Category Archives: Metagenomics & Bioinformatics

February 15, 2018

Posted on by

An especially interesting article on engineered bacteria in the treatment of colon cancer today: Chun Loong Ho and colleagues engineered an E. coli strain to bind to colon cancer cells and constitutively secrete an enzyme that can turn dietary derived glucosinolates (from cruciferous vegetables) into cancer fighting isothiocynates. Mice exposed to carcinogens and fed both the engineered bacteria and broccoli developed fewer and smaller colorectal tumors than exposed mice who were fed 1) neither bacteria or brocoli, 2) only bacteria, or 3) only broccoli.  Engineered probiotics anyone?

Also : A cultured community developed from wastewater that can reduce the greenhouse gas N2O to N2 and help mitigate global warming; the majority of Daphnia microbiomes are not passed from parent to offspring but absorbed from the surrounding environment; and the impacts of CRISPR-Cas9 selection pressure on phage evolution.

Events and jobs

Postdoctoral Scholars of Microbiology, School of Life Sciences – University of Nevada Las Vegas

*****************************

General microbiome

Review: The genome, microbiome and evolutionary medicine – Robert C. Brunham – cmaj

Pregnancy and early life

Survey of Staphylococcus aureus in a general pediatric population and focus on isolates with three clinically relevant toxin-encoding genes – Anne Filleron – World Journal of Pediatrics

Human skin microbiome

Review: Impact of Skin Microbiome on Attractiveness to Arthropod Vectors and Pathogen Transmission – Niels O. Verhulst – Skin and Arthropod Vectors

Human gut microbiome

Intestinal Microbial Community Differs between Acute Pancreatitis Patients and Healthy Volunteers – Xi Mei Zhang – Biomedical and Environmental Sciences

The microbiome in chronic kidney disease patients undergoing hemodialysis and peritoneal dialysis – Liliana Simões-Silva – Pharmacological Research

Review: Intestinal Microbiome Shifts, Dysbiosis, Inflammation, and Non-alcoholic Fatty Liver Disease – Emma T. Saltzman – Frontiers in Microbiology

Does Low-Protein Diet Influence the Uremic Toxin Serum Levels From the Gut Microbiota in Nondialysis Chronic Kidney Disease Patients? – Ana Paula Black – Journal of Renal Nutrition

The Effect of Oligofructose-Enriched Inulin on Faecal Bacterial Counts and Microbiota-Associated Characteristics in Celiac Disease Children Following a Gluten-Free Diet: Results of a Randomized, Placebo-Controlled Trial – Natalia Drabińska – Nutrients

Preprint: Spatial variation of the native colon microbiota in healthy adults – Kaitlin J Flynn – bioRxiv

Preprint: The intestinal microbiota predisposes to traveller’s diarrhoea and to the carriage of multidrug-resistant Enterobacteriaceae after travelling to tropical regions – Stefano Leo – bioRxiv

*****************************

Animal experiments

Influence of Eimeria falciformis Infection on Gut Microbiota and Metabolic Pathways in Mice – Guangping Huang – Infection and Immunity

The Antimicrobial Peptide CRAMP Is Essential for Colon Homeostasis by Maintaining Microbiota Balance – Teizo Yoshimura – The Journal of Immunology

Animal microbiome

*Good Daphnia parents do not control the offspring microbiome – Angela E. Douglas – Journal of Animal Ecology

Effect of antibiotic withdrawal in feed on chicken gut microbial dynamics, immunity, growth performance and prevalence of foodborne pathogens – Sanjay Kumar – PLOSone

Review: The Microbial Zoo in the C. elegans Intestine: Bacteria, Fungi and Viruses – Hongbing Jiang – Viruses

Effects of parental care on resource allocation into immune defense and buccal microbiota in mouthbrooding cichlid fishes – Isabel S. Keller – Evolution

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats – Guido Bonthond – PeerJ

Effect of ginkgo extract supplementation on in vitro rumen fermentation and bacterial profiles under different dietary conditions – Seongjin Oh – Animal Science Journal

Review: Animal host–microbe interactions – Bethany J. Hoye – Journal of Animal Ecology

Plant, root, and soil microbiome

Oilseed rape cultivation increases the microbial richness and diversity in soils contaminated with cadmium – Xin Wang – Journal of Soils and Sediments

Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters – Emine Gozde Ozbayram – Microorganisms

Bacterial Microbiota of Rice Roots: 16S-Based Taxonomic Profiling of Endophytic and Rhizospheric Diversity, Endophytes Isolation and Simplified Endophytic Community – Felix Moronta-Barrios – Microorganisms

Water and extremophile microbiome

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria – Catherine Gérikas Ribeiro – The ISME Journal

Distribution Patterns of Microbial Community Structure Along a 7000-Mile Latitudinal Transect from the Mediterranean Sea Across the Atlantic Ocean to the Brazilian Coastal Sea – Jin Zhou – Microbial Ecology

The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea – Yuzhi Wu – Extremophiles

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system – Caroline Souffreau – Environmental Microbiology

Chemical and Microbial Quality of Groundwater in Siloam Village, Implications to Human Health and Sources of Contamination – John Ogony Odiyo – International Journal of Environmental Research and Public Health

Microbial Ecology

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies – Mari Pent – Environmental Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Resistome

Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes – Wenguang Xiong – BMC Microbiome

*****************************

Probiotics / prebiotics

Effect of VSL#3 Probiotic in a Patient with Glycogen Storage Disease Type Ia and Irritable Bowel Disease-like Disease – Miguel Carnero-Gregorio – Probiotics and Antimicrobial Proteins

New Insight into Biofilm Formation Ability, the Presence of Virulence Genes and Probiotic Potential of Enterococcus sp. Dairy Isolates – Nikola Popović – Frontiers in Microbiology

Effectiveness and Safety of a Probiotic-Mixture for the Treatment of Infantile Colic: A Double-Blind, Randomized, Placebo-Controlled Clinical Trial with Fecal Real-Time PCR and NMR-Based Metabolomics Analysis – Maria Elisabetta Baldassarre – Nutrients

Fecal Microbiome Transplants

Long-term follow-up of the effects of fecal microbiota transplantation in combination with soluble dietary fiber as a therapeutic regimen in slow transit constipation – Xueying Zhang – Science China Life Sciences

Bioinformatics

Identification of fungi in shotgun metagenomics datasets – Paul D. Donovan – PLOSone

MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies – Ahmed A. Metwally – BMC Microbiome

Biotechnology

*Engineered commensal microbes for diet-mediated colorectal-cancer chemoprevention – Chun Loong Ho – Nature Biomedical Engineering

*Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9 – Pan Tao – Science Advances

Waste and Pollution

*Life on N2O: deciphering the ecophysiology of N2O respiring bacterial communities in a continuous culture – Monica Conthe – The ISME Journal

Metagenomic analysis of microbial community and function involved in cd-contaminated soil – Gang Feng – BMC Microbiology

*****************************

Microbes in the news

Humpback microbiome linked to seasonal, environmental changes – Phys.org

 

February 10, 2018

Posted on by

Check out the Environmental Microbiology * The New Microscopy themed issue from
Events and jobs from Current Opinion in Microbiology! Other highlights include bioinformatic and wet lab techniques, including fecal water preparation for metabolomics and SMRT, as well as a new version of Kraken with k-mer coverage (KrakenHLL)!

Jobs and events
PhD scholarships in Microbiome Synthetic Biology – Danmarks Tekniske Universitet

Human respiratory microbiome
Dysbiosis of inferior turbinate microbiota is associated with high total IgE levels in allergic rhinitis patients – Dong-Wook Hyun – Infection and Immunity

Human skin microbiome
Epidermal lipid composition, barrier integrity and eczematous inflammation are associated with skin microbiome configuration  – Hansjörg Baurecht – Journal of Allergy and Clinical Immunology

Human oral microbiome
Presence of archaea and selected bacteria in infected root canal system – Ewa Brzezińska-Błaszczyk – Canadian Journal of Microbiology

Human gut microbiome
Review: Understanding the Microbiome: Emerging Biomarkers for Exploiting the Microbiota for Personalized Medicine against Cancer – Meenakshi Rajpoot – Seminars in Cancer Biology

Animal microbiome
Exploring virulence of new and less studied species of Metarhizium spp. from Brazil for two-spotted spider mite control – Thiago Castro – Experimental and Applied Acarology

Plant, root, and soil microbiome
Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum – Myung Hwan Lee – Journal of Biotechnology

Effects of rhizosphere interactions of grass interspecies on the soil microbial properties during the natural succession in the Loess Plateau – Chao Zhang – European Journal of Soil Biology

Degradation of polycyclic aromatic hydrocarbons in soil mesocosms by microbial/plant bioaugmentation: Performance and mechanism – Fan-xin Kong – Chemosphere

The influence of tree species on soil properties and microbial communities following afforestation of abandoned land in northeast China – Na Yang – European Journal of Soil Biology

Diversity of the bacterial microbiome in the roots of four Saccharum species: S. spontaneum, S. robustum, S. barberi, and S. officinarum – Meng Dong – Frontiers in Microbiology

Water and extremophile microbiome
Current Opinion in Microbiology has a themed issue called Environmental Microbiology * The New Microscopy with many articles of interest, some including:

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea – Jiyoung Lee – Ocean Science Journal

The effect of temperature on the microbial communities of peak biogas production in batch biogas reactors – Guangliang Tian – Renewable Energy

The Effects of Antibiotics on Microbial Community Composition in an Estuary Reservoir during Spring and Summer Seasons – Zheng Xu – Water

Built environment
Review: Advances in concrete materials for sewer systems affected by microbial induced concrete corrosion: A review – Cyrill Grengg – Water Research

Microbial interactions
Comparative study on nutrient depletion-induced lipidome adaptations in Staphylococcus haemolyticus and Staphylococcus epidermidis – Yu Luo – Scientific Reports

The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp – Hung-Yu Liao – Journal of Hazardous Materials

Probiotics / prebiotics / antibiotics
Evolutionary trajectories to amoxicillin-clavulanic acid resistance in Escherichia coli are affected by growth media – Alasdair TM Hubbard – biorXiv

Bioinformatics
ComPAS: Community Preserving Sampling for Streaming Graphs – Sandipan Sikdar – arXiv

KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts – Florian P Breitwieser – bioRxiv

Techniques
Efficient non-cytotoxic fluorescent staining of halophiles – Ivan Maslov – Scientific Reports

Metabonomic Evaluation of Fecal Water Preparation Methods: The Effects of Ultracentrifugation – Sandi Yen – Current Metabolomics

SMRT-Cappable-seq reveals complex operon variants in bacteria – Bo Yan – bioRxiv

Microbes in the news
Are Hand Dryers Actually Full of Bacteria? A Viral Photo Doesn’t Tell the Whole Story – Maggie Astor – New York Times

Bacteria-infected mosquitoes might be good thing for Miami – Jennifer Kay – ABC News
Miami releases bacteria-infected mosquitoes to help fight Zika virus – KGUN9

UV Light That Is Safe for Humans but Bad for Bacteria and Viruses – GEN News

Stanford Global Health awards seed funding to nine projects – Stanford Medicine News Center

Microbes on the market
Seres Therapeutics Inc. (MCRB) Settles Into New 52-Week Low on February 08 Session – Equities.com

Tiffany’s other picks
Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain – Sylvie Janssens – mSystems

 

February 7, 2018

Posted on by

Today we have many “gut microbiota” and “water microbiome” articles, as well as quite a few reviews in “Food microbiology” sector. One article (among many interesting today) I would like to highlight is the one from Guillaume Bernard and how unraveling the microbial dark matter should be identified as a central priority for biologists.

Jobs

Microbiology Technician -R&D, Lille, France

Consultant Medical Microbiologist, Birmingham, UK

Events

1st International Conference on Microbial Food and Feed Ingredients (MiFFI2018): 2-4 May 2018, Denmark

12th Vaccine Congress, Budapest, Hungary

General microbiome

Synergistic gold–copper detoxification at the core of gold biomineralisation in Cupriavidus metallidurans  – L. Bütof – Metallomics

The role of the type VI secretion system vgrG gene in the virulence and antimicrobial resistance of Acinetobacter baumannii ATCC 19606 – Jianfeng Wang – PLOS One

Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria – Marike Palmer – Frontiers in Microbiology

Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery – Guillaume Bernard – Genome Biology and Evolution

Draft genome sequence of Paenibacillus strain LK1, a phytohormone producing bacterium – Kun Liu – 3 Biotech

Pregnancy and early life

Review: Urinary tract infection during pregnancy: current concepts on a common multifaceted problem – Kallirhoe Kalinderi – Journal of Obstetrics and Gynaecology

Human respiratory microbiome

In children, the microbiota of the nasopharynx and brochoalveolar lavage fluid are both similar and different – Kirsten M. Kloepfer – Pediatric Pulmonology

At the Root: Defining and Halting Progression of Early Chronic Obstructive Pulmonary Disease – Fernando J. Martinez – American Journal of Respiratory and Critical Care Medicine

Oral microbiome

Transcriptome of healthy gingival tissue from edentulous sites in patients with a history of generalized aggressive periodontitis – Tiago Taiete – Journal of Periodontology

Evaluation of oxidative status in patients with chronic periodontitis and polycystic ovary syndrome: A cross-sectional study – Ebru Saglam – Journal of Periodontology

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research – Irina Marie Velsko – bioRxiv

Presence of the esp gene in Enterococcus faecium derived from oropharyngeal microbiota of haematology patients – Milica Jovanović – Archives of Oral Biology

Short-term microbiological effects of photodynamic therapy in non-surgical periodontal treatment of residual pockets: A split-mouth RCT – Mônica Grazieli Corrêa – Lasers in Surgery and Medicine

Human skin microbiome

Platelet activation and aggregation by the opportunistic pathogen Cutibacterium (Propionibacterium) acnes – Frida Petersson – PLOS One

Human vaginal microbiome

Dysbiosis of the Vaginal Microbiota and Higher Vaginal Kynurenine/Tryptophan Ratio Reveals an Association with Chlamydia trachomatis Genital Infections – Noa Ziklo – Frontiers in Celular & Infection Microbiology

Human gut microbiome

Report: Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria – Christine M. Deje – Science

Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells – Liam Chung – Cell Host & Microbe

Longitudinal microbiome analysis of single donor fecal microbiota transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis – Michael Mintz – PLOS One

Infectious bursal disease virus infection leads to changes in the gut associated-lymphoid tissue and the microbiota composition – Li Li – PLOS One

Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades – Shinichiro Hirai – PLOS One

Gut microbiome and depression: what we know and what we need to know – Gal Winter – Reviews in the Neurosciences

Connection between BMI related plasma metabolite profile and gut microbiota – Filip Ottosson – The Journal of Clinical Endocrinology & Metabolism

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – Tanya T. Nguyen – Journal of Psychiatric Research

Maturation of the gut microbiome and risk of asthma in childhood – Jakob Stokholm – Nature Communications

Anaerobic 4-hydroxyproline utilization: discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity – Yolanda Y. Huang – Gut Microbes

Micro Integral Membrane Protein (MIMP), a Newly Discovered Anti-Inflammatory Protein of Lactobacillus Plantarum, Enhances the Gut Barrier and Modulates Microbiota and Inflammatory Cytokines – Yin M. – Cellular Physiology and Biochemistry

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations – Matthew A. Jackson – PeerJ

Animal experiments 

Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin – Lance W. Noll – PLOS One

Shift of uterine microbiota associated with antibiotic treatment and cure of metritis in dairy cows – Soo Jin Jeon – Veterinary Microbiology

Microbiota-derived Metabolic Factors Reduce Campylobacteriosis in Mice  – Xiaolun Sun – Gastroenterology

Comprehensive Profiling of Fecal Metabolome of Mice by Integrated Chemical Isotope Labeling-Mass Spectrometry Analysis – Bi-Feng Yuan – Analitical Chemistry

Influence of a diet enriched with virgin olive oil or butter on mouse gut microbiota and its correlation to physiological and biochemical parameters related to metabolic syndrome – Isabel Prieto – PLOS One

Injectable antimicrobials in commercial feedlot cattle and their effect on the nasopharyngeal microbiota and antimicrobial resistance – Devin B.Holman – Veterinary Microbiology

IL-6-mediated signaling pathways limit Chlamydia muridarum infection and exacerbate its pathogenicity in the mouse genital tract  – Xin Sun – Microbes and Infection

Gut microbial composition can differentially regulate bile acid synthesis in humanized mice – Dae Joong Kang – Hepatology Communications

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction – Youlian Zhou – mSystems

Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents – Leore T. Geller – Molecular & Cellular Oncology

Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet – Shasha Liu – Scientific Reports

Dietary supplementation with a nucleotide-rich yeast extract modulates gut immune response and microflora in weaned pigs in response to a sanitary challenge – S. M. Waititu – Animal

Animal microbiome 

Cellulose-dependent expression and antibacterial characteristics of surfactin from Bacillus subtilis HH2 isolated from the giant panda – Ziyao Zhou – PLOS One

Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection – Mirela D’arc – BMC Retrovirology

Temperature variation, bacterial diversity and fungal infection dynamics in the amphibian skin – Ana V. Longo – Molecular Ecology

Plant, root, and soil microbiome

Effects of an EPSPS-transgenic soybean line ZUTS31 on root-associated bacterial communities during field growth – Gui-Hua Lu – PLOS One

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities – Eric R. Hester – mSystems

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome – Collin M. Timm – mSystems

Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits – Thangasamy Saminathan – Frontiers in Plant Science

Links between nanoscale and macroscale surface properties of natural root mucilage studied by atomic force microscopy and contact angle – Robin Kaltenbach – Journal of Colloid and Interface Science

Induced Salt Tolerance of Perennial Ryegrass by a Novel Bacterium Strain from the Rhizosphere of a Desert Shrub Haloxylon ammodendron – Ao-Lei He – International Journal of Molecular Science

Water and extremophile microbiome 

High growth potential and nitrogen removal performance of marine anammox bacteria in shrimp-aquaculture sediment – LuongVan Duc – Chemosphere

Establishment and convergence of photosynthetic microbial biomats in shallow unit process open-water wetlands – Zackary L.Jones – Water Research

Review: Bioactive compounds from marine macroalgae and their hypoglycemic benefits – ChaoZhao – Trends in Food Science & Technology

A Short Comparison of Two Marine Planktonic Diazotrophic Symbioses Highlights an Un-quantified Disparity – Andrea Caputo – Frontiers in Marine Science

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O. Roger Anderson – Frontiers in Marine Science

Spatiotemporal dynamics of river viruses, bacteria and microeukaryotes – Thea Van Rossum  – bioRxiv

Trace Metal Requirements and Interactions in Symbiodinium kawagutii – Irene B. Rodriguez – Frontiers in Microbiology

Depth-Resolved Variations of Cultivable Bacteria and Their Extracellular Enzymes in the Water Column of the New Britain Trench – Qianfeng Liu – Frontiers in Microbiology

Cyanophage-encoded lipid desaturases: oceanic distribution, diversity and function – Sheila Roitman – The ISME Journal

Picoplankton distribution influenced by thermohaline circulation in the southern Adriatic – Tina Šilović – Continental Shelf Research

Evaluation of the relationship of picoplankton and viruses to environmental variables in a lagoon system (Çakalburnu Lagoon, Turkey) – Yucel-Gier – Chemistry and Ecology

Trophic-functional patterns of biofilm-dwelling ciliates at different water depths in coastal waters of the Yellow Sea, northern China – Mamun Abdullah Al – European Journal of Protistology

Distribution of bacterial communities along the spatial and environmental gradients from Bohai Sea to northern Yellow Sea – Shu-Xian Yu – PeerJ

Environmental Factors Support the Formation of Specific Bacterial Assemblages on Microplastics – Sonja Oberbeckmann – Frontiers in Microbiology

Abrupt changes in the composition and function of fungal communities along an environmental gradient in the high Arctic – Oriol Grau – Molecular Ecology

Built environment 

Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting – Yanan Yin – Canadian Journal of Microbiology

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Josh – Journal of Environmental Sciences

Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics – Ryan P. Bartelme – Frontiers in Microbiology

Food microbiology

Review: Recent advances in understanding the anti-obesity activity of anthocyanins and their biosynthesis in microorganisms – Lianghua Xie – Trends in Food Science & Technology

Review: Combining reformulation, active packaging and non-thermal post-packaging decontamination technologies to increase the microbiological quality and safety of cooked ready-to-eat meat products – Claudia N.Horita – Trends in Food Science & Technology

Review: Impact of curcumin nanoformulation on its antimicrobial activity – Anderson Clayton da Silva – Trends in Food Science & Technology

Review: Antimicrobial potential of legume extracts against foodborne pathogens: A review – M.C.Pina-Pérez – Trends in Food Science & Technology

Long-term kinetics of Salmonella Typhimurium ATCC 14028 survival on peanuts and peanut confectionery products – Maristela S. Nascimento – PLOS One

Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages – Marina Giello – Food Microbiology

Effects of microbial diversity on nitrite concentration in pao cai, a naturally fermented cabbage product from China – Zhaoxia Wang – Food Microbiology

Bacterial and fungal microbiota of spontaneously fermented Chinese products, Rubing milk cake and Yan-cai vegetable pickles – Xin Liu – Food Microbiology

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese – A. S. Bertuzzi – mSytems

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions – Nan Li – Scientific Reports

Phages and viruses

The Human Virome – Selene Zárate – Archives of Medical Research

Microreview: Contractile injection systems of bacteriophages and related systems – Nicholas M.I. Taylor – Molecular Microbiology

In vitro models for deciphering the mechanisms underlying the sexual transmission of viruses at the mucosal level – Julie Frouard – Virology

Bioinformatics

xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria – Eliot C. Bush – BMC Bioinformatics

Microbes in the news

Scientists say Earth’s atmosphere is raining viruses and bacteria down on the entire planet

Medicines from engineered bacteria offer promise — and pitfalls

Microbes on the market 

uBiome, the Leader in Microbial Genomics, Launches New Research Study Allowing SmartGut™ Patients to Assess the Impact of Diet and Lifestyle on Gut Conditions

February 1, 2018

Posted on by

The publication of a Springer manual entitled Mechanisms underlying host-microbiome interactions in pathopysiology of human diseases contains multiple interesting articles today, including reviews on the gut microbiome and preterm infant gut development, colerectal cancer, and metabolic disease, as well as a useful review of statistical models for mouse and human microbiome data. In addition, a revisitation of gut enterotypes via metabolomics, decreased Akkermansia muciniphila in psoriasis,  the bacterial communities of fiddler crabs, the impact of different wavelengths of light on hot spring bacteria, and two articles on the uses of metabarcoding in both 16S and eukaryotic microbiota analysis.

Events and jobs

Microbiology Manager – Covance – Indianapolis, Indiana

*****************************
Pregnancy and early life

*Review: Impact of Microbes on the Intestinal Development of the Preterm Infant – Elizabeth Humphrey – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Multi-site human microbiome

Review: Good and Bad Farming: The Right Microbiome Protects from Allergy – Markus Johannes Ege – Allergy Prevention and Exacerbation

Human gut microbiome

*Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes – Manoj Kumar Verma – Scientific Reports

Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – BMC Gasteroentrology

*The Akkermansia muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Review: The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer – Cheng-Bei Zhou – Critical Reviews in Microbiology

Editorial: Unveiling the gut virome in human health and diseases – Tao Zuo – International Journal of Clinical Virology

*Review: The Influence of the Microbiota on the Etiology of Colorectal Cancer – Melissa C. Kordahi – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

*Review: Altered Microbiota and Their Metabolism in Host Metabolic Diseases – Beng San Yeoh –  In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Review: The Gut Microbiome and Its Marriage to the Immune System: Can We Change It All? – Eva Untersmayr – Allergy Prevention and Exacerbation

*Review: Fecal Microbiota Transplants: Current Knowledge and Future Directions – Roxana Chis – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

*****************************

Animal experiments

Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice – Ann Wells – Journal of Proteome Research

The Changes of Colonic Bacterial Composition and Bacterial Metabolism Induced by an Early Food Introduction in a Neonatal Porcine Model – Chao Shi – Current Microbiology

Animal microbiome

*Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Transcriptional changes detected in fecal RNA of neonatal dairy calves undergoing a mild diarrhea are associated with inflammatory biomarkers – Fernanda Rosa – PLOSone

Tiny but mighty: The role of the rumen microbes in livestock production
K M Cammack – Journal of Animal Science

Effects of Spray-Dried Porcine Plasma on Fecal Microbiota in Nursery Pigs – Huyen Tran – Journal of Animal Science

Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows – Susakul Palakawong Na Ayudthaya – Biotechnology for Biofuels

Plant, root, and soil microbiome

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Stress-Tolerant Beneficial Microbes for Sustainable Agricultural Production – Reeta Goel – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 7. Springer

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire – Taylor K. Dunivin – PLOSone

Review: The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance – Msizi Mhlongo – Frontiers in Plant Science

Characterization of bacteria isolated from the Saffron (Crocus Sativus L.) rhizosphere – Majid Jami Al-Ahmadi – Journal of Horticultural Research

Review: Rhizoremediation – Plant Microbe Interactions in the Removal of Pollutants – Mehak Oberai – International Journal of Current Microbiology and Applied Sciences (IJCMAS)

Role of microbes in organic carbon decomposition and maintenance of soil ecosystem – Hina Khatoon – International Journal of Chemical Studies

Water and extremophile microbiome

Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing – Kazuhisa Okada – Scientific Reports

*Effect of light wavelength on hot spring microbial mat biodiversity – Akifumi Nishida – PLOSone

Microbial Ecology

Estimating taxon-specific population dynamics in diverse microbial communities – Benjamin J. Koch – Ecosphere

Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains – Eric Hong Jian Wong – Scientific Reports

Resistome

High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut – Lisa Ciesinski – PLOSone

*****************************
Probiotics / prebiotics

An Integrative Review on the Effect of Prebiotics, Probiotics, and Synbiotics on Infection After Colorectal Cancer Surgery – Sarah Williams Anderson – Aorn Journal

Phages and Viruses

Metagenomic Analysis of the Jinding Duck Fecal Virome – Lili Zhao – Current Microbiology

Bioinformatics

*Statistical Models and Analysis of Microbiome Data from Mice and Humans – Yinglin Xia – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases – Qingyu Chen – Journal of Data and Information Quality

Techniques

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving – Clinical Metabolomics

*16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer) – Clare Bird – PLOSone

*Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients – Ibrahim Hamad – PLOSone

*****************************
Microbes in the news

The Germ and the Gene: Gut Bacteria Research Takes a Step Forward – Ruairi MacKenzie – Technology Networks

These bacteria produce gold by digesting toxic metals – EurekaAlert

 

 

January 31, 2018

Posted on by

Today, research in prediabetes microbiome, bacteriophages in urinary microbiota, several reviews and a good number of papers focused in animal microbiome.

 

Human Microbiome

Review: Influence of functional food components on gut health – Murphy L.Y. Wan – Critical Reviews in Food Science and Nutrition

Review: Gut Microbiota and the Neuroendocrine System – Aitak Farzi – Neurotherapeutics

Laxative effect of repeated Daiokanzoto is attributable to decrease in aquaporin-3 expression in the colon – Risako Kon – Journal of Natural Medicines

Aberrant intestinal microbiota in individuals with prediabetes – Kristine H. Allin – Diabetologia

Perspective: The Potential for Topical Probiotic Treatment of Chronic Rhinosinusitis, a Personal Perspective – Anders U. Cervin – Frontiers in cellular and infection microbiology

The third tier in treatment: Attending to the growing connection between gut health and emotional well-being – Joseph Verdino – Health psychology open

Bifidobacteria and lactobacilli in the gut microbiome of children with non-alcoholic fatty liver disease: which strains act as health players? – Valerio Nobili – Archives of medical science

Kynurenic Acid: The Janus-Faced Role of an Immunomodulatory Tryptophan Metabolite and Its Link to Pathological Conditions – Elisa Wirthgen – Frontiers in immunology

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis – Susana Matamouros – Proceedings of the National Academy of Sciences of the United States of America

Review: Gut as an emerging organ for the treatment of diabetes – Martin Haluzik – The Journal of endocrinology

Bacteriophages Of The Urinary Microbiome – Taylor Miller-Ensminger – Journal of bacteriology

Commensal microbiota modulate gene expression in the skin – Jacquelyn S. Meisel – Microbiome

Host genetic variation and its microbiome interactions within the Human Microbiome Project – Raivo Kolde – Genome medicine

 

Animal Microbiome

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times – Joung-Soo Lim – Asian-Australasian journal of animal sciences

Effects of different dietary ratio of metabolizable glucose and metabolizable protein on growth performance, rumen fermentation, blood biochemical indices and ruminal microbiota of 8 to 10-month-old heifers – Jie Sun – Asian-Australasian journal of animal sciences

Effects of dietary fiber levels on cecal microbiota composition in geese – Yanpin Li – Asian-Australasian journal of animal sciences

Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua – Kiran G. Bapatla – Journal of Basic Microbiology

Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model – J.E. Libbey – Beneficial Microbes

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L. – D. Alberoni – Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2 – A. Yitbarek – Beneficial Microbes

Appropriate dose of Lactobacillus buchneri supplement improves intestinal microbiota and prevents diarrhoea in weaning Rex rabbits – Y. Zhou – Beneficial Microbes

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish – Thibault P. R. A. Legrand – Frontiers in microbiology

 

Plant/Soil Microbiome

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline – Martin Broberg – Microbiome

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan – Dong Zhu – Environmental science & technology

 

Environmental Microbiome

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

 

General Microbiome

Cross-regulatory circuit between AHR and microbiota – Jian Ji – Current Drug Metabolism

‘Massilimalia timonensis’ sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol – P. Afouda – New microbes and new infections

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies – Stefano Campanaro – Scientific Reports

January 29, 2018

Posted on by

An exciting fellowship in Ireland, along with some interesting techniques in today’s digest!

Events and jobs
APEX (APC Postdoctoral EXcellence) Fellowship – Ireland
Fellowships will be offered in the four thematic APC research areas of ‘Microbes to Molecules’, ‘Diet and Microbes at the Extremes of Life’, ‘Brain-Gut-Microbiota Axis’ and ‘Host-Microbe Dialogue’. Adhering to the MSCA principle of ‘individual-driven mobility’.

Multi-site human microbiome
Review: Rethinking Antimicrobial Prophylaxis in the Transplant Patient in the World of Emerging Resistant Organisms-Where Are We Today? – Lucy E Horton – Current Hematologic Malignancy Reports

Human gut microbiome
Metabolic mechanisms of interaction within a defined gut microbiota – Gregory Leonard Medlock – bioRxiv

Gastric bacterial flora in patients harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – Bmc Gastroenterology

Review: Molecular Paths linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections – M Serino – Journal of Molecular Biology
(DOI not availabe yet, linked to PubMed)

Animal microbiome
Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity – Julie Reveillaud – Microbiome

Microbiome structure influences infection by the parasite Crithidia bombi in bumble bees – Blair K Mockler – Applied And Environmental Microbiology

Plant, root, and soil microbiome
The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C A Mallon – The Isme Journal

Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades – Hee-Sung Bae – Applied And Environmental Microbiology

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence – Jia Liu – Microbiome

Water and extremophile microbiome
Bioavailability of mineral-bound iron to a snow algae-bacteria co-culture and implications for albedo-altering snow algae blooms – Z R Harrold – Applied And Environmental Microbiology

Built environment
Structure, variation, and assembly of the deterioration-associated microbiome of stone monuments – Qiang Li – Applied And Environmental Microbiology

Targeting Bacteria and Methanogens to Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure – Jemaneh Habtewold – Applied And Environmental Microbiology

Techniques
Novel method reveals a narrow phylogenetic distribution of bacterial dispersers in environmental communities exposed to low hydration conditions. – U S Krüger – Applied And Environmental Microbiology

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. – Garold Fuks – Microbiome

Microbes in the news
What To Do If You Are Worried About Flesh Eating Bacteria – Bruce Y. Lee – Forbes

Be aware: Certain bacteria may increase HIV risk for women – Hindustan Times (see yesterday’s post for the paper in from Lancet Infectious Diseases)

New Astronaut Food Recipe Combines Human Waste and Bacteria – Jonathan Kesh – Outer Places

‘Bug memories’ could help fight looming crisis – Jamie Morton – New Zealand Herald

January 26, 2018

Posted on by

Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany

2018 MICROBIOME CONFERENCES – Taconic

General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses

Technology

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics

Bioinformatics

Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv

January 25, 2018

Posted on by

Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

*****************************

Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

Review: Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

*****************************

Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice  – Feifei Lin – Food and Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista – British Journal of Nutrition

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

*Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

*****************************

Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

*****************************

Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology

 

January 24, 2018

Posted on by

General microbiome

Meta-analysis generates and prioritizes hypotheses for translational microbiome research – Claire Duvallet – microbial biotechnology

Resistance to Antibiotics: Are we prepared to Handle This Growing Ghost? – Ashima Kushwaha Bhardwaj – Omics Ebook Group

Pregnancy and early life

Neonate gut and respiratory microbiota: coordinated development through time and space – Alex Grier – bioRxiv

Human oral microbiome

Oral Microbiome Studies: Potential Diagnostic and Therapeutic Implications – A. Mira – Advances in Dental Research (SAGE Journals)

Rebalancing the Caries Microbiome Dysbiosis: Targeted Treatment and Sugar Alcohols – L. Zhan – Advances in Dental Research (SAGE Journals)

The Caries Microbiome: Implications for Reversing Dysbiosis – A.C.R. Tanner – Advances in Dental Research (SAGE Journals)

In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P. D. Marsh – Advances in Dental Research (SAGE Journals)

Getting to Know “The Known Unknowns”: Heterogeneity in the Oral Microbiome – R. A. Burne – Advances in Dental Research (SAGE Journals)

Human gut microbiome

Adaptive Immune Education by Gut Microbiota Antigens – Qing Zhao – Immunology

Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Characterization of the fecal microbiota differs between age groups in Koreans – Sun-Young Kook – Intestinal Research

Diet, microbiota and inflammatory bowel disease: review – Bruna Luísa Radavelli – Nutrition & Food Science

The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori – Ingeborg Klymiuk – Frontiers in Microbiology

Gut Microbial Diversity in Women with Polycystic Ovary Syndrome Correlates with Hyperandrogenism – Pedro J Torres – JCEM

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Celiac Disease Patients and Controls – Sudarshan A Shetty – bioRxiv

Animal experiments 

Modeling Host-Microbiome Interactions in Caenorhabditis elegans – Teklu K. Gerbaba – Journal of Nematology

The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota – Zoya Alteber – Immunology & Cell Biology

A metagenomics approach to the intestinal microbiome structure and function in high fat diet-induced obesity mice fed with oolong tea polyphenols – Mei Cheng – Food & Function

Animal microbiome

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica – Juan G. Abarca – Frontiers in Microbiology

Functional Characteristics of the Flying Squirrel’s Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling – Hsiao-Pei Lu – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

Out of sight, but no longer out of mind – towards an increased recognition of the role of soil microbes in plant speciation – József Geml – New Phytologist

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

Assembly and ecological function of the root microbiome across angiosperm plant species – Connor R. Fitzpatrick – PNAS

A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome – Jaderson Silveira Leite Armanhi – Frontiers in Plant Science

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function – Baneshwar Singh – Frontiers in Microbiology

Water and extremophile microbiome

Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation – Peike Gao – Applied Microbiology and Biotechnology

Evidence for Coupling of the Carbon and Phosphorus Biogeochemical Cycles in Freshwater Microbial Communities – O Roger Anderson – Frontier in Marine Science

Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields – Teresa Cerqueira – Environmental Microbiology

Bioinformatics

Predictive functional profiles using metagenomic 16S rRNA data: a novel approach to understanding the microbial ecology of aquaculture systems – Ángel Martín Ortiz-Estrada – Reviews in Agriculture

[MSc Thesis] Optimizing the Reconstruction of Microbial Population Genomes from Metagenomes – Bhavya Nalagampalli Papudeshi – San Diego State University, ProQuest Dissertations Publishing

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Extension of the viral ecology in humans using viral profile hidden Markov models – Zurab Bzhalava – PLOS One

Metataxonomic approach to decipher the polymicrobial burden in diabetic foot ulcer and its biofilm mode of infection – Karthika Suryaletha – International Wound Journal

A strategy for association study on intestinal microbiome and brain metabolome across lifespan of rats – Tianlu Chen – Analytical Chemistry

Techniques

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows – Jueeli D. Vaidya – Frontiers in Microbiology

Microbes in the news

Hyperandrogenism may alter gut microbiome in PCOS

Ed’s non-microbiology picks 

Using Fungi to Fix Bridges

Cooperating with machines – Jacob W. Crandall – Nature Communications

An investigation into the nutritional composition and cost of gluten-free versus regular food products in the UK – L. Fry – Journal of Human Nutrition and Dietetics

Prevalence and Trends in Prepregnancy Normal Weight — 48 States, New York City, and District of Columbia, 2011–2015 – CDC / Morbidity and Mortality Weekly Report

Exposed subsurface ice sheets in the Martian mid-latitudes – Colin M. Dundas – Science

Shorter sleep duration and longer sleep onset latency are related to difficulty disengaging attention from negative emotional images in individuals with elevated transdiagnostic repetitive negative thinking – Jacob A. Nota – Journal of Behavior Therapy and Experimental Psychiatry

January 19, 2018

Posted on by

Today’s digest features a review on gut microbial glycerol metabolism as a source of Acrolein, and an interesting article on the impact of climate cooling on ecosystem community structure and function in alpine soils. Happy reading!

 

Careers and Events

Research Fellow – National University of Singapore

Postdoctoral Fellow – Boston Children’s Hospital, Harvard Medical School

Scientific Officer/Senior Scientific Officer – The Cancer Research UK Beatson Institute

Staff Clinician – National Institutes of Health (NIH) National Heart, Blood and Lung Institute (NHLBI)

Human respiratory microbiome

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children – Marianne S. Muhlebach – Plos Pathogens

Human skin microbiome

Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis – Maja-Lisa Clausen – JAMA Dermatology

Human gut microbiome

Review : Genetic and microbiome influence on lipid metabolism and dyslipidemia – Maria Matey Hernandez – Physiological Genomics

Review : Bile acids in glucose metabolism in health and disease – Hagit Shapiro – Journal of Experimental Microbiology

*Review: Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source – Jianbo Zhang – mBio

Review: How does ‘metabolic surgery’ work its magic? New evidence for gut microbiota – Peck Bailey C.E – Current Opinion in Endocrinology, Diabetes and Obesity

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease – Gavin M. Douglas – Microbiome

Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease – Ahmed Moustafa – Clinical and translational gastroenterology

Animal experiments

Flaxseed-enriched diets change milk concentration of the antimicrobial danofloxacin in sheep – Jon Andoni Otero – BMC Veterinary Research

Colonization of the cervicovaginal space with Gardnerella vaginalis leads to local inflammation and cervical remodeling in pregnant mice – Luz-Jeannette Sierra – Plos One

Kudingcha and Fuzhuan Brick Tea Prevent Obesity and Modulate Gut Microbiota in High-Fat Diet Fed Mice – Guijie Chen – Molecular Nutrition and Food Research

Plant, root, and soil microbiome

*Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling – Linwei Wu – ISME Journal

Cultivable fungi present in Antarctic soils: taxonomy, phylogeny, diversity, and bioprospecting of antiparasitic and herbicidal metabolites – Eldon C. Q. Gomes – Extremophiles

Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots – Petr Kohout – The ISME Journal

A large-scale field study of bacterial communities in cereal aphid populations across Morocco – Samir Fakhour – FEMS Microbiology Ecology

Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress – Aaron S. David – Ecology

Water and extremophile microbiome

Brief Report: Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean – Olga Sánchez – Environmental Microbiology Reports

Development of a mediated whole cell-based electrochemical biosensor for joint toxicity assessment of multi-pollutants using a mixed microbial consortium – Guanyue Gao – Analytica Chimica Acta

The acute effects of erythromycin and oxytetracycline on enhanced biological phosphorus removal system: shift in bacterial community structure – Zhetai Hu – Environmental Science and Pollution Research

Probiotics / prebiotics

Valorization of Brewer’s spent grain to prebiotic oligosaccharide: production, xylanase catalyzed hydrolysis, in-vitro evaluation with probiotic strains and in a batch human fecal fermentation model – Mursalin Sajib – Journal of Biotechnology

In vitro fermentation of gum acacia – impact on the faecal microbiota – Sehad Alarifi -International Journal of Food Sciences and Nutrition

A bioluminescent test system reveals valuable antioxidant properties of lactobacillus strains from human microbiota – Maria Marsova – World Journal of Microbiology and Biotechnology

Yeasts / Fungi

Review: Sequence-based classification and identification of Fungi – David Hibbett – Mycologia

Phages and viruses

Detection of bovine Deltapapillomavirus DNA in peripheral blood of healthy sheep (Ovis aries) – S. Roperto – Transboundary and Emerging Diseases

Metagenomics

In-depth resistome analysis by targeted metagenomics – Val F. Lanza – Microbiome

Metabolomics

Qualitative metabolomics profiling of serum and bile from dogs with gallbladder mucocele formation – Jody L. Gookin – Plos One

Bioinformatics

A distance-based approach for testing the mediation effect of the human microbiome -Jie Zhang – Bioinformatics

Anitha’s non-microbiology picks

NASA test proves pulsars can function as a celestial GPS

The dark side of light: how artificial lighting is harming the natural world

Ultrathin 2-D metals get their own periodic table