Review: Current State of Knowledge on Implications of Gut Microbiome for Surgical Conditions – Edmund B. Chen – Journal of Gastrointestinal Surgery
Review: Maintenance of intestinal homeostasis by mucosal barriers – Ryu Okumura – Inflammation and Regeneration
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Animal experiments
*Food withdrawal alters the gut microbiota and metabolome in mice – Xiaojiao Zheng – The FASEB Journal
Animal microbiome
*Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera) – Jane Ludvigsen – International Journal of Systematic and Evolutionary Microbiology
*Host Age Affects the Development of Southern Catfish Gut Bacterial Community Divergent From That in the Food and Rearing Water – Zhimin Zhang – Frontiers in Microbiology
*The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data – Eria A. Rebollar – Frontiers in Microbiology
Gut Microbiota-Regulated Pharmacokinetics of Berberine and Active Metabolites in Beagle Dogs After Oral Administration – Ru Feng – Frontiers in Pharmacology
Strongyle Infection and Gut Microbiota: Profiling of Resistant and Susceptible Horses Over a Grazing Season – Allison Clark – Frontiers in Physiology
Review: Opinion: Pesticides Could Alter Amphibian Skin Microbiomes and the Effects of Batrachochytrium dendrobatidis – Krista A. Mccoy – Frontiers in Microbiology
Preprint: Earthworms and Cadmium – heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils? – Maja Šrut – bioRxiv
Effect of Dietary Non-phytate Phosphorus Levels on the Diversity and Structure of Cecal Microbiota in Meat Duck from 1 to 21 d of age – S J Dai – Poultry Science
Rumen bacterial community structure impacts feed efficiency in beef cattle – Henry A Paz – Journal of Animal Science
Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein – E A Latham – Journal of Animal Science
Plant, root, and soil microbiome
*Dynamic changes in microbial communities during the bioremediation of herbicide (chlorimuron-ethyl and atrazine) contaminated soils by combined degrading bacteria – Jian Wang – PLOSone
Comparison of Microbial Community Structure in Kiwifruit Pollens – Min-Jung Kim – The Plant Pathology Journal
*Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces – Haitao Wang – Environmental Science and Technology
Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China – Baihui Ren – Scientific Reports
Preprint: Social Motility: Interaction between two sessile soil bacteria leads to emergence of surface motility – Lucy M McCully – bioRxiv
Water and extremophile microbiome
Sulphate-reducing bacteria (SRB) in the Yangtze Estuary sediments: Abundance, distribution and implications for the bioavailibility of metals – Zuo-shun Niu – Science of The Total Environment
Bacterial community succession and degradation patterns of hydrocarbons in seawater at low temperature – Leendert Vergeynst – Journal of Hazardous Materials
Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition – Emily B. Graham – PeerJ
Organic carbon source and salinity shape sediment bacterial composition in two China marginal seas and their major tributaries – Kai Wang – Science of The Total Environment
Nitrate amendment reduces biofilm biomass and shifts microbial communities in remote, oligotrophic ponds – Carmella Vizza – Freshwater Science
Microbial Ecology
Bacterial interspecies quorum sensing in the mammalian gut microbiota – Karina Bivar Xavier – Comptes Rendus Biologies
Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass – Aoife Joyce – Frontiers in Microbiology
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Probiotics / prebiotics
*Results from a Randomized Placebo-Controlled Clinical Trial of a RBX2660—a Microbiota-based Drug for the Prevention of Recurrent Clostridium difficile Infection – Erik R Dubberke – Clinical Infectious Dieases
Outer Membrane Vesicles From Probiotic and Commensal Escherichia coli Activate NOD1-Mediated Immune Responses in Intestinal Epithelial Cells – María-Alexandra Cañas – Frontiers in Microbiology
Fecal Transplants
Recruitment of feces donors among blood donors: Results from an observational cohort study – Simon Mark Dahl Jørgensen – Gut Microbes
Fecal microbiota transplantation associated with 10 years of stability in a patient with SPMS – Seraj Makkawi – Neurology, Neuroimmunology & Neuroinflammation
Phages and viruses
Metagenomic analysis of ssDNA viruses in surface seawater of Yangshan Deep-Water Harbor, Shanghai, China – Hongming Wang – Marine Genomics
*The viral structure of the Cuatro Ciénegas Basin, a unique oasis in Northern Mexico, reveals a highly diverse population at a small geographic scale – B. Taboada – Applied and Environmental Microbiology
Waste and Pollution
Metataxonomy and functionality of wood-tar degrading microbial consortia – Lorenzo Brusetti – Journal of Hazardous Materials
Variations in the denitrifying microbial community and functional genes during mesophilic and thermophilic anaerobic digestion of cattle manure – Kaiyu Zhang – Science of The Total Environment
Techniques
Electrochemical detection of viable bacteria in urine and antibiotic selection – Noriyuki Nakamura – Biosensors and Bioelectronics
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Microbes in the news
Nova-like explosion of spinning live bacteria explained – A’ndrea Elyse Messer – Phys.org
New ‘NanoZymes’ use light to kill bacteria – Science Daily
The Germs That Love Diet Soda – Moises Velasquez-Manoff
Bacteria can pass on memory to descendants, researchers discover – Melody Pupols – Phys.org
Charting an underexplored landscape: The genitourinary microbiome – Medical Press
A long digest today – lots of science on the gut, environment, and some interesting editorials on techniques, bioinformatics, and methodologies applied to microbiome studies.
General microbiome
[pre print] Oscillating bacterial expression states generate herd immunity to viral infection – Christopher J. R. Turkington – bioRxiv
Retraction: Microbiome restoration diet improves digestion, cognition and physical and emotional wellbeing – The PLOS ONE Editors – PLOS ONE
DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy – Elisa Banchi – PLOS ONE
Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome – Zachary S. Ballard – ACS Nano
Unraveling Interactions between the Microbiome and the Host Immune System To Decipher Mechanisms of Disease – Catherine A. Lozupone – mSystems
Making Millennial Medicine More Meta – Peter J. Turnbaugh – mSystems
Pregnancy and early life
Neonatal intestinal dysbiosis in necrotizing enterocolitis – Naomi-Liza Denning – Molecular Medicine
Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units – Zhi-Hui Zou – Annals of Clinical Microbiology and Antimicrobials
* The Effect of Early Limited Formula on Breastfeeding, Readmission, and Intestinal Microbiota: A Randomized Clinical Trial – Valerie J. Flaherman – The Journal of Pediatrics
Multi-site human microbiome
The Complex Interplay between Chronic Inflammation, the Microbiome, and Cancer: Understanding Disease Progression and What We Can Do to Prevent It – Heather Armstrong – Cancers
Human oral microbiome
Salivary microbial profiles in relation to age, periodontal, and systemic diseases – Ronaldo Lira-Junior – PLOS ONE
Human respiratory microbiome
Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective – Georgios D. Kitsios – mSystems
Host-Microbe Interactions in Airway Disease: toward Disease Mechanisms and Novel Therapeutic Strategies – Emily K. Cope – mSystems
Human gut microbiome
The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome – Christopher John Kiely – Gut Microbes
Species Level Description of the Human Ileal Bacterial Microbiota – Heidi Cecilie Villmones – Nature
* Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates – Francesco Multinu – mSphere
* Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature
In this issue: Effect of gut microbiome on mucosal immunity and enteric diseases – Kumar, Himanshu – International Reviews of Immunology
Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis – Dragos Ciocan – Nature
Clostridium difficile Exposures, Colonization, and the Microbiome: Implications for Prevention – Sara L. Revolinski – Infection Control and Hospital Epidemiology
* Of Microbes and Minds: A Narrative Review on the Second Brain Aging – Riccardo Calvani – Frontiers in Medicine
Microbiome: Viral hormones activate human insulin signalling – Ashley York – Nature
Modulation of Gut Microbiota: A Novel Paradigm of Enhancing the Efficacy of Programmed Death-1 and Programmed Death Ligand-1 Blockade Therapy – Yiming Wang – Frontiers in Immunology
* Assessing the Influence of Vegan, Vegetarian and Omnivore Oriented Westernized Dietary Styles on Human Gut Microbiota: A Cross Sectional Study – Carmen Losasso – Frontiers in Microbiology
Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies – Melanie Tramontano – Nature
Animal experiments
Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment – Katherine E. Dahlhausen – PeerJ
Low dose brain estrogen prevents menopausal syndrome while maintaining the diversity of the gut microbiomes in estrogen-deficient rats – Sunmin Park – American Journal of Physiology-Endocrinology and Metabolism
Oral supplementation of Bifidobacterium longum strain BR-108 alters cecal microbiota by stimulating gut immune system in mice irrespectively of viability – Yuko Makioka – Bioscience, Biotechnology, and Biochemistry
Animal microbiome
Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok – Martha Zakrzewski – Nature
Changes in Larval Mosquito Microbiota Reveal Non-target Effects of Insecticide Treatments in Hurricane-Created Habitats – Joseph P. Receveur – Microbial Ecology
Dissecting cause and effect in host-microbiome interactions using the combined worm-bug model system – Marina Ezcurra – Biogerontology
Plant, root, and soil microbiome
[pre print] Diversity analysis and function prediction of rhizo- and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range – Dandan Cheng – PeerJ pre prints
Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application – A. N. Naliukhin – Eurasian Soil Science
Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification – Jun Lou – PeerJ
Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions – Alfonso Méndez-Bravo – PLOS ONE
Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields – Xuhong Song – PLOS ONE
Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6 – Betina Cecilia Agaras – PLOS ONE
Water and extremophile microbiome
Microbial communities underpinning mesophilic anaerobic digesters treating food wastewater or sewage sludge: a full-scale study – Joonyeob Lee – Bioresource Technology
Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought – Debra A. Davis – Microorganisms
Diversity and assembly patterns of activated sludge microbial communities: A review – Yu Xia – Biotechnology Advances
Temperature-induced changes in a microbial community under autotrophic denitrification with sulfide – Michal Sposob – Process Biochemistry
Metagenomic Exploration of Microbial Signatures on Periyar River Sediments from the Periyar Tiger Reserve in the Western Ghats – Aparna Chakkamadathil Rajeev – Genome Announcements
Occurrence and seasonal dynamics of RNA viral genotypes in three contrasting temperate lakes – Ian Hewson – PLOS One
Shifts in dissolved organic matter and microbial community composition are associated with enhanced removal of fecal pollutants in urban stormwater wetlands – Xiao Huang – Water Research
Effect of semi-permeable cover system on the bacterial diversity during sewage sludge composting – Tatiana Robledo-Mahón – Journal of Environmental Management
* Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth? – S. K. Schmidt – Antonie van Leeuwenhoek
Rapid alterations to marine microbiota communities following an oil spill – Brad J. Gemmell – Ecotoxicology
Microbial communities and their potential for degradation of dissolved organic carbon in cryoconite hole environments of Himalaya and Antarctica – Aritri Sanyal – Microbiological Research
Built environment
Microbiome Profiles of Commercial Broilers Through Evisceration and Immersion Chilling During Poultry Slaughter and the Identification of Potential Indicator Microorganisms – John A. Handley – Frontiers in Microbiology
Food microbiology
Characterization of Bacteria in Nigerian Yogurt as Promising Alternative to Antibiotics in Gastrointestinal Infections – Anthony Opeyemi Ayeni – Journal of Dietary Supplements
Probiotics / prebiotics
Polyphenols’ Gut Microbiota Metabolites: Bioactives or Biomarkers? -Francisco A. Tomas-Barberan – Journal of Agriculture and Food Chemistry
* A Multi-strain Probiotic Reduces the Fatty Liver Index, Cytokines and Aminotransferase levels in NAFLD Patients: Evidence from a Randomized Clinical Trial – Nazarii Kobyliak – Journal of Gastrointestinal and Liver Diseases
Bioinformatics
Species classifier choice is a key consideration when analysing low-complexity food microbiome data – Aaron M. Walsh – Microbiome
Data and Statistical Methods To Analyze the Human Microbiome – Levi Waldron – mSystems
* Discovery of enzymes for toluene synthesis from anoxic microbial communities – Beller HR – Nature
Techniques
Community Assembly Processes of the Microbial Rare Biosphere – Xiu Jia – Trends in Microbiology
* Metabolomics: A High-Throughput Platform for Metabolite Profile Exploration – Jing Cheng – Computational Systems Biology
[Patent] Spectrometric Analysis of Microbes – Zoltan Takats
* Development and evaluation of a culture-free microbiota profiling platform (MYcrobiota) for clinical diagnostics – Stefan A. Boers – European Journal of Clinical Microbiology & Infectious Diseases
Comparative analysis of four commercial on-farm culture methods to identify bacteria associated with clinical mastitis in dairy cattle – Jair C. Ferreira – PLOS One
Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics – Casey M. Theriot – mSystems
Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research – Nicole A. Hynson – mSystems
Microbiomes In Natura: Importance of Invertebrates in Understanding the Natural Variety of Animal-Microbe Interactions – Jillian M. Petersen – mSystems
Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies – Isabelle Laforest-Lapointe – mSystems
Microbes on the market
DuPont Expands Microbiome Research Program, Adds Second Partnership with Fermentation Specialist
Science, publishing, and career
Biocodex Microbiota Foundation Awards Grants to Two Innovative Researchers in the Microbiome Field
Early-Career Systems Microbiology Scientists – Jack A. Gilbert – mSystems
Ed’s non-microbiology picks (can use your own name of course!) (cool non-microbiology science)
Self-employed people happier and more engaged at work, study finds
Health Care Spending in the United States and Other High-Income Countries
Ancient DNA Is Rewriting Human (and Neanderthal) History
How exercise in old age prevents the immune system from declining
A packed microbiome digest today, particularly if you want to indulge in a gut microbiome review or some soil microbiome discoveries. There is also a nice microbial perspective on the life‐history evolution of marine invertebrate larvae!
Events
Report of the San Francisco Bay Area Microbiome Meetup group
Jobs
Scientific Officer (Microbiology) – Hyper Recruitment Solutions – Wiltshire, UK
Assistant professor in Reproductive Health Sciences with focus on the microbiome – Karolinska Institutet – Sweden
Human respiratory microbiome
Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites – Elizabeth Copeland – Frontiers in Cellular and Infection Microbiology
Human gut microbiome
Can microbiology affect psychiatry? A link between gut microbiota and psychiatric disorders – Ewelina Gulas – Psychiatria Polska
A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America – Homero San-Juan-Vergara – Scientific Reports
Preprint: Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids – Sara C. Di Rienzi – BioRxiv
A systematic review of studies on the faecal microbiota in anorexia nervosa: future research may need to include microbiota from the small intestine – Hanna Ferløv Schwensen – Eating and Weight Disorders – Studies on Anorexia, Bulimia and Obesity
Systematic Review: Gut Microbiota in Fecal Samples and Detection of Colorectal Neoplasms – Efrat L. Amitay – Gut Microbes
How are the expression patterns of gut antimicrobial peptides modulated by human gastrointestinal diseases? A bridge between infectious, inflammatory, and malignant diseases – Paulo André Dias Bastos – Journal of the European Peptide Society EPS
Animal experiments
Prebiotic attenuation of olanzapine-induced weight gain in rats: analysis of central and peripheral biomarkers and gut microbiota – Amy Chia-Ching Kao – Translational Psychiatry
Adverse effect of early-life high-fat/high-carbohydrate (“Western”) diet on bacterial community in the distal bowel of mice – Sandra InfanteVillamil – Nutrition Research
Animal microbiome
A microbial perspective on the life‐history evolution of marine invertebrate larvae: If, where and when to feed – Tyler J. Carrier – Marine Ecology
The significance of the diversity and composition of the cecal microbiota of the Tibetan swine – Weiping Yang – Annals of Microbiology
A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios – Jianping Quan – Scientific Reports
Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs – Maelle Sevellec – Microbiome
Plant, root, and soil microbiome
Comparison of crop productivity and soil microbial activity among different fertilization patterns in red upland and paddy soils – Liu Kai-lou – Acta Ecologica Sinica
Application of manure containing tetracyclines slowed down the dissipation of tet resistance genes and caused changes in the composition of soil bacteria – WenguangXiong – Ecotoxicology and Environmental Safety
Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation – Shuai Zhao – Scientific Reports
Glyphosate application increased catabolic activity of gram-negative bacteria but impaired soil fungal community – Yehao Liu – Environmental Science and Pollution Research
Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years – Youfa Luo – Environmental Science and Pollution Research
Water and extremophile microbiome
Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of cooccurring macroalgae – Melissa Y Chen – Molecular Ecology
Bioinformatics
Review and perspective on mathematical modeling of microbial ecosystems – Antonella Succurro – Biochemical Society Transactions
Techniques
DNA extraction for streamlined metagenomics of diverse environmental samples – Clarisse Marotz – BIOTECHNIQUES
Microbes in the news
Sensitive Microbial Test Identifies Previously Undetectable Bacteria – Genetic Engineering & Biotechnology News
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
Poor fitness linked to weaker brain fiber, higher dementia risk
Fewer Infants Died In States That Allowed Affordable Care Act
Today’s digest is full of exciting papers and a great think piece on the questionable research practices.
General Microbiome
REVIEW:The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Flandroy L. Science of The Total Environment
REVIEW: Designer microbiomes for environmental, energy and health biotechnology. Strous M. Current Opinion in Microbiology
Microbiome and atrial fibrillation. Mishima RS. International Journal of Cardiology
Gut Microbiome
REVIEW:Role of gut microbiota and oxidative stress in the progression of non-alcoholic fatty liver disease to hepatocarcinoma: Current and innovative therapeutic approaches. Borrelli A. Redox Biology
Prebiotics/Probiotics
In vitro digestibility and prebiotic potential of curdlan (1 → 3)-β-d-glucan oligosaccharides in Lactobacillus species. Shi Y. Carbohydrate Polymers
No appendix necessary: Fecal transplants and antibiotics can resolve Clostridium difficile infection. Joshi T. Journal of Theoretical Biology.
Preprint
Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria. McLean JS. bioRxiv
Ethical Shades of Gray: Questionable Research Practices in Health Professions Education. Artino AR. bioRxiv
Plant, Soil, and Water Microbiome
Biogeography and ecological processes affecting root-associated bacterial communities in soybean fields across China. Zhang B. Science of The Total Environment
Shift in the microbial community composition of surface water and sediment along an urban river. Wang L. Science of The Total Environment
REVIEW:Veterinary antibiotics (VAs) contamination as a global agro-ecological issue: A critical view. Kuppusamy S. Agriculture, Ecosystems & Environment
Rubber plantation ageing controls soil biodiversity after land conversion from cassava. Peerawat M. Agriculture, Ecosystems & Environment
Animal Experiment and Microbiome
Gut microbiota modulates alcohol withdrawal-induced anxiety in mice. Xiao HW. Toxicology Letters
Microbes in the News
Mosquitoes infected with bacteria to make them infertile released in battle against viruses.
-The Independent
Computer models reveal best way to kill deadly bacteria
-Phys.Org
Bacteria produce gold by digesting toxic metals
-Phys.Org
SA start-up tackles deadly global bacteria
-SBS
Microbiome Digest - Bik's Picks 