Category Archives: Human oral

October 11, 2018

Posted on by

The effects of chronic ethanol ingestion on the fruit fly microbiota, engineering the mosquito microbiota to produce an antiplasmodial effector, how temperature change affects an ecosystems biodiversity and function.

General microbiome

Changes in temperature alter the relationship between biodiversity and ecosystem functioning – Francisca C García – PNAS

Human respiratory microbiome

Respiratory Microbiota Predicts Clinical Disease Course of Acute Otorrhea in Children With Tympanostomy Tubes – Wing Ho Man – The Pediatric Infectious Disease Journal

Human oral microbiome

Carious status and supragingival plaque microbiota in hemodialysis patients – Qi Yue – PLOS ONE

Human gut microbiome

Review: Fecal Microbiota Transplantation for the Management of Clostridium difficile Infection – Raghavendra Paknikar – Surgical Infections

Review: Diet, gut microbiome and indoxyl sulphate in chronic kidney disease patients – Chih-Yu Yang – Nephrology

Animal experiments

Risks Related to High-Dosage Recombinant Antimicrobial Peptide Microcin J25 in Mice Model: Intestinal Microbiota, Intestinal Barrier Function and Immune Regulation – Haitao Yu – Journal of Agricultural and Food Chemistry

Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet – Sun Min Lee – Frontiers in Microbiology

Animal microbiome

Pre-print: Chronic ethanol ingestion impairs Drosophila melanogaster health in a microbiome-dependent manner – James Angus Chandler – bioRxiv

Blood meal-induced inhibition of vector-borne disease by transgenic microbiota – Jackie L Shane – Nature Communications

Plant, root, and soil microbiome

Friends or foes in the rhizosphere: traits of fluorescent Pseudomonas that hinder Azospirillum brasilense growth and root colonization – Guillermo A Maroniche – FEMS Microbiology Ecology

Water and extremophile microbiome

Seasonal variation of extracellular enzymatic activity in marine snow-associated microbial communities and their impact on the surrounding water – Ingrid Ivančić – FEMS Microbiology Ecology

Food microbiology

Comparative evaluation of spoilage-related bacterial diversity and metabolite profiles in chilled beef stored under air and vacuum packaging – Ahmad Rois Mansur – Food Microbiology

Assessment of the non-lactic acid bacteria microbiota in fresh cucumbers and commercially fermented cucumber pickles brined with 6% NaCl – Ilenys M Pérez-Díaz – Food Microbiology

Bioinformatics

Bayesian Inference of Microbial Community Structure from Metagenomic Data Using BioMiCo – Katherine A Dunn – Microbiome Analysis (Book)

Metabolomics

Targeted Metabolic Profiling Indicates Apple Rootstock Genotype-Specific Differences in Primary and Secondary Metabolite Production and Validate Quantitative Contribution From Vegetative Growth – Rachel Leisso – Frontiers in Plant Science

Techniques

Analyzing Metabolic Pathways in Microbiomes – Mobolaji Adeolu – Microbiome Analysis (Book)

More microbes

Prevalence of Yersinia Species in the Ileum of Crohn’s Disease Patients and Controls – Guillaume Le Baut – Frontiers in Cellular and Infection Microbiology

October 10, 2018

Posted on by

Microbiota conservation and diversity in butterfly species, air and waterborne microbiota of a pharmaceutical plant, the a study on the oral microbiota of rugby players.

General microbiome

Preserving microbial diversity – Maria G Dominguez Bello – Science

Pregnancy and early life

Evaluation of patient- versus provider-collected vaginal swabs for microbiome analysis during pregnancy – Kristine M Wylie – BMC Research Notes

Human skin microbiome

The microbiome of the “sterile” pustules in palmoplantar pustulosis – Kana Masuda-Kuroki – Experimental Dermatology

Human oral microbiome

Oral health and microbiota status in professional rugby players: A case-control study – Matthieu Minty – Journal of Dentistry

Oral Bacteriome Compositions Identified by 16S rRNA Metagenomics in a Randomly Selected “Healthy” Nigerian Male and Female Subjects – Kingsley C Anukam – International Journal of Research and Reports in Dentistry

Human gut microbiome

Review: The Gut-Brain Axis and the Microbiome: Mechanisms and Clinical Implications – Vadim Osadchiy – Clinical Gastroenterology and Hepatology

Animal experiments

Replication Study: Intestinal inflammation targets cancer-inducing activity of the microbiota – Kathryn Eaton – eLIFE

Animal microbiome

Pre-print: Conserved microbiota among young Heliconius butterfly species – Bas van Schooten – PeerJ

Gastrointestinal Microbial Flora in Wild and Captive Olive Baboons (Papio anubis) – Senelwa Davis Lugano – American Journal of Infectious Diseases and Microbiology

Plant, root, and soil microbiome

Rhizosphere microbiome structure alters to enable wilt resistance in tomato – Min-Jung Kwak – Nature Biotechnology

Apple rootstocks of different nitrogen tolerance affect the rhizosphere bacterial community composition – Xiaofen Chai – Journal of Applied Microbiology

Effects of consecutive monoculture of sweet potato on soil bacterial community as determined by pyrosequencing – Huan Li – Journal of Basic Microbiology

Ectomycorrhizal fungi may not act as a barrier inhibiting host plant absorption of heavy metals – Yangze Tang – Chemosphere

Pre-print: Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances – Rodrigo G Taketani – PeerJ

Water and extremophile microbiome

Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas – NV Pimenov – Microbiology

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles – Sheila Powell – The ISME Journal

High diversity of thermophilic cyanobacteria in Rupite hot spring identified by microscopy, cultivation, single-cell PCR and amplicon sequencing – Otakar Strunecky – Extremophiles

Built environment

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance – Filippo Pacchioni – BMC Microbiology

Food microbiology

Review: The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others – Jose F Garcia-Marzcorro – Nutrients

Phages and viruses

Characterization of dog serum virome from Northeastern Brazil – MN Weber – Virology

Bioinformatics

‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets – Bhusan K Kuntal – The ISME Journal

Techniques

A Simple In Vitro Gut Model for Studying the Interaction between Escherichia coli and the Intestinal Commensal Microbiota in Cecal Mucus – Matthew E Mokszycki – Applied and Environmental Microbiology

Science, career, and publishing

Inoculating science against potential pandemics and information hazards – Kevin M Esvelt – PLOS Pathogens

October 8, 2018

Posted on by

The Digest is back with a lot of plant and soil microbiome papers. Highlights include how nematodes may alter microbial communities to benefit the host, a review on host-microbe interactions affecting acne, and a common garden study on causal relationship between plant phenotype and its rhizosphere microbiome.

General microbiology

A Candida auris Outbreak and Its Control in an Intensive Care Setting – David W. Eyre et al. – New England Journal of Medicine

** Diplogastrellus nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host – Cristina C. Ledón-Rettig et al. – PNAS

Cross-talk between MarR-like transcription factors coordinates the regulation of motility in uropathogenic Escherichia coli – Courtney L. Luterbach & Harry L.T. Mobley – Infection and Immunity

Antibiotic resistance

Environmental dimensions of antibiotic resistance: Assessment of basic science gaps – Kornelia Smalla et al. – FEMS Microbiology Ecology

Human skin microbiome

** Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris – Alan M. O’Neill & Richard L. Gallo – Microbiome

Human oral microbiome

Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing – Zhifang Zhou et al. – PeerJ

Human repiratory microbiome

Genomics, Microbiomics, Proteomics, and Metabolomics in Bronchopulmonary Dysplasia – Charitharth Vivek Lal et al. – Seminars in Perinatology

Human gut microbiome

Association of metformin administration with gut microbiome dysbiosis in healthy volunteers – Ilze Elbere et al. – PLoS One

Oral probiotic combination of Lactobacillus and Bifidobacterium alters the gastrointestinal microbiota during antibiotic treatment for Clostridium difficile infection – T. J. De Wolfe et al. – PLoS One

Review: Impact of the gut microbiota on chemical risk assessment – Tine Rask Licht & Martin Iain Bahl – Current Opinion in Toxicology

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye – Rajagopalaboopathi Jayasudha et al. – Journal of Biosciences

The Microbiome and Radiation Induced-Bowel Injury: Evidence for Potential Mechanistic Role in Disease Pathogenesis – Tomoko Kumagai et al. – Nutrients

Impact of Agaricus bisporus Mushroom Consumption on Gut Health Markers in Healthy Adults – Julie Hess et al. – Nutrients

Animal experiments

Effect of probiotic treatment on the clinical course, intestinal microbiome, and toxigenic Clostridium perfringens in dogs with acute hemorrhagic diarrhea – Anna-Lena Ziese et al. – PLoS One

Caloric restriction promotes functional changes involving short-chain fatty acid biosynthesis in the rat gut microbiota – Alessandro Tanca et al. – Scientific Reports

Animal microbiome

Evidence for Gut-Associated Serratia symbiotica in Wild Aphids and Ants Provides New Perspectives on the Evolution of Bacterial Mutualism in Insects – François Renoz et al. – Microbial Ecology

Plant, root and soil microbiome

Vertical stratification of bacteria and the chemical compounds in crude oil-contaminated soil layers of the semi-deserted Dzungharian Basin – Jiang-Ke Yang et al. – PLoS One

Dynamics of Changes in Microbiological Composition of Stored Sediments – Aleksandra Sałata et al. – Journal of Ecological Engineering

Review: Nano-scale undead drivers of microbial life, biogeochemical turnover and ecosystem functions – Yakov Kuzyakov & Kyle Mason-Jones – Soil Biology and Biochemistry

Response of microbial communities to different organochlorine pesticides (OCPs) contamination levels in contaminated soils – Yu Du et al. – Chemosphere

Changes in the soil microbial communities of alpine steppe at Qinghai-Tibetan Plateau under different degradation levels – Heng Zhou et al. – Science of The Total Environment

Responses of the endophytic bacterial communities of Juncus acutus to pollution with metals, emerging organic pollutants and to bioaugmentation with indigenous strains – Evdokia Syranidou et al. – Frontiers in Plant Science

Desert and steppe soils exhibit lower autotrophic microbial abundance but higher atmospheric CO2 fixation capacity than meadow soils – Kang Zhao et al. – Soil Biology and Biochemistry

Bacterial microbiota and metabolic character of traditional sour cream and butter in Buryatia, Russia – Jie Yu et al. – Frontiers in Microbiology

Interactions between soil properties, soil microbes and plants in remnant-grassland and old-field areas: a reciprocal transplant approach – Monique E. Smith et al. – Plant and Soil

Exploration of the Biosynthetic Potential of the Populus Microbiome – Patricia M. Blair et al. – mSystems

Soil microbial community structure in the rhizosphere of Robinia pseudoacacia L. seedlings exposed to elevated air temperature and cadmium-contaminated soils for 4  years – X. Jia et al. – Science of The Total Environment

** Plant Phenotypic Traits Eventually Shape Its Microbiota：A Common Garden Test – Yunshi Li et al. – Frontiers in Microbiology

Soil Type-Dependent Interactions of P-Solubilizing Microorganisms with Organic and Inorganic Fertilizers Mediate Plant Growth Promotion in Tomato – Isaac Kwadwo Mpanga et al. – Agronomy

Water and extremophile microbiome

Distinct community structure and microbial functions of biofilms colonizing microplastics – Lingzhan Miao et al. – Science of The Total Environment

Mature biofilm communities on synthetic polymers in seawater – Specific or general? – Inga V. Kirstein et al. – Marine Environmental Research

Phages and viruses

Virome definition in cerebrospinal fluid of patients with neurological complications after hematopoietic stem cell transplantation – C. Pou et al. – Journal of Clinical Virology

Metagenomic sequencing from mosquitoes in China reveals a variety of insect and human viruses – Pengpeng Xiao et al. – Frontiers in Cellular and Infection Microbiology

Technology

Review: Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies – Christopher Staley & Michael J. Sadowsky –

Bioinformatics

Postnovo: Post-Processing Enables Accurate and FDR-Controlled De Novo Peptide Sequencing – Samuel E. Miller et al. – Journal of Proteome Research

4 October, 2018

Posted on by

Today’s digest is full of exciting wine and animal microbiome studies!😁🐌🍷

General Microbiome

Editorial: Microbe and host lipids.Nigou J. Biochimie

Obesity alters composition and diversity of the oral microbiota in patients with type 2 diabetes mellitus independently of glycemic control.Tam J. PLoS One

Impact of the preoperative use of synbiotics in colorectal cancer patients: A prospective, randomized, double-blind, placebo-controlled study. Polakowski CB

The time response of anaerobic digestion microbiome during an organic loading rate shock. Braz GHR. Applied Microbiology and Biotechnology

REVIEW: Childhood weight gain and oral microbiota.Greenhill C. Nature Reviews Endocrinology

Glycan recognition at the saliva – Oral microbiome interface.Cross BW, Ruhl S. Cellular Immunology.

Loss of murine Paneth cell function alters the immature intestinal microbiome and mimics changes seen in neonatal necrotizing enterocolitis. Lueschow SR. PLoS One

Direct Utilization of Organic Nitrogen by Phytoplankton and Its Role in Nitrogen Cycling Within the Southern California Bight. Morando M. Frontiers in Microbiology.

Persistence and reversal of plasmid-mediated antibiotic resistance.Lopatkin AJ. Nature Communications

Gut Microbiome

REVIEW: Effects of Metabolites Derived From Gut Microbiota and Hosts on Pathogens.Li Z.Frontiers in Cellular and Infection Microbiology

Food and Wine Microbiome

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines. Morgan SC. International Journal of Food Microbiology

Techniques

Comparison of sampling methods for profiling cervicovaginal microbiome in rhesus macaques. Schmidt BA. Journal of  Medical Primatology.

Qiita: rapid, web-enabled microbiome meta-analysis.Gonzalez A. Nature Methods

Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.Rotimi AM. BMC Bioinformatics

Animal Microbiome and Experiments

White spot syndrome virus (WSSV) infection impacts intestinal microbiota composition and function in Litopenaeus vannamei.Wang Jl; Fish and Shellfish Immunology

Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density.Zheng W. PLoS One

<i>Diplogastrellus</i> nematodes are sexually transmitted mutualists that alter the bacterial and fungal communities of their beetle host.Ledón-Rettig CC. PNAS

The response of ruminal fermentation, epithelium-associated microbiota, and epithelial barrier function to severe feed restriction in pregnant ewes.Hu F. Journal of Animal Science

Rabbit Microbiota Changes Throughout the Intestinal Tract. Velasco-Galilea M. Frontiers in Microbiology

Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups. Tulstrup MV. Communications Biology

Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages.Black EM. Microbiology Open

Effect of Different Disinfectants on Bacterial Aerosol Diversity in Poultry Houses.Jiang L. Frontiers in Microbiology

Effects of organic acid and medium chain fatty acid blends on the performance of sows and their piglets.  Lan R. Animal Science Journal

Microbial community composition and electricity generation in cattle manure slurry treatment using microbial fuel cells: effects of inoculum addition. Xie B. Environmental Science and Pollution Research

Plant, Soil, and Air Microbiome

Response of soil enzymes, functional bacterial groups, and microbial communities exposed to sudan I-IV. Teng Y. Ecotoxicology and Environmental Safety

Erratum: “Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification”.Salvetti E. Applied and Environmental Microbiology

Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado. de Araujo ASF. Communications Biology

Application of phosphate solubilizing bacteria in immobilization of Pb and Cd in soil.Yuan Z. Environmental Science and Pollution Research

Inland Waters and Marine Microbiome

Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities.Dittmann KK. Environmental Microbiology Reports

Novel T4 bacteriophages associated with black band disease in corals.Buerger P. Environmental Microbiology

Environmental conditions affect activity and associated microorganisms of marine sponges.Batista D. Marine Environmental Research

The link between the microbial ecology, gene expression, and biokinetics of denitrifying polyphosphate-accumulating systems under different electron acceptor combinations.Vieira A. Applied Microbiology and Biotechnology

Antibiotics/Probiotics

Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes. Cairns J. Communications Biology

Metabolome/ Proteomics

Metaproteomics Study of the Gut Microbiome.Lai LA. Methods Molecular Biology: Functional Proteomics

COMMENTARY: Making the Case for Functional Proteomics. Perkins RC. Methods Molecular Biology: Functional Proteomics

REVIEW:Metabolome analysis for investigating host-gut microbiota interactions.Chen MX. Journal of Formosan Medical Association

September 28, 2018

Posted on by

Happy Friday! Today we have a long Digest with several interesting reviews and preprints. Learn about the fallopian tube microbiome, the bacterial communities in Icelandic volcanic deposits, the effect of ammonia on anaerobic digesters, skin defense peptides that modulate a frog’s resistance to a pathogen, and a new tool for constructing pan-genomes from shotgun metagenomic data. Enjoy!

General Microbiome
The mammalian mycobiome: A complex system in a dynamic relationship with the host
– Ghee Chuan Lai – WIREs Systems Biology and Medicine

Niche and fitness differences determine invasion success and impact in laboratory bacterial communities. – Shao-peng Li – ISMEJ

Pregnancy and Early Life
Fallopian tube microbiota: evidence beyond DNA. -Elise S Pelter – Future Microbiology

Human Oral Microbiome
Titanium as a modifier of the peri‐implant microbiome structure – Diane Daubert – Clinical Implant Dentistry and Related Research

Human Gut Microbiome
Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis. – Yan He – Microbiome

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease – Federica Ungaro – Gut Microbes

Obesity-Linked Gut Microbiome Dysbiosis Associated with Derangements in Gut Permeability and Intestinal Cellular Homeostasis Independent of Diet. – Ravinder Nagpal – Journal of Diabetes Research

Preprint: Social relationships, social isolation, and the human gut microbiota – Kimberly Dill-McFarland – bioRxiv

Review: Gut Microbiota: IgA Protects the Pioneers – Whitman B. Schofield – Current Biology

Review: The Gut Microbiota and Dysbiosis in Autism Spectrum Disorders. – Heather K. Hughes – Current Neurology and Neuroscience Reports

Animal Experiments
Modulation of Pulmonary Microbiota by Antibiotic or Probiotic Aerosol Therapy: A Strategy to Promote Immunosurveillance against Lung Metastases. – Valentino Le Noci – Cell Reports

Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells – A. Butera – Scientific Reports

Fermented Astragalus in diet altered the composition of fecal microbiota in broiler chickens – Hongxing Qiao – AMB Express

Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan‐rich hemicellulose extract in diet – Yvonne Konkol – BJU International

Animal Microbiome
Microbiota and skin defense peptides may facilitate coexistence of two sympatric Andean frog species with a lethal pathogen. – Sandra V. Flechas – ISMEJ

Green forage and fattening duration differentially modulate cecal microbiome of Wanxi white geese. – Xingyong Chen – PLoS One

Plant, root, and soil microbiome
Succession and diversity of microbial communities in landfills with depths and ages and its association with dissolved organic matter and heavy metals. – Si-jia Liu – Science of The Total Environment

Characterization of the bacterial communities on recent Icelandic volcanic deposits of different ages.– Bo Byloos – BMC Microbiology

Linking microbial co-occurrences to soil ecological processes across a woodland-grassland ecotone. – Samiran Banerjee – Ecology and Evolution

Water and Extremophile Microbiome
Independent and interactive effects of reduced seawater pH and oil contamination on subsurface sediment bacterial communities – António Louvado – Environmental Science and Pollution Research

Effects of nutrient enrichment on surface microbial community gene expression in the oligotrophic North Pacific Subtropical Gyre – J. C. Robidart – ISMEJ

Food and Industrial Microbiology
Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study – Elsa Sandberg Nielsen – Food & Function

Relationship between microbial community, operational factors and ammonia inhibition resilience in anaerobic digesters at low and moderate ammonia background concentrations. – Y. Lu – New Biotechnology

Microbial Community Enhances Biodegradation of Bisphenol A Through Selection of Sphingomonadaceae. – Seungdae Oh – Microbial Ecology

Bioinformatics
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data. – Florian Plaza Oñate – Bioinformatics

Preprint: A unified framework for unconstrained and constrained ordination of microbiome read count data – Stijn Hawinkel – bioRxiv

September 25, 2018

Posted on by

Events and jobs

4th Annual European Microbiome Congress – London UK – November 14-15 2018

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

General microbiome

Review: “Under the Skin” and into the Gut: Social Epidemiology of the Microbiome – Jennifer Beam Dowd – Current Epidemiology Reports

Review: Concurrent cross‐reactivity of microbiota‐derived epitopes to both self and pathogens may underlie the “Hygiene hypothesis” – David Usharauli – Scandinavian Journal of Immunology

Pregnancy and early life

Influence of non-polio enteroviruses and the bacterial gut microbiota on oral poliovirus vaccine response: a study from south India – Ira Praharaj – The Journal of Infectious Diseases

A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space – Samanta Michelini – Microbiome

Human respiratory microbiome

Review: Paradigms of Lung Microbiota Functions in Health and Disease, Particularly, in Asthma – Elliot Mathieu – Frontiers in Physiology

Different Upper Airway Microbiome and Their Functional Genes Associated with Asthma in Young Adults and Elderly Individuals – Jin‐Jae Lee – Allergy

Human oral microbiome

In-vivo shift of the microbiota in oral biofilm in response to frequent sucrose consumption – Annette Carola Anderson – Scientific Reports

Human gut microbiome

Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects – Mireia Lopez-Siles – Frontiers in Cellular and Infection Microbiology

Influence of gender and menopausal status on gut microbiota – Jose A.Santos-Marcos – Maturitas

Review: High-protein diets for weight management: Interactions with the intestinal microbiota and consequences for gut health. A position paper by the my new gut study group – François Blachier – Clinical Nutrition

Review: Review of the effects of sliver nanoparticle exposure on gut bacteria – Jiangyan Li – Journal of Applied Toxicology

Review: Interactions between Bitter Taste, Diet and Dysbiosis: Consequences for Appetite and Obesity – Alexandria Turner – Nutrients

Review: Progress in characterizing the linkage between Fusobacterium nucleatum and gastrointestinal cancer – Yang Liu – Journal of Gastroenterology

The Amount of Bifidobacterium Genus in Colorectal Carcinoma Tissue in Relation to Tumor Characteristics and Clinical Outcome – Keisuke Kosumi – The American Journal of Pathology

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

Animal experiments

Commensal microbiota induces colonic barrier structure and functions that contribute to homeostasis – Christina L. Hayes – Scientific Reports

Palmatine ameliorated murine colitis by suppressing tryptophan metabolism and regulating gut microbiota – Xiao-Jun Zhang – Pharmacological Research

Behavioral response to fiber feedingis cohort-dependent and associated with gut microbiota composition in mice – Lucy J.Mailing – Behavioural Brain Research

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets – John J Miklavcic – The Journal of Nutrition

Goji Berry Modulates Gut Microbiota and Alleviates Colitis in IL‐10‐Deficient Mice – Yifei Kang – Molecular Nutrition and Food Research

Konjaku flour reduces obesity in mice by modulating the composition of the gut microbiota – Yongbo Kang – International Journal of Obesity

Polysaccharide from fermented Momordica charantia L. with Lactobacillus plantarum NCU116 ameliorates type 2 diabetes in rats – He Gao – Carbohydrate Polymers

Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy – Andreassen M – Allergy and Immunology

In vitro experiments

Dietary fatty acids sustain growth of human gut microbiota – Richard Agans – Applied and Environmental Microbiology

Animal microbiome

Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri) – Xiao-Ling Wan – Scientific Reports

Differences in the Gut Microbiota Establishment and Metabolome Characteristics Between Low- and Normal-Birth-Weight Piglets During Early-Life – Na Li – Frontiers in Microbiology

Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves – Bridget E. Fomenky – Scientific Reports

Evaluation of microbial communities associated with the liquid and solid phases of the rumen of cattle offered a diet of perennial ryegrass or white clover – Jenna M. Bowen – Frontiers in Microbiology

Possibilities of early life programming in broiler chickens via intestinal microbiota modulation – Luis A Rubio – Poultry Science

A Comparative Analysis of Microbial DNA Preparation Methods for Use With Massive and Branching Coral Growth Forms – Alejandra Hernandez-Agreda – Frontiers in Microbiology

Plant, root, and soil microbiome

Interactions of mycorrhiza and protists in the rhizosphere systemically alter microbial community composition, plant shoot-to-root ratio and within-root system nitrogen allocation – Gunnar J. Henkes – Frontiers in Environmental Science

Combined effects of biochar addition and nitrogen fertilizer reduction on the rhizosphere metabolomics of maize (Zea mays L.) seedlings – Nan Cheng – Plant and Soil

Does sulfur fertilizer influence Cu migration and transformation in colloids of soil pore water from the rice (Oryza sativa L.) rhizosphere? – Lijuan Sun – Environmental Pollution

The Alleopathic Compound Luteolin from Peanut Litter Affects Peanut Nodule Formation and the Rhizosphere Microbial Community – Hong-Wei Wang – Agronomy Journal

Seasonal comparison of bacterial communities in rhizosphere of alpine cushion plants in the Himalayan Hengduan Mountains – Shuai Chang – Plant Diversity

The effect of a medic-wheat rotational system and contrasting degrees of soil disturbance on nematode functional groups and soil microbial communities – Johan Habig – Agriculture, Ecosystems & Environment

Soil-microbial communities indexing from mangroves rhizophere and barren sandy habitats – Kandasamy Saravanakumar – Physiological and Molecular Plant Pathology

Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil – Boxi Wang – PLOS One

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of Solfatara Crater (Campi Flegrei, southern Italy) – Crognale Simona – FEMS Microbiology Ecology

Responses of arbuscular mycorrhizal fungi to long-term inorganic and organic nutrient addition in a lowland tropical forest – Merlin Sheldrake – The ISME Journal

Genetic correlation network prediction of forest soil microbial functional organization
Bin Ma – The ISME Journal

Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach – M. H. Hemmat-Jou – Ecotoxicology

Water and extremophile microbiome

Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs – Nathaniel W. Fortney – Frontiers in Microbiology

Methanogens and iron-reducing bacteria: the overlooked members of mercury methylating microbial communities in boreal lakes – Andrea G. Bravo – Applied and Environmental Microbiology

Metagenomics reveals microbial diversity and metabolic potentials of seawater and surface sediment from a hadal biosphere at the Yap Trench – Xinxu Zhang – Frontiers in Microbiology

Dynamics and determinants of amoeba community, occurrence and abundance in subtropical reservoirs and rivers – Kexin Ren – Water Research

Microbial Ecology

Review: A coexistence theory in microbial communities – Marina Dohi – Royal Society Open Science

Inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier – Data in Brief

Resistome

Selection for increased quorum-sensing cooperation in Pseudomonas aeruginosa through the shut-down of a drug resistance pump – Ron D. Oshri – The ISME Journal

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

Fecal Transplants

A Systematic Review of the Efficacy and Safety of Fecal Microbiota Transplant for Clostridium difficile Infection in Immunocompromised Patients – Oluwaseun Shogbesan – Canadian Journal of Gastroenterology and Hepatology

Faecal microbiota transplantation as a treatment for inflammatory bowel disease: a national survey of adult and paediatric gastroenterologists in the UK – James Roger Mcilroy – Frontline Gastroenterology

Introduction to the joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) faecal microbiota transplant guidelines – Benjamin H. Mullish – The Journal of Hospital Infection

Phages and viruses

Detection of Viruses in Clinical Samples Using Metagenomic Sequencing and Targeted Sequence Capture – Kristine M. Wylie – Journal of Clinical Microbiology

Waste and Pollution

Pathogens, faecal indicators and human‐specific microbial source‐tracking markers in sewage – Cristina García‐Aljaro – Journal of Applied Microbiology

September 24, 2018

Posted on by

General microbiology

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt, PHYSICAL REVIEW LETTERS

Small at Size, Big at Impact: Microorganisms for Sustainable Development – Nasib Singh, Microbial Bioprospecting for Sustainable Development

Population Genomics of Archaea: Signatures of Archaeal Biology from Natural Populations – David J. Krause, Population Genomics

Pregnancy and early life

Sharing of human milk oligosaccharides degradants within bifidobacterial communities in faecal cultures supplemented with Bifidobacterium bifidum – Aina Gotoh, Scientific Reports

Multi-site human microbiome

Gut–Liver Axis: How Do Gut Bacteria Influence the Liver? – Peter Christopher Konturek, Medical Sciences

Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health – Kathrin Beyer, Plos One

Optimal immunosuppressor induces stable gut microbiota after liver transplantation – Jian-Wen Jiang, World Journal of Gastroenterology

Human respiratory microbiome

The Microbiome and Tuberculosis: Early Evidence for Cross Talk – Sivaranjani Namasivayam, mBio

Trans-maternal Helicobacter pylori exposure reduces allergic airway inflammation in offspring through regulatory T-cells – Andreas Kyburz, Journal of Allergy and Clinical Immunology

Human oral microbiome

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situbiofilm model – Stefan Rupf, Scientific Reports

Human gut microbiome

In silico Identification of Metagenomic Signature Describing Neurometabolic Potential of Normal Human Gut Microbiota – A. S. Kovtun, Russian Journal of Genetics

Gut microbiota modulates drug pharmacokinetics – Juanhong Zhang, Drug Metabolism Reviews

Active Site Flexibility Revealed in Crystal Structures of Parabacteroides merdae β‐Glucuronidase from the Human Gut Microbiome – Michael S. Little, Protein Science

Structural and Functional Analysis of the Gut Microbiome for Toxicologists – Robert G. Nichols, Current Protocols in Toxicology

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet, Neurogastroenterology and Motility

Animal experiments

Response of goose intestinal microflora to the source and level of dietary fiber – Haizhu Zhou, Poultry Science

Microbiota modulation by eating patterns, dietary and macronutrient composition; impact on food intake – Elizabeth A. Klingbeil, American Journal of Physiology

Water and extremophile microbiome

Accounting for bacterial overlap between raw water communities and contaminating sources improves the accuracy of signature-based microbial source tracking – Moa Hägglund, Frontiers in Microbiology

Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N – Beatriz Fernández-Gómez, ISME

Single-cell genomics uncover Pelagibacter as the putative host of the extremely abundant uncultured 37-F6 viral population in the ocean – Francisco Martinez-Hernandez, ISME

Microbial Community Function in Electroactive Biofilm-based Constructed Wetlands – Ramírez Vargas, Biogeosciences

Fungal endophyte‐infected leaf litter alters in‐stream microbial communities and negatively influences aquatic fungal sporulation – Emily R. Wolfe, Synthesising Ecology

Salt marsh denitrification is impacted by oiling intensity six years after the Deepwater Horizon oil spill – Corianne Tatariw, Environmental Pollution

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination – Blaise P. Bougnom, Environmental Research

Plant, root, and soil microbiome

Phosphate solubilizing bacteria with glucose dehydrogenase gene for phosphorus uptake and beneficial effects on wheat – Muhammad Suleman, Plos One

Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests – Pengyu Zhao, PeerJ

Aphid Colonization Affects Potato Root Exudate Composition and the Hatching of a Soil Borne Pathogen – Grace A. Hoysted, Frontiers in Plant Sciences

Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions – Michael James Van Oosten, BMC Plant Biology

Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France) – Jorge R. Osman, Antonie van Leeuwenhoek

Plant roots alter microbial functional genes supporting root litter decomposition – Shengjing Shi, Soil Biology and Biochemistry

Bacterial community response to a preindustrial‐to‐future CO2 gradient is limited and soil‐specific in Texas Prairie grassland – Swastika Raut, Global Change Biology

Built environment

Houseplants as home health monitors – C. Neal Stewart Jr., SYNTHETIC BIOLOGY

Characterization of Aspergillus niger Isolated from the International Space Station – Jillian Romsdahl, mSystems

Food microbiology

Microbiological Changes during Ripening of Chihuahua Cheese Manufactured with Raw Milk and Its Seasonal Variations – Cristina Sánchez-Gamboa, Foods

Supplementation in mushroom crops and its impact on yield and quality – Jaime Carrasco, AMB Express

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro‐Inflammatory Markers in a Caco‐2/endothelial Cell Co‐Culture Model – Ting Wu, Molecular Nutrition and Food Research

Techniques

A critical evaluation of the use of gas chromatography- and high performance liquid chromatography-mass spectrometry techniques for the analysis of microbial metabolites in human urine after consumption of orange juice – José Luis Ordóñez, Journal of Chromatography A

Recovering cellular biomass from fluids using chemical flocculation – Paul A. Kenward, Environmental Microbiology Reports

Influence of support media supplementation to reduce the inhibition of anaerobic digestion by phenol and ammonia: Effect on degradation performances and microbial dynamics – Simon Poirier, Data in Brief

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC – Dhavalkumar Patel, Biotech

Bioinformatics

Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development – Dipannita Hazra, Microbial Bioprospecting for Sustainable Development

Metabolomics

Paradoxes in leaky microbial trade – Yoav Kallus, Nature Communications

Antibiotics

Amycomicin is a potent and specific antibiotic discovered with a targeted interaction screen – Gleb Pishchany, PNAS

Microbes in the news

Subculture show converts Storefront for Art and Architecture into living lab – The Architects Newspaper, Ali Oriaku

19 September, 2018

Posted on by

Today’s midweek digest includes a brilliant review on the occurrence of HGT within human holobiont and a new approach to analysing microbiome data

General Microbiome

REVIEW: Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.Sitaraman R. Microbiome

Epidemiological aspects of healthcare-associated infections and microbial genomics.Mirande C. Europeans Journal of Clinical Microbiology and Infectious Diseases

Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study. Lee SH. Journal of Clinical Medicine

REVIEW: Proteomics and the microbiome: pitfalls and potential.Lin H. Expert Review of Proteomics

Biological films adhering to the oral soft tissues: structure, composition and potential impact on taste perception.Neyraud E. Journal of Texture Studies

Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. Flaherty BR. Microbiome

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.Jarett JK. Microbiome

The Extended Genotype: Microbially Mediated Olfactory Communication.Carthey AJR. Trends in Ecology and Evolution

Ceftriaxone administration disrupts intestinal homeostasis, mediating non-inflammatory proliferation and dissemination of commensal enterococci.Chakraborty R. Infection and Immunity

Gut Microbiome

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.Martínez I. eLIFE

Human gut <i>Bacteroides</i> capture vitamin B<sub>12</sub> via cell surface-exposed lipoproteins.Wexler AG. eLIFE

Structural basis for the role of serine-rich repeat proteins from <i>Lactobacillus reuteri</i> in gut microbe-host interactions.Sequeira S. PNAS

Rapid and complete dehalogenation of halonitromethanes in simulated gastrointestinal tract and its influence on toxicity. Yin J. Chemosphere.

Diet: Cause or Consequence of the Microbial Profile of Cholelithiasis Disease?Gutiérrez-Díaz I. Nutrients

Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-κB activation through gut microbiota disturbance. Jang HM. Scientific Reports

Salmonella stimulates pro-inflammatory signalling through p21-activated kinases bypassing innate immune receptors.Sun H. Nature Microbiology

Lung Microbiome

Deciphering the Lung Microbiome: Implications for Lung Health and Disease.Johnson MM. Respiration

Plant and Soil Microbiome

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. Sánchez-Soto Jiménez MF. PeerJ.

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing. Li Z. Current Microbiology

Molecular characterization and detection of 16SrIII group phytoplasma associated with Huanglongbing symptoms.Wulff NAA. Phytopathology

Water Microbiome

Analysis of Bacterial Community Structure of Activated Sludge from Wastewater Treatment Plants in Winter. Xu S. BioMed Research International

Biological As(III) oxidation in biofilters by using native groundwater microorganisms.Crognale S. Science of the Total Environment

Animal Experiments and Microbiome

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. Bredon M. Microbiome

The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome.Dranse HJ. PeerJ

Techniques

KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA.Randolph TW. The Annals of Applied Statistics

September 15, 2018

Posted on by

Have a nice weekend! Today, we have several papers, covering different aspects of the microbiome! Some highlights (in bold): the role of microbiota in cancer immunotherapy success; interesting study about the lung microbiota and smoking; changes in gut microbiota in asthma patients, microbiota changes in high-salt feces; an interesting article about the potential effect of dogs in veteran rehabilitation; a review about periodontitis and the microbiome; a ecophylogenetic study about mammalian microbiome, and more!

 

Human and General Microbiome

Metagenomic Approaches for Understanding New Concepts in Microbial Science – Luana de Fátima Alves – International Journal of Genomics

Review: Epigenetic Mechanisms Link Maternal Diets and Gut Microbiome to Obesity in the Offspring – Yuanyuan Li – Frontiers in Genetics

Review: NLRP3 inflammasome in colitis and colitis-associated colorectal cancer – Agampodi Promoda Perera – Mammalian Genome

Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study – He Xu – Frontiers in Microbiology

Review: Roles of intestinal microbiota in response to cancer immunotherapy – Jing Cong – European Journal of Clinical Microbiology & Infectious Diseases

Intestinal dysbiosis and hormonal neuroendocrine secretion in the fibromyalgic patient: Relationship and correlations – Giovanni Tomasello – Biomedical Papers

Macroecology to Unite All Life, Large and Small – Ashley Shade – Trends in Ecology and Evolution

Dichotomous development of the gut microbiome in preterm infants – Thao T. B. Ho – Microbiome

Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome – Ann C. Gregory – Respiratory Research

A metagenome-wide association study of gut microbiota in asthma in UK adults – Qi Wang – BMC Microbiology

The Cutaneous Microbiome and Wounds: New Molecular Targets to Promote Wound Healing – Taylor R. Johnson – International Journal of Molecular Sciences

Phthalate Exposure and Odds of Bacterial Vaginosis Among U.S. Reproductive-Aged Women, NHANES 2001-2004 – Ruth J.Geller – Reproductive Toxicology

Para-cresol production by Clostridium difficile affects microbial diversity and membrane integrity of Gram-negative bacteria – Ian J. Passmore – PLoS Pathogens

Salt in stools is associated with obesity, gut halophilic microbiota and Akkermansia muciniphila depletion in humans – E. H. Seck – International Journal of Obesity

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota – Z.F. Kispal – Journal of Pediatric Urology

The Gut-Brain Axis in Alzheimer’s Disease and Omega-3. A Critical Overview of Clinical Trials – Francesca La Rosa – Nutrients

Associations between Flavonoid Intakes and Gut Microbiota in a Group of Adults with Cystic Fibrosis – Li Li – Nutrients

Review: Insights into the Human Virome Using CRISPR Spacers from Microbiomes – Claudio Hidalgo-Cantabrana – Viruses

Review: Probiotics in the Treatment of Colorectal Cancer –  Robert Hendler – Medicines

Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease – Shu Mei Teo – Cell Host and Microbe

Human skin volatiles: Passive sampling and GC × GC-ToFMS analysis as a tool to investigate the skin microbiome and interactions with anthropophilic mosquito disease vectors – Alexis P. Roodt – Journal of Chromatography B

Commentary: Regulating stool for microbiota transplantation – Pilar N. Ossorio – Gut Microbes

Associations between the gut microbiota and host responses to high altitude – J. Philip Karl – Gastrointestinal and Liver Physiology

Exploring service dogs for rehabilitation of veterans with PTSD: A microbiome perspective – Andrew J.,Billera Hoisington – Rehabilitation Psychology

Mucosal associated invariant T cells from human breast ducts mediate a Th17-skewed response to bacterially exposed breast carcinoma cells – Nicholas A. Zumwalde – Breast Cancer Research

Periodontitis and the microbiome: a systematic review and meta-analysis – Fabrizio Guerra – Minerva Stomatologica

Formal Comment: The microbiome and the human: A reply to Parke and colleagues – Tobias Rees – PLoS Biology

Microbiota-gut-brain research: a critical analysis – Katarzyna B. Hooks – Behavioral and Brain Sciences

 

Animal Microbiome

Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota – Christopher A. Gaulke – mBio

The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis – Agnieszka D. Truax – Cell Host and Microbe

American ginseng microbial metabolites attenuate DSS-induced colitis and abdominal pain – Chong-Zhi Wang – International Immunopharmacology

Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome – Heidi Pauer – PLoS ONE

Bacterial community composition in the salivary glands of triatomines (Hemiptera: Reduviidae) – Michele Souza Lima – PLoS Neglected Tropical Diseases

Postnatal Administration of Lactobacillus rhamnosus HN001 Ameliorates Perinatal Broad-Spectrum Antibiotic-Induced Reduction in Myelopoiesis and T cell Activation in Mouse Pups – Eva Fuglsang – Molecular Nutrition and Food Research

Absorption of Codonopsis pilosula Saponins by Coexisting Polysaccharides Alleviates Gut Microbial Dysbiosis with Dextran Sulfate Sodium-Induced Colitis in Model Mice – Yaping Jing – BioMed Research International

Tributyrin Supplementation Protects Immune Responses and Vasculature and Reduces Oxidative Stress in the Proximal Colon of Mice Exposed to Chronic-Binge Ethanol Feeding – B. Glueck – Journal of Immunology Research

Fecal Hyodeoxycholic Acid Is Correlated With Tylosin-Induced Microbiome Changes in Growing Pigs – Michaela P. Trudeau – Frontiers in Veterinary Science

Yeast Probiotics Shape the Gut Microbiome and Improve the Health of Early-Weaned Piglets – Jinqiang Xu – Frontiers in Microbiology

Probiotic Bacillus amyloliquefaciens C-1 Improves Growth Performance, Stimulates GH/IGF-1, and Regulates the Gut Microbiota of Growth-Retarded Beef Calves – Renjia Du – Frontiers in Microbiology

The Microbiome of the Gastrointestinal Tract of a Range-Shifting Marine Herbivorous Fish – Jacquelyn Jones – Frontiers in Microbiology

Intestinal Microbiome-Metabolome Responses to Essential Oils in Piglets – Yuan Li – Frontiers in Microbiology

Review: Managing the Microbial Community of Marine Fish Larvae: A Holistic Perspective for Larviculture – Olav Vadstein – Frontiers in Microbiology

Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement – H. Myint – Beneficial Microbes

Effects of short-term fasting on in vivo rumen microbiota and in vitro rumen fermentation characteristics – Jong Nam Kim – Asian-Australian Journal of Animal Sciences

The effect of exposure to high altitude and low oxygen on intestinal microbial communities in mice – Wei Zhang – PLoS ONE

 

Food Microbiome

Lactic Acid Bacterium Population Dynamics in Artisan Sourdoughs Over One Year of Daily Propagations Is Mainly Driven by Flour Microbiota and Nutrients – Fabio Minervini – Frontiers in Microbiology

Effect of Pressure, Reconstituted RTE Meat Microbiota, and Antimicrobials on Survival and Post-pressure Growth of Listeria monocytogenes on Ham – Januana S. Teixeira – Frontiers in Microbiology

 

Plant Microbiome

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla – Mohamed S. Sarhan – Microbes and Environments

Root exudates drive the soil-borne legacy of aboveground pathogen infection – Jun Yuan – Microbiome

Review: Mycorrhizal microbiomes – Mika T. Tarkka – Mycorrhiza

 

Bioinformatics

GePMI: A statistical model for personal intestinal microbiome identification – Zicheng Wang – npj Biofilms and Microbiomes

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes – Suzanne M. Kosina – BMC Microbiology

 

Other

Temporal variability and stability of the fecal microbiome: the Multiethnic Cohort Study – Benjamin C Fu – Cancer Epidemiology, Biomarkers & Prevention

A flavin-based extracellular electron transfer mechanism in diverse Gram-positive bacteria – Samuel H. Light – Nature

 

September 10, 2018

Posted on by

In the today’s digest: an article on detection limits and bias with DNA extraction kits and primer choice, a novel R package to analyze timeseries in the 16S microbiome data in perturbation studies, a study on how fecal microbiota transplantation induces changes in gut microbial and metabolomic profiles of pediatric ulcerative colitis patients, plus an invitation for the first worldwide online open access course via Twitter about science and microbiology starting October 2.

Event

Third Annual Microbiome Symposium at Stanford, September 24 at the Stanford Faculty Club, Palo Alto, CA.

Human gut microbiome

*Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients – David J Nusbaum – FEMS Microbiology Ecology

Review: Sample preparation and recent trends in volatolomics for diagnosing gastrointestinal diseases – Tomasz Majchrzak – TrAC Trends in Analytical Chemistry

Special Report: The role of gut microbiota in lupus: what we know in 2018? – Lorena Ruiz – Expert Review of Clinical Immunology

Human gut virome

The Intestinal Virome and Immunity – Jessica A. Neil and Ken Cadwell – J Immunology

Human lung microbiome

The Human Respiratory Microbiome: The End of the Beginning? – Alicia B. Mitchell and Allan R. Glanville – Essentials in Lung Transplantation

Human oral microbiome

Review: The oral microbiome – friend or foe? – Kilian Mogens – Eur J Oral Science

Animal microbiome

Ultrahigh-throughput functional profiling of microbiota communities – Stanislav S. Terekhova – PNAS

Water microbiome

*Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing – Jakob Brandt and Mads Albertsen – Frontiers in Microbiology

Application of untargeted metabolomics for the detection of pathogenic Naegleria fowleri in an operational drinking water distribution system – Zhihao Yu – Water Research

Soil microbiome

Investigation on microbial community in remediation of lead-contaminated soil by Trifolium repensL. – Chenjing Liu – Ecotoxicology and Environmental Safety

Bioinformatics

*The Block Bootstrap Method for Longitudinal Microbiome Data – Pratheepa Jeganathan – arXiv

*Course

#EUROmicroMOOC: Trends in Microbiology [The first worldwide online open access microbiology course via Twitter]