August 18, 2017

Human Microbiome: Gut

Worse inflammatory profile in omnivores than in vegetarians associates with the gut microbiota composition – Ana Carolina Franco-de-Moraes – Diabetology & Metabolic Syndrome (BMC)

News and views: Spondyloarthropathies: Ruminococcus on the horizon in arthritic disease – Lars Vereecke & Dirk Elewaut – Nature Reviews Rheumatology

Increased human intestinal barrier permeability plasma biomarkers zonulin and FABP2 correlated with plasma LPS and altered gut microbiome in anxiety or depression – Bruce R Stevens – Gut (BMJ)

 

Human Microbiome: Respiratory tract

Strain level Streptococcus colonization patterns during the first year of life – Meredith Wright – Frontiers in Microbiology

State of the art: The airway microbiota in early cystic fibrosis lung disease – Katherine B. Frayman – Pediatric Pulmonology (Wiley)

 

Human Microbiome: Mouth

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols – Yenkai Lim – Scientific Reports

 

Built microbiome

Bacterial diversity among four healthcare-associated institutes in Taiwan – Chang-Hua Chen – Scientific Reports

 

Animal Microbiome

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

Microbiota in the coelomic fluid of two common coastal starfish species and characterization of an abundant Helicobacter-related taxon – Satoshi Nakagawa – Scientific Reports

Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation – M. Glymenaki – Scientific Reports

Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis – Koji Watanabe – PLoS Pathogens

Gut microbiota of a long-distance migrant demonstrates resistance against environmental microbe incursions – Alice Risely – Molecular Ecology (Wiley)

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs – Hui Yang –  Frontiers in Microbiology

Research Highlight: Tell me who you are and I’ll tell you what you eat – Irene Vacca – Nature Reviews Microbiology

Mucus organisation is shaped by colonic content; a new view – J. B. J. Kamphuis – Scientific Reports

Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice – Jose F. Garcia-Mazcorro – European Journal of Nutrition

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model – Jonathan B. Clayton – BioRxiv

Milk microbiome and bacterial load following dry cow therapy without antibiotics in dairy cows with healthy mammary gland – Erika C. R. Bonsaglia –  Scientific Reports

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome – David Casero – Microbiome (BMC)

 

Probiotics, Prebiotics and Synbiotics

Secretome of intestinal bacilli: a natural guard against pathologies – Olga N. Ilinskaya – Frontiers in Microbiology

The Probiotic Combination of Bifidobacterium longum subsp. infantis CECT 7210 and Bifidobacterium animalis subsp. lactis BPL6 Reduces Pathogen Loads and Improves Gut Health of Weaned Piglets Orally Challenged with Salmonella Typhimurium – Emili Barba-Vidal –  Frontiers in Microbiology

Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 attenuate D-galactosamine-induced liver injury by modifying the gut microbiota – Daiqiong Fang – Scientific Reports

Administration of two probiotic strains during early childhood does not affect the endogenous gut microbiota composition despite probiotic proliferation – Martin Frederik Laursen – BMC Microbiology

A randomized synbiotic trial to prevent sepsis among infants in rural India – Pinaki Panigrahi – Nature

 

Pathogen Research

High-Resolution Microbiome Profiling for Detection and Tracking of Salmonella enterica – Christopher J. Grim – Frontiers in Microbiology

In situ architecture, function, and evolution of a contractile injection system – Désirée Böck – Science

 

Bioactive compounds

Onion Peel Ethylacetate Fraction and Its Derived Constituent Quercetin 4`-O-Β-D Glucopyranoside Attenuates Quorum Sensing Regulated Virulence and Biofilm Formation – Hanan AlYousef – Frontiers in Microbiology

Promysalin is a salicylate-containing antimicrobial with a cell-membrane-disrupting mechanism of action on Gram-positive bacteria – Rahul D. Kaduskar – Scientific Reports

 

Bacteriophages

Selection of Functional Quorum Sensing Systems by Lysogenic Bacteriophages in Pseudomonas aeruginosa  – Miguel-Angel Saucedo-Mora – Frontiers in Microbiology

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca – Teagan L. Brown – PLoS ONE

 

Soil and Environmental Microbiology

Distinct Seasonal Patterns of Bacterioplankton Abundance and Dominance of Phyla α-Proteobacteria and Cyanobacteria in Qinhuangdao Coastal Waters Off the Bohai Sea – Yaodong He – Frontiers in Microbiology

The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard – Giorgia Novello – Frontiers in Microbiology

Perspective: How microbes survive in the open ocean – Jonathan P. Zehr – Science

Ecophysiology of freshwater Verrucomicrobia inferred from metagenome-assembled genomes – Shaomei He – BioRxiv

Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter – Quanchao Zeng – PeerJ preprints

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes – Cheng Wang – Microbiome (BMC)

 

Bioinformatics and Genomics

Abundance-based reconstitution of microbial pan-genomes from whole-metagenome shotgun sequencing data – Florian Plaza Oñate – BioRxiv

Evaluation of the impact of Illumina error correction tools on de novo genome assembly – Mahdi Heydari –  BMC Bioinformatics

 

Non-microbiology picks

A pathology atlas of the human cancer transcriptome – Mathias Uhlen – Science

Increasing Symptoms in Irritable Bowel Symptoms With Ingestion of Galacto-Oligosaccharides Are Mitigated by α-Galactosidase Treatment – C J Tuck – The American Journal of Gastroenterology

Lessons from between the white lines for isolated data scientists – Benjamin S Baumer ​- PeerJ preprints

 

August 17, 2017

After two days of holidays on Microbiome Digest, today our blog is a bit longer with many papers in the part of water, soil and gut microbiome. Moreover, check new tools which can be used to deal with microbiome data (MicrobiomeDB and MetaMeta) and some interesting news about microbes in the “Microbes in the news” section. Enjoy the summer (in the lab or on the beach) while reading what is new in microbial world.

Events and jobs

Quality Control Manager, Microbiology, Technical Operations, Marlborough, Massachusetts, US

Assistant/Associate Professor – Microbiology and Immunology (Job ID #83258), Chicago, US

General microbiome

A macroecological theory of microbial biodiversity – William R. Shoemaker – Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms – Jonathan Friedman – Nature Ecology & Evolution

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla – Eric Becraft – bioRxiv

Review: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life – Anja Spang – Science

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria – Arnauld Vinçon-Laugier – Frontiers in Microbiology

Advances in the analysis of “less-conventional” human body fluids: an overview of the ce- and hplc-ms applications in the years 2015–2017 – Monica Di Venere – Electrophoresis

Pregnancy and early life

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly A.Lackey – Journal of Microbiological Methods

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants – Danping Zhu – Scientific Reports

Multi-site human microbiome

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid –  Philipp Kirstahler – bioRxiv

Oral microbiome

Oral microbial community assembly under the influence of periodontitis – Hongju Chen – PLOS One

Subgingival Microbiome of Gingivitis in Chinese Undergraduates – Ke Deng – Chinese Journal of Dental Research

Human skin microbiome

Review: What is new in the pathophysiology of acne, an overview – B. Dréno – Journal of the European Academy of Dermatology and Venerology

The Role of the Skin and Gut Microbiome in Psoriatic Disease – Di Yan – Current Dermatology Reports

Human vaginal microbiome

The Vaginal Microbiome and its Potential to Impact Efficacy of HIV Pre-exposure Prophylaxis for Women –  Jennifer Velloza – Current HIV/AIDS Reports

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment – Cornelia Gottschick – Microbiome

 

Human gut microbiome

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – bioRxiv

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska- Gut Pathogens

Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism –  Wenzhen Ji – Molecular Medicine Reports

Brain-gut-microbiota axis and mental health – Timothy G. Dinan – Psychosomatic Medicine

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells – Mei San Tang – Inflamatory Bowel Diseases

Gut microbiome response to short-term dietary interventions in reactive hypoglycemia subjects – Sara Quercia –  Diabetes Metabolism Research and Reviews

The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces – Donjete Statovci –  Frontiers in Immunology

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects – Elena Buelow – Microbiome

Future prospect of faecal microbiota transplantation as a potential therapy in asthma – Y Kang  – Allergologia et Immunopathologia

Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients With Rheumatoid Arthritis – Annalisa Pianta – Arthritis & Rheumatology

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska – Gut Pathogens

The impact of age and gut microbiota on Th17 and Tfh cells in K/BxN autoimmune arthritis – Fei Teng – Arthritis Research & Therapy

Amoxapine Demonstrates Incomplete Inhibition of β-Glucuronidase Activity from Human Gut Microbiota – Wei Yang –  SLAS Discovery

Animal experiments 

Role of intestinal microbiome in American ginseng-mediated colon cancer protection in high fat diet-fed AOM/DSS mice –  C.-Z. Wang –  Clinical and Translational Oncology

The influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens – Zifeng Han – Infection and Immunity

Animal microbiome 

Microbiota of little penguins and short-tailed shearwaters during development – Meagan L. Dewar – PLOS One

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLOS One

Brief Communication: Climate warming reduces gut microbiota diversity in a vertebrate ectotherm – Elvire Bestion – Nature Ecology & Evolution

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Andrea Springer – Ecology and Evolution

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLOS One

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community – Marcus J. Pennington – Scientific Reports

Plant, root, and soil microbiome

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach – Thanyaporn Ruangdech – Agriculture and Natural Resources

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient – Eric J. Chapman – European Journal of Soil Biology

Bacteria from the rhizosphere and tissues of As-hyperaccumulator Pteris vittata and their role in arsenic transformation – Yong-HeHan – Chemosphere

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize – LinChen – Pedosphere

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates – Yanglei Yi – Frontiers in Microbiology

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants – Anna C. Santamans – PLOS One

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China – Guangyu Li – International Journal of Environmental Research and Public Health

Microbial volatile compounds alter the soil microbial community – Jun Yuan –  Environmental Science and Pollution Research

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G. Marshall – Marine Genomics

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils – Ruo-Nan Wu – Microbial Ecology

Biophysical processes supporting the diversity of microbial life in soil – Robin Tecon – FEMS Microbiology Reviews

Water and extremophile microbiome 

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond – Patrick J. Kearns – Aquatic Microbial Ecology

Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques –  Samuel Bryson – Thesis, Oregon State University

Effects of alkali types on waste activated sludge (WAS) fermentation and microbial communities – Xiaoling Li – Chemosphere

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern –  María José León –  International Journal of Systematic and Evolutionary

Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis – Emad I. Hussein – Microbiology Open

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters – Dahe Zhao – Applied Microbiology and Biotechnology

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing – M Jongman – Journal of Applied Microbiology

Report: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga – Haim Treves – Current Biology

The effects of morphology and neighbouring seaweeds on macroalgal microbiota – Thesis, The University of British Columbia

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system – Jing-Zhe Jiang – PLOS One

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre – Stephanie A. Sommer – Molecular Ecology

Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem – Mohd Ezhar Mohd Noor –  bioRxiv

The organizing effects of elevated CO2 on competition among estuarine primary producers – Craig S. Young – Scientific Reports

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation – Mamoru Oshiki – Genome Announcements

Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology

Early photosynthetic eukaryotes inhabited low-salinity habitats – Patricia Sánchez-Baracaldo – PNAS

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs – Sunita J.Varjani – Bioresource Technology

Probiotics / prebiotics

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure – Gurjeet Kaur – Journal of Proteomics

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Phages and viruses

Phage in urban wastewater have the potential to disseminate antibiotic resistance – Gayathri Upeksha Gunathilaka – International Journal of Antimicrobial Agents

Bioinformatics

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments – Francislon Silva de Oliveira – bioRxiv

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling – Vitor C. Piro – Microbiome

A bioarchitectonic approach to the modular engineering of metabolism – Cheryl A. Kerfeld – Philosophical Transactions of the Royal Society B

Techniques

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems – Joanne B. Emerson – Microbiome

A Note: A simple methodology to collect culturable bacteria from feces of Anopheles darlingi (Diptera: Culicidae) – Andrelisse Arruda – Journal of Microbiological Methods

Biotechnology

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks – Keaton Larson – Environmental Science & Technology

Microbial communities as biosensors for monitoring urban environments – Fangqiong Ling – Microbial Biotechnology

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Review: Purification and reuse of non-point source wastewater via Myriophyllum-based integrative biotechnology: A review – Liu F – Bioresource Technology

Improvements in algal lipid production: a systems biology and gene editing approach –  Avik Banerjee – Critical Reviews in Biotechnology

Microbes in the news 

Scientists Make Food From Bacteria, Water, Electricity, and a Whole Lot of Patience

Are you lonesome tonight? Why we, like Elvis, turn to food for comfort

Scientists See Bacteria Responding Electrically to Physical Stimuli for the First Time

Killing bacteria by hacking plastics with silver and electricity

Human Gut Microbes May Help Suppress MS, New Research Suggests 

Unexpected Microbial Life in Glacial Clay Could Offer Antibiotic Solutions

 

 

 

August 14, 2017

A burst of articles for your Monday digest. Quite a few highlights emerge from this Digest. There can be racial disparity in gastrointestinal cancer risk. The stress we experience now might influence our children’s aging in the future. And you might want to think twice about choosing between 16S and metagenomic sequencing, depending on the type of samples you have.

Jobs

Research Technician – Molecular Biology and Microbiology Department – Tufts University

General microbiology

*Letter: Pilot study to determine whether microbial contamination levels in hospital washrooms are associated with hand-drying method – M.H. Wilcox et al. – Journal of Hospital Infection

History matters: heterotrophic microbial community structure and function adapt to multiple stressors – Alexander Feckler et al. – Global Change Biology

Pregnancy and early life

Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates – Alicja Nogacka et al. – Microbiome

Pregnancy-induced changes in metabolome and proteome in ovine uterine flushings – Jared J. Romero – Biology of Reproduction

Evolution of newborns urinary metabolomic profiles according to age and growth – Aurélien Scalabre et al. – Journal of Proteome Research

Human oral microbiome

Effect of fermented milk containing Lactobacillus rhamnosus SD11 on oral microbiota of healthy volunteers: A randomized clinical trial – P. Rungsri et al. – Journal of Dairy Science

Human lung microbiome

Microbiome in lung explants of idiopathic pulmonary fibrosis: a case-control study in patients with end-stage fibrosis – Kitsios GD – Thorax

Human gut microbiome

**Racial Disparity in Gastrointestinal Cancer Risk – Hassan Ashktorab et al. – Gastroenterology

Master Thesis: A study of the effects of diet on human gut microbial community structure and mercury metabolism – Ria Saha – University of Ottawa

*Investigation into the stability and culturability of Chinese enterotypes – Yeshi Yin
et al. – Scientific Reports

Bangladesh Environmental Enteric Dysfunction (BEED) study: protocol for a community-based intervention study to validate non-invasive biomarkers of environmental enteric dysfunction – Mahfuz M – BMJ Open

Metabolomics

“Omics” in Human Colostrum and Mature Milk: Looking to Old Data with New Eyes – Flaminia Bardanzellu et al. – Nutrients

Animal experiments

Stability and efficacy of frozen and lyophilized fecal microbiota transplant (FMT) product in a mouse model of Clostridium difficile infection (CDI) – Zhi-Dong Jiang et al. – Anaerobe

Rat: The activity of Hou-Po-Da-Huang-Tang is improved through intestinal bacterial metabolism and Hou-Po-Da-Huang-Tang selectively stimulate the growth of intestinal bacteria associated with health – Xing-Yan Liu et al. – Biomedicine & Pharmacotherapy

Mouse: Navy and black bean supplementation primes the colonic mucosal microenvironment to improve gut health – Jennifer M. Monk et al. – The Journal of Nutritional Biochemistry

Mouse: Human Gut-Derived Commensal Bacteria Suppress CNS Inflammatory and Demyelinating Disease – Ashutosh Mangalam et al. – Cell Reports

Mouse: Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition – Michail Mamantopoulos et al. – Immunity

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice – Koji Yasuda et al. – mSystems

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome – Timothy A. Johnson et al. – mBio

Animal microbiome

*The Effects of Captivity on the Mammalian Gut Microbiome – Valerie J. McKenzie et al. – Integrative and Comparative Biology

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep – Janine Kamke et al. – BMC Research Notes

High diversity and unique composition of gut microbiomes in pygmy (Kogia breviceps) and dwarf (K. sima) sperm whales – Patrick M. Erwin et al. – Scientific Reports

Virome comparisons in wild-diseased and healthy captive giant pandas – Wen Zhang and Shixing Yang et al. – Microbiome

Gut microbiomes of free-ranging and captive Namibian cheetahs: diversity, putative functions, and occurrence of potential pathogens – Wasim uddin et al. – Molecular Ecology

Plant, root and soil microbiome

Ecological and functional effects of fungal endophytes on wood decomposition – Lauren C. Cline et al. – Functional Ecology

Spatial Distribution Patterns of Root-Associated Bacterial Communities Mediated by Root Exudates in Different Aged Ratooning Tea Monoculture Systems – Yasir Arafat et al. – International Journal of Molecular Sciences

Book chapter: The Rhizosphere and Plant Nutrition Under Climate Change – Tarek Alshaal et al. – Essential Plant Nutrients

Fungal Diversity in Tomato Rhizosphere Soil under Conventional and Desert Farming Systems – Elham A. Kazerooni et al. – Frontiers in Microbiology

Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans – Zongzhuan Shen et al. – Microbial Ecology

*Characterisation and risk assessment of polycyclic aromatic hydrocarbons (PAHs) in soils and plants around e-waste dismantling sites in southern China – Yujie Wang et al. – Environmental Science and Pollution Research

Water and extremophile microbiome

**Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing – Michael Tessler et al. – Scientific Reports

Interplay of hydrology, community ecology and pollutant attenuation in the hyporheic zone – Ignacio Peralta-Maraver et al. – Science of The Total Environment

Responses of coral-associated bacterial communities to local and global stressors – Jamie McDevitt-Irwin et al. – Frontiers in Marine Science

Built environment microbiome

Variability of indoor fungal microbiome of green and non-green low-income homes in Cincinnati, Ohio – Kanistha Coombs et al. – Science of The Total Environment

Food microbiome

Bacterial diversity of the Colombian fermented milk “Suero Costeño” assessed by culturing and high-throughput sequencing and DGGE analysis of 16S rRNA gene amplicons – Karina Edith Motato – Food Microbiology

Bioinformatics

*Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson et al. – Briefings in Bioinformatics

Big data management challenges in health research—a literature review – Xiaoming Wang et al. – Briefings in Bioinformatics

Microbes in the news

*FDA: Don’t use these liquid drug or dietary supplement products for infants – Sara Nealeigh – Bradenton Herald

Core bacteria in the gut of horses showed some stability over time in study – HorseTalk

Are Doctors Wrong About Finishing Your Antibiotics? – Paul A. Offit – Daily Beast

*Bacteria at the beach: High levels found at nearly a dozen locations in past two weeks – Sarah Reese – NWI Times

Microbes on the market

OptiBiotix Health PLC (OPTI) Rating Reiterated by FinnCap – Anthony Sawyer – Week Herald

Non-microbiology picks

**Review: Transgenerational Effects of Early Environmental Insults on Aging and Disease Incidence – Mirela Ambeskovic et al. – Neuroscience & Biobehavioral Reviews

Air-quality implications of widespread adoption of cool roofs on ozone and particulate matter in southern California – Scott A. Epstein et al. – PNAS

August 13, 2017

Read about commensal fungi, the “nemabiome,” and a follow-up NYT article on the common topic of dirty sponges.

General microbiome

Commensal Fungi in Health and Disease – Jose J. Limon, Cell Host & Microbe

Circadian Coordination of Antimicrobial Responses – Paola Tognini, Cell Host & Microbe

Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities – Alejandra L. Ibáñez de Aldecoa, Frontiers in Microbiology

Pregnancy and early life

Culture independent assessment of human milk microbial community in lactational mastitis – Shriram H. Patel, Scientific Reports

Human gut microbiome

The Gut Microbiota, Food Science, and Human Nutrition: A Timely Marriage – Michael J. Barratt, Cell Host & Microbe

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis, Cell Host & Microbe

Gut microbial profile in primary biliary cholangitis: Towards bioindicators – Sara Lemoinne, Clinics and Research in Hepatology and Gastroenterology

Human oral microbiome

Microbes and Host Response: A relationship in health and disease – Alpdogan Kantarci, Oral Diseases

Human nearly-sterile sites

Profiling the Urinary Microbiome in Men with Positive versus Negative Biopsies for Prostate Cancer – Eva Shrestha, The Journal of Urology

Animal experiments

Beef, Chicken, and Soy Proteins in Diets Induce Different Gut Microbiota and Metabolites in Rats – Zhu Y, Frontiers in Microbiology

Commentary: Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome – Blessing O. Anonye, Frontiers in Immunology

Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies – Emily L Pascoe, ISME

Animal microbiome

The use of nemabiome metabarcoding to explore gastro-intestinal nematode species diversity and anthelmintic treatment effectiveness in beef calves – Russell W. Avramenko, International Journal for Parasitology

Plant, root, and soil microbiome

Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils – Qing Cao, Environmental Pollution

Compatible Rhizosphere-Competent Microbial Consortium Adds Value to the Nutritional Quality in Edible Parts of Chickpea – Sudheer K. Yadav, Journal of Agricultural and Food Chemistry

Isolation and Characterization of a Phosphorus-Solubilizing Bacterium from Rhizosphere Soils and Its Colonization of Chinese Cabbage (Brassica campestris ssp. chinensis) – Zhen Wang, Frontiers in Microbiology

Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research – Julia A. Vorholt, Cell Host & Microbe

Pearl Millet Genetic Traits Shape Rhizobacterial Diversity and Modulate Rhizosphere Aggregation – Papa M. S. Ndour, Frontiers in Plant Science

Water and extremophile microbiome

Phylogenetically conserved resource partitioning in the coastal microbial loop – Samuel Bryson, ISME

Probiotics/Prebiotics

Characterization of the Culturable Subpopulations of Lactobacillus in the Chicken Intestinal Tract as a Resource for Probiotic Development – Bishnu Adhikari, Frontiers in Microbiology

Microbes in the news

We Need to Talk Some More About Your Dirty Sponges – Joanna Klein, New York Times

University of California at San Francisco Recruiting MS Patients for Gut Bacteria Study – Carolina Henriques, Multiple Sclerosis News Today

This paper battery is powered by bacteria in your spit – Jeremy Deaton, Popular Science

August 12, 2017

Events and jobs

Research Technician – Molecular Biology and Microbiology Department – Tufts University – Application Due:Open Until Filled

Postdoctoral Research Associate – University of Exeter – Application closing date: 07/09/2017

Noninvasive Ileal Sampling Technology for Human Microbiome Studies – Reduction-to-Practice Challenge, InnoCentive – Deadline: Nov 08 2017, 23:59 EST

General microbiome

A Supervised Statistical Learning Approach For Accurate Legionella pneumophila Source Attribution During Outbreaks – A Buultjens – bioRxiv

Animal microbiome 

Microbial population analysis of the midgut of Melophagus ovinus via high-throughput sequencing – DY Duan – Parasites & Vectors

Coadministration of isomalto-oligosaccharides augments metabolic health benefits of cinnamaldehyde in high fat diet fed mice – DP Singh – Biofactors

Water microbiome and extremophiles 

Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater – AP de Mora – bioRxiv

Techniques

Correlated expression of archaeal ammonia oxidation machinery across disparate environmental and culture conditions – P Carini – bioRxiv

Genome-based exploration of the specialized metabolic capacities of the genus Rhodococcus – A Ceniceros – BMC Genomics

Preservation of three-dimensional spatial structure in the gut microbiome – Y Hasegawa – bioRxiv

Rapid and scalable preparation of bacterial lysates for cell-free gene expression – A Didovyk – ACS Synth Biol.

Microbes in the news 

Does colon cleansing wipe out our gut microbiome? – The New York Times

Space invaders: the challenges of studying microbes in space – BMC Blog

Origins of DNA folding suggested in archaea – Science Daily

Bombed bin trucks, breeding bacteria, dirty water: Yemen’s cholera explosion – The Guardian

Seven filthy food habits and how dirty they really are – CNN

Promoting local booze and bacteria at Martha in Kensington – Philly.com

Watchdog group finds excessive bacteria in South Korea McDonald’s burger – UPI

Rebiotix Tries To Get One Up Over Seres – Seeking Alpha

Plants love microbes – and so do farmers – Phys.org

How the microbiome could tackle antibiotic resistant infections in the lungs – Imperial College London

Small molecule inhibitor prevents or impedes tooth cavities in a preclinical model – Medical Xpress

For bacteria that cheat, food is at the forefront – Science Daily

Microbiome Sequencing Services Market: Global Industry Size, Share, Growth, Outlook, Opportunities and Forecast 2017 To 2025 – Research Corridor  – Digital Journal

August 11, 2017

General microbiome
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins – Andreas Zanzoni – Microbiome

Pregnancy and early life
Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates – Alicja Nogacka – Microbiome

Multi-site human microbiome
Probiotics protect mice from CoCrMo particles-induced osteolysis – Zhenheng Wang – International Journal of Nanomedicine

Human respiratory microbiome
The temporal dynamics of the tracheal microbiome in tracheostomised patients with and without lower respiratory infections – Marcos Pérez-Losada – PLoS One

Human skin microbiome
Review: Impact of nasopharyngeal microbiota on the development of respiratory tract diseases – S. Esposito – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome
Community characteristics of the gut microbiomes of competitive cyclists – Lauren M. Petersen – Microbiome

Bile microbiota in primary sclerosing cholangitis: Impact on disease progression and development of biliary dysplasia – Pedro Pereira – PLoS One

Assessment of therapeutic response in Crohn’s disease using quantitative dynamic contrast enhanced MRI (DCE-MRI) parameters: A preliminary study – Jianguo Zhu – Medicine

Review: Bridging the Gap between Gut Microbial Dysbiosis and Cardiovascular Diseases – Kimberley Lau – Nutrients

Animal experiments
Statin therapy causes gut dysbiosis in mice through a PXR-dependent mechanism – Jose A. Caparrós-Martín – Microbiome

The Microbiome Activates CD4 T-cell-mediated Immunity to Compensate for Increased Intestinal Permeability – Karen L.Edelblum – Cellular and Molecular Gastroenterology and Hepatology

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas J. Sharpton – bioRxiv

Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice – Phillip T. Brooks – Microbiome

Characterizing the gut (Gallus gallus) microbiota following the consumption of an iron biofortified Rwandan cream seeded carioca (Phaseolus Vulgaris L.) bean-based diet – Spenser Reed – PLoS One

Gut dysbiosis in mice genetically selected for low antibody production – Ana Carolina da Silva Santos – Gut Pathogens

Plant, root, and soil microbiome
Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome – Yunzeng Zhang – Microbiome

Water and extremophile microbiome
Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Phages and viruses
Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples – Dagmara W. Lewandowska – Microbiome

HIV DNA-Adenovirus Multiclade Envelope Vaccine Induces Gp41 Antibody Immunodominance in Rhesus Macaques – Qifeng Han – Journal of Virology

Techniques
A method for measuring sulfide toxicity in the nematode Caenorhabditis elegans – Leonid Livshits – MethodsX

A novel plant-based-sea water culture media for in vitro cultivation and in situ recovery of the halophyte microbiome – Mohamed Y.Saleh – Journal of Advanced Research

Genomes
Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements – Rupa Iyer – Genomics Data

Description of ‘Arabia massiliensis’ gen. nov., sp. nov., ‘Gordonibacter massiliensis’ sp. nov., and ‘Bacilliculturomica massiliensis’ gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman – S.I. Traore – New Microbes and New Infections

Science, publishing, and career
By now, you may have all heard of the Google Engineer fired over his criticism of diversity efforts. The full memo is here. My particular thoughts resonate with the Atlantic article below, because it reminds me of how important science communication is, and how quickly it devolves into black and white:
The Most Common Error in Media Coverage of the Google Memo – Conor Friedersdorf – The Atlantic

August 10, 2017

Human urinary microbiome

The microbiome in urogenital schistosomiasis and induced bladder pathologies – Adewale S. Adebayo – PLoS Negl Trop Dis

Human gut microbiome

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes – Lena Takayasu – PLoS ONE

Plant, root, and soil microbiome

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence – Yun Kit Yeoh – Nature Communications

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy – Rumakanta Sapkota – Frontiers in Plant Science

Water and extremophile microbiome

Active microorganisms thrive among extremely diverse communities in cloud water – Pierre Amato – PLoS ONE

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan – Satoshi Hiraoka – Frontiers in Microbiology

Built environment

The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science

Microbes in the news

For Healthy Skin, Just Add…Bacteria? – Adam Hurly – GQ

Microbes on the market

Reality vs. hype: A macro look at the microbiome market – Juliet Preston – MedCityNews

Science, publishing, and career

Prof claims victory over ‘#manel’ at microbiome conference – Dan Jackson – Campus Reform