Author Archives: xinhuang7

December 25, 2018

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Merry Christmas to those of you who celebrate, and Happy Holidays to those of you taking a break! Today’s Digest is dense, so get prepared. This Digest includes many articles in Animal Experiments and Plant, Root and Soil Microbiome. It also features finding antimicrobial resistance in indoor dust, how commensals help maintain epithelial homeostasis, and a carnivorous plant farming microbes for digesting preys. Enjoy!

Antimicrobial resistance

Bioaccumulation of antibiotics in crops under long-term manure application: Occurrence, biomass response and human exposure – Fangkai Zhao et al. – Chemosphere

Preprint: From genotype to antibiotic susceptibility phenotype in Enterobacteriaceae: a clinical perspective – Etienne Ruppé et al. – bioRxiv

Review: Action of Antimicrobial Peptides against Bacterial Biofilms – Muhammad Yasir et al. – Materials

** Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors – Ashkaan K. Fahimipour et al. – mSystems

Pregnancy and early life

Maternal antibiotic prophylaxis affects Bifidobacterium spp. counts in the human milk, during the first week after delivery – M. Padilha et al. – Beneficial Microbes

Human oral microbiome

Preprint: Microbiome composition comparison in oral and atherosclerotic plaque from patients with and without periodontitis – Daichi Isoshima et al. – bioRxiv

Meta-review: Barrett’s esophagus and esophageal cancer: Links to microbes and the microbiome – Teminioluwa A. Ajayi et al. – PLoS Pathogens

Human respiratory microbiome

Lower airway microbiota associates with inflammatory phenotype in severe preschool wheeze – Polly F.M. Robinson et al. – Journal of Allergy and Clinical Immunology

Human gut microbiome

Population-Based Gut Microbiome Associations With Hypertension – Hamdi Jama et al. – Circulation Research

Response to: Population-Based Gut Microbiome Associations With Hypertension – Claire J. Steves & Matthew A. Jackson – Circulation Research

Gut Microbiota and Endothelial Dysfunction Markers in Obese Mexican Children and Adolescents – Khemlal Nirmalkar et al. – Nutrients

Gut mucosal-associated microbiota better discloses Inflammatory Bowel Disease differential patterns than faecal microbiota – Annamaria Altomare et al. – Digestive and Liver Disease

Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT – R. Murphy et al. – Beneficial Microbes

Review: Synthetic consortia of nanobody-coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis-associated diseases and co-morbidities – Kenneth Timmis et al. – Microbial Biotechnology

Human gut-microbiome-brain axis

Review: A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis – S. Du Preez et al. – Systematic Reviews

Built environment microbiome

Carbapenem-resistant Enterobacteriaceae dispersal from sinks is linked to drain position and drainage rates in a laboratory model system – P.Aranega Bou et al. – Journal of Hospital Infection

Enriching Beneficial Microbial Diversity of Indoor Plants and Their Surrounding Built Environment With Biostimulants – Alexander Mahnert et al. – Frontiers in Microbiology

Food microbiome

Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China – Yan Zhu & Yingying Cao et al. – PeerJ

Animal experiments

Gut microbiota profiling in Norwegian weaner pigs reveals potentially beneficial effects of a high-fiber rapeseed diet – Özgün Candan Onarman Umu et al. – PLoS One

** Mouse: Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis – Mayara Grizotte-Lake et al. – Immunity

Non-isoflavones Diet Incurred Metabolic Modifications Induced by Constipation in Rats via Targeting Gut Microbiota – Jialin Liu & Ruirui Chang et al. – Frontiers in Microbiology

Genetic Effects on the Gut Microbiota Assemblages of Hybrid Fish From Parents With Different Feeding Habits – Wuhui Li, Junmei Liu & Hui Tan et al. – Frontiers in Microbiology

Mouse: Aspirin eugenol ester regulates cecal contents metabolomic profile and microbiota in an animal model of hyperlipidemia – Ning Ma et al. – BMC Veterinary Research

Effects of Early Intervention with Maternal Fecal Microbiota and Antibiotics on the Gut Microbiota and Metabolite Profiles of Piglets – Chunhui Lin et al. – Metabolites

Mouse: Impact of Cyanocobalamin and Methylcobalamin on Inflammatory Bowel Disease and the Intestinal Microbiota Composition – Xuan Zhu et al. – Journal of Agricultural and Food Chemistry

Impact of probiotics on development and behaviour in Drosophila melanogaster – a potential in vivo model to assess probiotics – E. Gómez et al. – Beneficial Microbes

Effects of chronic caffeine exposure during adolescence and subsequent acute caffeine challenge during adulthood on rat brain serotonergic systems – M.R. Arnold et al. – Neuropharmacology

Mouse: A Microtube Array Membrane (MTAM) Encapsulated Live Fermenting Staphylococcus epidermidis as a Skin Probiotic Patch against Cutibacterium acnes – Albert-Jackson Yang et al. – International Journal of Molecular Sciences

Animal microbiome

Wild bees and their nests host Paenibacillus bacteria with functional potential of avail – Alexander Keller et al. – Microbiome

Field-level clothianidin exposure affects bumblebees but generally not their pathogens – Dimitry Wintermantel et al. – Nature Communications

Plant, root and soil microbiome

** Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant – Dagmara Sirová & Jiří Bárta et al. – Microbiome

The influence of Bt maize cultivation on communities of arbuscular mycorrhizal fungi revealed by MiSeq sequencing – Huilan Zeng et al. – Frontiers in Microbiology

Evaluation of the possible persistence of potential human pathogenic bacteria in olive orchards irrigated with treated urban wastewater – Adriano Sofo et al. – Science of The Total Environment

Relationships between the properties of Spitsbergen soil, number and biodiversity of rhizosphere microorganisms, and heavy metal concentration in selected plant species – Agnieszka Hanaka et al. – Plant and Soil

Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils – Tianzhu Meng et al. – Applied Microbiology and Biotechnology

Shift of millet rhizosphere bacterial community during the maturation of parent soil revealed by 16S rDNA high-throughput sequencing – Lixia Xu et al. – Applied Soil Ecology

Molecular characterization of eukaryotic algal communities in the tropical phyllosphere based on real-time sequencing of the 18S rDNA gene – Huang Zhu et al. – BMC Plant Biology

The impact of carbon addition on the organisation of rhizosheath of chickpea – Sheikh M. F. Rabbi et al. – Scientific Reports

Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long-term biodiversity experiment – Marc W. Schmid et al. – Molecular Ecology

Review: The role of water in plant-microbe interactions – Kyaw Aung et al. – The Plant Journal

Toxicity of phthalate esters to lettuce (Lactuca sativa) and the soil microbial community under different soil conditions – Tingting Ma et al. – PLoS One

Water and extremophile microbiome

Review: Acidithiobacillus ferrooxidans – Raquel Quatrini & D. Barrie Johnson – Trends in Microbiology

Phages and viruses

Perspective: Minimum Information about an Uncultivated Virus Genome (MIUViG) – Simon Roux et al. – Nature Biotechnology

Data: Whole-genome of Mexican-crAssphage isolated from the human gut microbiome – Melany Cervantes-Echeverría et al. – BMC Research Notes

Virome analysis of tick-borne viruses in Heilongjiang Province, China – Fei Meng et al. – Ticks and Tick-borne Diseases

Preprint: Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and mutation – Nicolas M Suarez et al. – bioRxiv

Simultaneous Detection of Beta and Gamma Human Herpesviruses by Multiplex qPCR Reveals Simple Infection and Coinfection Episodes Increasing Risk for Graft Rejection in Solid Organ Transplantation – Yessica Sánchez-Ponce et al. – Viruses

Finer-Scale Phylosymbiosis: Insights from Insect Viromes – Brittany A. Leigh – mSystems

Technology

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota – Ana Popovic et al. – Microbiome

Preprint: Optimization of DNA extraction from human urinary samples for mycobiome community profiling – A. Lenore Ackerman et al. – bioRxiv

Bioinformatics

Combining multiple functional annotation tools increases coverage of metabolic annotation – Marc Griesemer & Jeffrey A. Kimbrel et al. – BMC Genomics

Scientific Communication and Education

Preprint: The economy and environmental attitudes: Does a good economy make citizens care more about the environment? – Stephanie Marie Rizio & Yoshihisa Kashima – bioRxiv

Preprint: Professional medical writing support and the quality, ethics and timeliness of clinical trial reporting: a systematic review – Obaro Evuarherhe et al. – bioRxiv

Preprint: A data-driven approach to reduce gender disparity in invited speaker programs at scientific meetings – Ann-Maree Vallence – bioRxiv

December 4, 2018

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A short and sweet Digest today. Many preprints, so take them with a grain of salt. Interesting highlights include skin odor and microbiome, plant derived alternative to antibiotics for growth promotion, and host specialization for bee gut symbionts.

General microbiology

Preprint: The genome of the fungal pathogen Verticillium dahliae reveals extensive bacterial to fungal gene transfer – Xiaoqian Shi et al. – bioRxiv

Antibiotic resistance

Preprint: Antimicrobial Resistance Surveillance Among Gram Negative Bacterial Isolates from Patients in Khartoum State Hospitals – Hana Salaheldin Elbadawi et al. – bioRxiv

Preprint: Linking the Resistome and Plasmidome to the Microbiome – Thibault Stalder et al. – bioRxiv

Human skin microbiome

** Understanding the microbial basis of body odor in pre-pubescent children and teenagers – Tze Hau Lam et al. – Microbiome

Animal experiments

** The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids – Peng Huang, Yan Zhang, Kangpeng Xiao & Fan Jiang et al. – Microbiome

Animal microbiome

** Preprint: Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5 – Kirsten M Ellegaard et al. – bioRxiv

Preprint: Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades – Nicholas D Youngblut et al. – bioRxiv

Water and extremophile microbiome

Preprint: Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia – Vitalii Timofeev et al. – bioRxiv

Phages and viruses

Preprint: Dengue and Chikungunya among Febrile Outpatients in Kinshasa, Democratic Republic of Congo: a cross-sectional study – Sam Proesmans et al. – bioRxiv

Preprint: Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression – Lauren M. Oko et al. – bioRxiv

Scientific communication

Preprint: Cross-Lagged Panel Model in Medical Research: A Cautionary Note – Satoshi Usami et al. – bioRxiv

Preprint: Which author is which? Gender Authorship Position in Aquaculture Literature – Morgan Chow et al. – bioRxiv

November 20, 2018

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Here’s your Digest before the US Thanksgiving holiday with a burst of human gut microbiome/animal experiment papers. Science publishes a special edition on diet and health, how do human gut microbes fare against mouse gut commensals, and watch out for the water used in your microbiome studies!

Jobs

Open Rank Tenure Track Faculty Position – Baylor College of Medicine

General microbiology

Preprint: Natural strain diversity reveals novel biofilm regulation in squid-colonizing Vibrio fischeri – Ella R. Rotman et al. – bioRxiv

Preprint: Genotyping of Salmonella spp. on the basis of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) – Calvin Jiksing et al. – bioRxiv

Pregnancy and early life

Iron-containing micronutrient powders modify the effect of oral antibiotics on the infant gut microbiome and increase post-antibiotic diarrhoea risk: a controlled study in Kenya – Daniela Paganini et al. – Gut

Human skin microbiome

Review: The epithelial immune microenvironment (EIME) in atopic dermatitis and psoriasis – Teruki Dainichi et al. – Nature Immunology

Human oral microbiome

The Effect of Influenza Virus on the Human Oropharyngeal Microbiome – Elisa Ramos-Sevillano et al. – Clinical Infectious Diseases

Human vaginal microbiome

Review: Ecological dynamics of the vaginal microbiome in relation to health and disease – Shirley Greenbaum et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Preprint: Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome – Benjamin D. Ross et al. – bioRxiv

Review: Calorie restriction and its impact on gut microbial composition and global metabolism – Xiaojiao Zheng et al. – Frontiers of Medicine

Fecal microbiota transplantation with frozen capsules for a patient with refractory acute gut graft-versus-host disease – Satoshi Kaito et al. – Blood Advances

Review: Salts and energy balance: A special role for dietary salts in metabolic syndrome –
Christopher W.Brey et al. – Clinical Nutrition

IL23R-protective coding variant promotes beneficial bacteria and diversity in the ileal microbiome in healthy individuals without inflammatory bowel disease – Martha Zakrzewski et al. – Journal of Crohn’s and Colitis

In vitro: A four-strain probiotic exerts positive immunomodulatory effects by enhancing colonic butyrate production in vitro – Frédéric Moens et al. – International Journal of Pharmaceutics

Review: Obesity and Cancer Risk: Emerging biological mechanisms and perspectives – Konstantinos I. Avgerinos et al. – Metabolism

Review: Endocrine regulation of gut function – a role for glucagon-like peptide-1 in the pathophysiology of irritable bowel syndrome – Dervla O’Malley – Experimental Physiology

The Human Metabolism of Nuts Proanthocyanidins Does not Reveal Urinary Metabolites Consistent with Distinctive Gut Microbiota Metabotypes – Adrián Cortés‐Martín et al. – Molecular Nutrition & Food Research

Review: The role of dietary factors in inflammatory bowel diseases: new perspectives – Yi Quan Zhou et al. – Journal of Digestive Diseases

Review: Interaction of gut microbiota with dysregulation of bile acids in the pathogenesis of nonalcoholic fatty liver disease and potential therapeutic implications of probiotics – Jiezhong Chen et al. – Journal of Cellular Biochemistry

Review: Cross-Talk Between Gluten, Intestinal Microbiota and Intestinal Mucosa in Celiac Disease: Recent Advances and Basis of Autoimmunity – Atul Munish Chander et al. – Frontiers in Microbiology

Review: Control and dysregulation of redox signalling in the gastrointestinal tract – Eric L. Campbell & Sean P. Colgan – Nature Reviews Gastroenterology & Hepatology

** Review: The gut microbiota at the intersection of diet and human health – Christopher L. Gentile & Tiffany L. Weir – Science

Review: Gut Microbiota and Their Neuroinflammatory Implications in Alzheimer’s Disease – Vo Van Giau et al. – Nutrients

Review: Gut microbiota in diabetes and HIV: Inflammation is the link – Vicente Estrada & Noemi Gonzalez – EBioMedicine

Human gut-microbiome-brain axis

Can the gut be the missing piece in uncovering PD pathogenesis? – Guillaume Chapelet et al. – Parkinsonism & Related Disorders

Human multi-site microbiome

Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions – Lara Costantini et al. – Scientific Reports

Review: Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption – Jessica L.Metcalf – Forensic Science International: Genetics

Boston Type I Keratoprosthesis: Antibacterial Resistance and Microbiota Evaluation of Soft Contact Lenses – Emilio A.Torres-Netto et al. – American Journal of Ophthalmology

Food microbiome

Combined effects of thymol, carvacrol and packaging on the shelf-life of marinated chicken – Layal Karam et al. – International Journal of Food Microbiology

Effect of post-harvest interventions on surficial carrot bacterial community dynamics, pathogen survival, and antibiotic resistance – Vaishali Dharmarha et al. – International Journal of Food Microbiology

The potential use of probiotic and beneficial bacteria in the Brazilian dairy industry – Monique Colombo et al. – Journal of Dairy Research

Animal experiments

In vitro: Environmental pollutant-mediated disruption of gut microbial metabolism of the prebiotic inulin – Jessie Hoffman et al. – Anaerobe

Assessment of the adverse impacts of aflatoxin B1 on gut-microbiota dependent metabolism in F344 rats – Jun Zhou et al. – Chemosphere

Dietary Tomato Powder Inhibits High-Fat Diet-Promoted Hepatocellular Carcinoma with Alteration of Gut Microbiota in Mice Lacking Carotenoid Cleavage Enzymes – Hui Xia et al. – Cancer Prevention Research

Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs – Eric F.Lucking et al. – EBioMedicine

Microbiota-Derived Lactate Activates Production of Reactive Oxygen Species by the Intestinal NADPH Oxidase Nox and Shortens Drosophila Lifespan – Igor Iatsenko et al. – Immunity

A polysaccharide extracted from Astragalus membranaceus residue improves cognitive dysfunction by altering gut microbiota in diabetic mice – Yameng Liu et al. – Carbohydrate Polymers

Mouse: Role of Bile Acids and GLP-1 in Mediating the Metabolic Improvements of Bariatric Surgery – Vance L. Albaugh et al. – Gastroenterology

Evaluation of Sialyllactose Supplementation of a Prebiotic-Containing Formula on Growth, Intestinal Development, and Bacterial Colonization in the Neonatal Piglet – Marcia H Monaco et al. – Current Developments in Nutrition

Mouse: The Probiotic Effectiveness in Preventing Experimental Colitis Is Correlated With Host Gut Microbiota – Sharmila Suwal et al. – Frontiers in Microbiology

Soy-Induced Fecal Metabolome Changes in Ovariectomized and Intact Female Rats: Relationship with Cardiometabolic Health – Victoria J. Vieira-Potter et al. – Scientific Reports

** Selective colonization ability of human fecal microbes in different mouse gut environments – Wei Zhou et al. – The ISME Journal

Rat: Potential Involvement of Peripheral Leptin/STAT3 Signaling in the Effects of Resveratrol and Its Metabolites on Reducing Body Fat Accumulation – Andrea Ardid-Ruiz et al. – Nutrients

Bacteria engineered to produce IL-22 in intestine induce expression of REG3G to reduce ethanol-induced liver disease in mice – Tim Hendrikx et al. – Gut

Effects of polystyrene microplastics on the composition of the microbiome and metabolism in larval zebrafish – Zhiqin Wan et al. – Chemosphere

Animal microbiome

The microbiome of Escherichia coli and culture-negative nonsevere clinical mastitis: Characterization and associations with linear score and milk production – A.K. Vasquez et al. – Journal of Dairy Science

Plant, root and soil microbiome

Community diversity and potential functions of rhizosphere-associated bacteria of nickel hyperaccumulators found in Albania – Séverine Lopez et al. – Science of The Total Environment

Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum – Ye Sun et al. – International Journal of Systematic and Evolutionary Microbiology

Linking bacterial community composition to soil salinity along environmental gradients – Kristin M. Rath et al. – The ISME Journal

Soil microbial community composition closely associates with specific enzyme activities and soil carbon chemistry in a long-term nitrogen fertilized grassland – Yue Li et al. – Science of The Total Environment

Water and extremophile microbiome

Periodic and spatial spreading of alkanes and Alcanivorax bacteria in deep waters of the Mariana Trench – Wen-Li Li et al. – Applied and Environmental Microbiology

Distinct bacterial and archaeal diversities and spatial distributions in surface sediments of the Arctic Ocean – Yuguang Wang et al. – FEMS Microbiology Letters

Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands – Dean J Horton et al. – FEMS Microbiology Letters

Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river – Yuzhan Yang et al. – FEMS Microbiology Letters

Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments – Luis J. Perez Calderon et al. – MicrobiologyOpen

Phages and viruses

Preprint: Complete genome of a Measles virus from Roraima state, Brazil – Catia Meneses et al. – bioRxiv

Safety Studies of Pneumococcal Endolysins Cpl-1 and Pal – Marek Harhala et al. – Viruses

Technology

Preprint: Controlling complex microbial communities: a network-based approach – Marco Tulio Angulo et al. – bioRxiv

** H2Oh No! The importance of reporting your water source in your in vivo microbiome studies – Jacqueline A. Barnett & Deanna L. Gibson – Gut Microbes

Bioinformatics

Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut – Yoshihisa Wakita et al. – BMC Microbiology

Non-microbiology picks

Preprint: Benchmarking university medical centres for responsible metrics. A cross sectional study on timely results dissemination across 36 German centres – Susanne Wieschowski et al. – bioRxiv

November 15, 2018

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Here’s your Thursday Digest. Highlights include a photo competition to showcase your research, Titanium ion enhancing fresh flower longevity, and an update on the UNITE database for fungal classification.

Event

** BMC ‘Research in progress’ photo competition – deadline tomorrow, November 16.

General microbiology

Review: The birth, evolution and death of metabolic gene clusters in fungi – Antonis Rokas et al. – Nature Reviews Microbiology

Considerations When Designing a Microbiome Study: Implications for Nursing Science – Katherine A. Maki et al. – Biological Research For Nursing

Review: Probiotics in human health and disease: from nutribiotics to pharmabiotics – Eun-Sook Lee et al. – Journal of Microbiology

Antimicrobial resistance

Review: Genome-based prediction of bacterial antibiotic resistance – Michelle Su et al. – Journal of Clinical Microbiology

Pregnancy and early life

Colonization of Cutibacterium avidum during infant gut microbiota establishment – Vanesa Natalin Rocha Martin et al. – FEMS Microbiology Ecology

Human skin microbiome

The proteomic and metabolomic characterization of exercise-induced sweat for human performance monitoring: A pilot investigation – Sean W. Harshman et al. – PLoS One

Human oral microbiome

In vitro: The effect of the stress hormone cortisol on the metatranscriptome of the oral microbiome – Ana E. Duran-Pinedo et al. – npj Biofilms and Microbiomes

Human gut microbiome

Alterations of fecal bacterial communities in patients with lung cancer – Wei-Quan Zhang et al. – American Journal of Translational Research

Temporal Variability of Escherichia coli Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics – Taylor K. S. Richter et al. – mSphere

Review: An insight into the intestinal web of mucosal immunity, microbiota, ​and diet and their role in inflammation and infection – Eliana Marino & Yu Anne Yap – Frontiers in Immunology

Human multisite microbiome

Determinants of the urinary and serum metabolome in children from six European populations – Chung-Ho E. Lau et al. – BMC Medicine

Human gut-microbiome-brain axis

Alteration of gut microbiota-associated epitopes in children with autism spectrum disorders – Mingbang Wang et al. – Brain, Behavior, and Immunity

Metabolomics

Metabolomic biomarkers and novel dietary factors associated with gestational diabetes in China – Xuyang Chen et al. – Metabolomics

Animal experiments

An Interleukin-23-Interleukin-22 Axis Regulates Intestinal Microbial Homeostasis to Protect from Diet-Induced Atherosclerosis – Aliia R. Fatkhullina et al. – Immunity

Gut microbiota dysbiosis correlates with a low-dose PCB126-induced dyslipidemia and non-alcoholic fatty liver disease – Yulang Chi et al. – Science of The Total Environment

Animal microbiome

The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status – Sarah M. Hird et al. – mSphere

Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation – Wei Xu et al. – Scientific Reports

Food microbiome

An integrated metagenomic/metaproteomic investigation of microbiota in dajiang-meju, a traditional fermented soybean product in Northeast China – Mengxi Xie et al. – Food Research International

Plant, root and soil microbiome

The ability of plants to produce strigolactones affects rhizosphere community composition of fungi but not bacteria – Lilia Costa Carvalhais et al. – Rhizosphere

Root exudates induce soil macroaggregation facilitated by fungi in subsoil – Vera L. Baumert et al. – Frontiers in Environmental Science

Long-term combined application of manure and chemical fertilizer sustained higher nutrient status and rhizospheric bacterial diversity in reddish paddy soil of Central South China – Xinwei Cui et al. – Scientific Reports

** Titanium Ions Inhibit the Bacteria in Vase Solutions of Freshly Cut Gerbera jamesonii and Extend the Flower Longevity – Cai-Xia Li et al. – Microbial Ecology

Ectomycorrhizal fungi inoculation alleviates simulated acid rain effects on soil ammonia oxidizers and denitrifiers in Masson pine forest – Yan Li et al. – Environmental Microbiology

Compounded disturbance chronology modulates the resilience of soil microbial communities and N-cycle related functions – Kadiya Calderón et al. – Frontiers in Microbiology

Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials – Sihang Yang et al. – Science of The Total Environment

Silver Toxicity Thresholds for Multiple Soil Microbial Biomarkers – Sotirios Vasileiadis et al. – Environmental Science & Technology

Ectomycorrhizal fungal communities and their functional traits mediate plant-soil interactions in trace element contaminated soils – Marta Gil-Martínez et al. – Frontiers in Plant Science

Modulation of litter decomposition by the soil microbial food web under influence of land use change – Amber Heijboer et al. – Frontiers in Microbiology

Water and extremophile microbiome

Response and recovery of microbial communities subjected to oxidative and biological treatments of 1,4-dioxane and co-contaminants – Yu Miao et al. – Water Research

In situ real-time quantification of microbial communities: Applications to cold and dry volcanic habitats – Linda S.Powers et al. – Global Ecology and Conservation

Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis – Martin Alexander Fischer et al. – Microbial Biotechnology

Importance of soil texture to the fate of pathogens introduced by irrigation with treated wastewater – Olabiyi Obayomi et al. – Science of The Total Environment

Active pathways of anaerobic methane oxidation across contrasting riverbeds – Li-dong Shen et al. – The ISME Journal

Drying and rainfall shape the structure and functioning of nitrifying microbial communities in riverbed sediments – Maria Isabel Arce et al. – Frontiers in Microbiology

Microbes in space

Inner Workings: Hunting for microbial life throughout the solar system – Adam Mann – PNAS

Confirmation of Microbial Ingress from Space – N. C. Wickramasinghe et al. – Advances in Astrophysics

Phages and viruses

Review: Targeting mechanisms of tailed bacteriophages – Franklin L. Nobrega et al. – Nature Reviews Microbiology

Viral diversity of Rhipicephalus microplus parasitizing cattle in southern Brazil – William Marciel de Souza et al. – Scientific Reports

Review: Respiratory Viral Infection-induced Microbiome Alterations and Secondary Bacterial Pneumonia – Shigeo Hanada et al. – Frontiers in Immunology

Technology

Review: Model Microbial Consortia as Tools for Understanding Complex Microbial Communities – Haruta, Shin & Yamamoto, Kyosuke – Current Genomics

Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer – Manasi S. Shah et al. – PLoS One

Bioinformatics

** The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications – Rolf Henrik Nilsson et al. – Nucleic Acids Research

Bioinformatics tools to assess metagenomic data for applied microbiology – Otávio G. G. Almeida & Elaine C. P. De Martinis – Applied Microbiology and Biotechnology

Pan-genomic analysis provides novel insights into the association of E. coli with human host and its minimal genome – Zhi-Kai Yang et al. – Bioinformatics

Microbes in the news

You Are What Your Bacteria Eat – Patricia Conway & Jorgen Schlundt – Innovation Magazine

November 2, 2018

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Your Friday Digest features plentiful of soil/plant and gut microbiome papers. Highlights include correlation between infant metabolic functions and diet/gestational weight gain, profiling human gut microbiomes across India, and the absence of a placenta microbiota. There are many other more articles worth reading, enjoy!

General microbiology

Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota – Michael A. Henson & Poonam Phalak – PLoS Computational Biology

A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli – Olga V Alikina et al. – FEMS Microbiology Letters

Pregnancy and early life

Long-lasting effect of oral azithromycin taken by women during labour on infant nutrition: Follow-up cohort of a randomized clinical trial in western Gambia – Anna Roca et al. – PLoS One

** Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes – Aimee M. Baumann-Dudenhoeffer et al. – Nature Medicine

Antibiotic and acid-suppression medications during early childhood are associated with obesity – Christopher M Stark et al. – Gut

** Lack of detection of a human placenta microbiome in samples from preterm and term deliveries – Jacob S. Leiby et al. – Microbiome

Human oral microbiome

Multi-species oral biofilm promotes reconstructed human gingiva epithelial barrier function – Lin Shang et al. – Scientific Reports

Review: Administration of systemic antibiotics during non-surgical periodontal therapy—a consensus report – B. Pretzl et al. – Clinical Oral Investigations

Human repiratory microbiome

Sputum Microbiome is Associated with 1-Year Mortality Following COPD Hospitalizations – Fernando Sergio Leitao Filho et al. – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

The co-existence of elevated high sensitivity C-reactive protein and homocysteine levels is associated with increased risk of metabolic syndrome: A 6-year follow-up study – Jinkwan Kim & Sangshin Pyo – PLoS One

** LogMPIE, pan-India profiling of the human gut microbiome using 16S rRNA sequencing – Ashok Kumar Dubey et al. – Scientific Data

Association between Neutrophil-to-Lymphocyte Ratio and Gut Microbiota in a Large Population: a Retrospective Cross-Sectional Study – Hee-Young Yoon et al. – Scientific Reports

Microbial nitrogen limitation in the mammalian large intestine – Aspen T. Reese et al. – Nature Microbiology

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles – Trishla Sinha et al. – Gut Microbes

Anti-Inflammatory Activities of Pentaherbs formula and Its Influence on Gut Microbiota in Allergic Asthma – Miranda Sin-Man Tsang et al. – Molecules

Identification of TMAO-producer phenotype and host–diet–gut dysbiosis by carnitine challenge test in human and germ-free mice – Wei-Kai Wu et al. – Gut

Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin – Zhen He et al. – Gut

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers – Vanessa L. Hale et al. – Genome Medicine

Comment: Targeting the microbiome: from probiotics to fecal microbiota transplantation – Alexander Khoruts – Genome Medicine

Human vaginal microbiome

Review: Endometrial microbes and microbiome: Recent insights on the inflammatory and immune “players” of the human endometrium – Silvia D’Ippolito et al. – American Journal of Reproductive Immunology

Animal experiments

Effect of dietary fiber content on nutrient digestibility and fecal microbiota composition in growing-finishing pigs – Mathilde Le Sciellour et al. – PLoS One

Effects of ultraviolet radiation and nutrient level on the physiological response and organic matter release of the scleractinian coral Pocillopora damicornis following thermal stress – Lucile Courtial et al. – PLoS One

Dog: Balance of saccharolysis and proteolysis underpins improvements in stool quality induced by adding a fiber bundle containing bound polyphenols to either hydrolyzed meat or grain-rich foods – Matthew I. Jackson & Dennis E. Jewell – Gut Microbes

Ventilator-induced lung injury is aggravated by antibiotic mediated microbiota depletion in mice – Sandra-Maria Wienhold & Mario Macrì et al. – Critical Care

Mouse: Dioxin-like PCB 126 increases intestinal inflammation and disrupts gut microbiota and metabolic homeostasis – Michael C. Petriello et al. – Environmental Pollution

Review: Innate Immune Influences on the Gut Microbiome: Lessons from Mouse Models – Susan J. Robertson et al. – Trends in Immunology

Animal microbiome

Milk microbiome diversity and bacterial group prevalence in a comparison between healthy Holstein Friesian and Rendena cows – Paola Cremonesi & Camilla Ceccarani et al. – PLoS One

Comparing the bacterial communities of wild and captive golden mantella frogs: Implications for amphibian conservation – Luiza F. Passos et al. – PLoS One

Insect anal droplets contain diverse proteins related to gut homeostasis – Tianzhong Jing et al. – BMC Genomics

Plant, root and soil microbiome

Putative Nitrogen-fixing bacteria Associated with The Rhizosphere and Root Endosphere of wheat plants grown in an Andisol from southern Chile – Joaquin I. Rilling et al. – Frontiers in Microbiology

Land-use intensity rather than plant functional identity shapes bacterial and fungal rhizosphere communities – Ricardo Schöps et al. – Frontiers in Microbiology

Microbial expression profiles in the rhizosphere of two maize lines differing in N use efficiency – Shamina Imran Pathan et al. – Plant and Soil

The rhizosphere of the halophytic grass Sporobolus robustus Kunth hosts rhizobium genospecies that are efficient on Prosopis juliflora (Sw.) DC and Vachellia seyal (Del.) P.J.H. Hurter seedlings – Fatoumata Fall et al. – Systematic and Applied Microbiology

Rhizosphere responses to environmental conditions in Radix pseudostellariae under continuous monoculture regimes – Hongmiao Wu et al. – Agriculture, Ecosystems & Environment

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress – Rupali Gupta et al. – Microbiological Research

Review: Multifaceted interactions between endophytes and plant: Developments and Prospects – Naveen K. Arora et al. – Frontiers in Microbiology

Enhancing phytoextraction of HMs at real scale, by combining Salicaceae Trees with microbial consortia – CARMINE GUARINO et al. – Frontiers in Environmental Science

PhD Dissertation: Implications of land-use legacy on soil microbiomes of urban grasslands – Grant Lafayette Thompson – Cornell University

Body size determines soil community assembly in a tropical forest – Lucie Zinger et al. Molecular Ecology

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes – Joshua Ladau et al. – mSystems

Water and extremophile microbiome

Microbial diversity and antibiotic resistance in a final effluent-receiving lake – Kinga Bondarczuk & Zofia Piotrowska-Seget – Science of The Total Environment

Non‐random processes determine the colonization of groundwater sediments by microbial communities in a pristine porous aquifer – Lucas Fillinger et al. – Environmental Microbiology

Food microbiome

Changes of microbial community and metabolite in kimchi inoculated with different microbial community starters – Seong-Eun Park et al. – Food Chemistry

Phages and viruses

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow – A. Bal et al. – BMC Infectious Diseases

Technology

A high-throughput sequencing assay to comprehensively detect and characterize unicellular eukaryotes and helminths from biological and environmental samples – Matthew V. Cannon et al. – Microbiome

Bioinformatics

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification – Daniel J. Nasko et al. – Genome Biology

* Species-level functional profiling of metagenomes and metatranscriptomes – Eric A. Franzosa et al. – Nature Methods

Striped UniFrac: enabling microbiome analysis at unprecedented scale – Daniel McDonald et al. – Nature Methods

Mechanistic microbiota models – Tal Nawy – Nature Methods

Microbes in the news

Club STEAM Powered students study bacteria, genetics – Cassie Gibb – The Southeast Sun

Media alert: New articles in The CRISPR Journal – MARY ANN LIEBERT, INC. – EurekAlert!

Electric shocks kill bacteria – Vienna University of Technology – PHYS.org

The Mad Science of Fermentation’s Funky Flavors – Joe Ray – Wired

How Nuclear Testing Transformed the Land in Nevada and New Mexico – Kealey Boyd – Hyperallergic

October 19, 2018

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Today’s Digest provides much food for thought. Highlights include how to identify keystone species, a seminal review on the long-term and short-term effects of C-section on mom and child’s health, and a new de novo assembler for short metagenomic reads.

General microbiology

Antibiotic export by efflux pumps affects growth of neighboring bacteria – Xi Wen et al. – Scientific Reports

Proteomic analysis of four Clostridium botulinum strains identifies proteins that link biological responses to proteomic signatures – Brooke L. Deatherage Kaiser et al. – PLoS One

Biodiversity‐function relationships in methanogenic communities – Pawel Sierocinski et al. – Molecular Ecology

Solubilization and degradation of polychlorinated biphenyls (PCBs) by naturally occurring facultative anaerobic bacteria – Gathanayana Pathiraja et al. – Science of the Total Environment

An improved neutral community model for temporal observations in microbial communities – Li Jie & Shen Xuzhu – Ecological Modelling

** Identifying Keystone Species In The Microbial Community Based On Cross-sectional Data – Min Li et al. – Current Gene Therapy

Does quorum sensing interference affect the fitness of bacterial pathogens in the real world? – Yiying Liu et al. – Environmental Microbiology

Pregnancy and early life

Microbiota and Derived Parameters in Fecal Samples of Infants with Non-IgE Cow’s Milk Protein Allergy under a Restricted Diet – María Díaz et al. – Nutrients

** Review: Short-term and long-term effects of caesarean section on the health of women and children – Jane Sandall et al. – Lancet

Human skin microbiome

The Skin Microbiota in Patients Hospitalized for Cellulitis and Association With Outcome – Duncan R Cranendonk et al. – Clinical Infectious Diseases

Human multi-site microbiome

Continuous Antibiotic Prophylaxis in Pediatric Urology – Douglas W.Storm et al. – Urologic Clinics of North America

Human gut microbiome

Impact of antibiotic use on survival in patients with advanced cancers treated on immune checkpoint inhibitor phase I clinical trials – S Sen et al. – Journal of Experimental Medicine

Review: Visceral pain: gut microbiota, a new hope? – Matteo M Pusceddu & Melanie G Gareau – Journal of Biomedical Science

Review: Vulnerability of long-term care facility residents to Clostridium difficile infection due to microbiome disruptions – Beth Burgwyn Fuchs et al. – Future Microbiology

Fecal Microbiota Transplant for Recurrent Clostridium Difficile Infection in Pediatric Inflammatory Bowel Disease – Cho, Stanley et al. – Journal of Pediatric Gastroenterology and Nutrition

Transcriptome meta-analysis identifies immune signature comprising of RNA binding proteins in ulcerative colitis patients – Saima Naz et al. – Cellular Immunology

Alterations of Gut Microbiome in the Patients With Severe Fever With Thrombocytopenia Syndrome – Honghai Xu et al. – Frontiers in Microbiology

Review: Role of Gut Microbiota in the Development and Treatment of Colorectal Cancer – LIN C. et al. – Digestion

Human gut-microbiome-brain axis

A primer on investigating the role of the microbiome in brain and cognitive development – Caroline Kelsey et al. – Developmental Psychology

Animal experiments

Grape polyphenols reduce gut-localized reactive oxygen species associated with the development of metabolic syndrome in mice – Peter Kuhn et al. – PLoS One

Host developmental toxicity of BPA and BPA alternatives is inversely related to microbiota disruption in zebrafish – Tara R Catron et al. – Toxicological Sciences

Liver Injury, Endotoxemia, and Their Relationship to Intestinal Microbiota Composition in Alcohol-Preferring Rats – Brunella Posteraro et al. – Alcoholism Clinical & Experimental Research

Liver tumorigenesis is promoted by a high saturated-fat diet specifically in male mice and is associated with hepatic expression of the proto-oncogene Agap2 and enrichment of the intestinal microbiome with Coprococcus – Kim B Pedersen et al. – Carcinogenesis

Animal microbiome

Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises – Chava L. Weitzman et al. – Royal Society Open Science

Review: Understanding the Milk Microbiota – Stephanie A.Metzger et al. – Veterinary Clinics of North America: Food Animal Practice

Evolution of the nasopharyngeal bacterial microbiota of beef calves from spring processing to 40 days after feedlot arrival – Christopher McMullen et al. – Veterinary Microbiology

Plant, root and soil microbiome

Review: The impact of microbes in the orchestration of plants’ resistance to biotic stress: a disease management approach – Matthew Chekwube Enebe & Olubukola Oluranti Babalola – pplied Microbiology and Biotechnology

Genome and evolution of the arbuscular mycorrhizal fungus Diversispora epigaea (formerly Glomus versiforme) and its bacterial endosymbionts – Xuepeng Sun et al. New Phytologist

Facilitation promotes invasions in plant-associated microbial communities – Wei, Zhong et al. – Ecology Letters

Water and extremophile microbiome

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations – David A. Aromokeye et al. – Frontiers in Microbiology

Bacterial community changes in a glacial-fed Tibetan lake are correlated with glacial melting – Keshao Liu et al. – Science of The Total Environment

Food microbiology

Review: Fermentation trip: amazing microbes, amazing metabolisms – Rong Feng et al. – Annals of Microbiology

Phages and viruses

Complete Genome Sequence of the Model Halovirus PhiH1 (ΦH1) – Mike Dyall-Smith et al. – Genes

Technology

Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer – Sae Ashikawa et al. – Journal of Medical Microbiology

The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study – Jan Tkadlec et al. – Clinical Microbiology and Infection

Bioinformatics

BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results – Aitor Blanco-Míguez et al. – PLoS One

Review: Integrating–omics data into genome-scale metabolic network models: principles and challenges – Charlotte Ramon et al. – Essays in Biochemistry

** High-quality genome sequences of uncultured microbes by assembly of read clouds – Alex Bishara et al. – Nature Biotechnology

Microbes in the news

Cecilia Jonsson Serenades Sewage Bacteria – Sofia Bergmann – Berlin Art Link

October 8, 2018

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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

September 11, 2018

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Today’s Digest has a ton of reviews on human gut microbiome, and also features a new bacterial growth theory, how antibiotics limit microbial metabolites penetrate the gut and discovery of bacteria from corals that inhibit the growth of a human pathogen.

General microbiology

Microbial exposure and human health – Anukriti Sharma & Jack A Gilbert – Current Opinion in Microbiology

** Consistent microbial dynamics and functional community patterns derived from first principles – Hadrien Delattre et al. – ISME J

Preprint: The Helicobacter pylori biofilm involves a multi-gene stress-biased response including a structural role for flagella – Skander Hathroubi et al. – bioRxiv

Human gut microbiome

Review: The intestinal epithelial response to damage – Laura Weichselbaum & Ophir D. Klein – Science China Life Sciences

Review: Metabolic Abnormalities in Diabetes and Kidney Disease: Role of Uremic Toxins – Laetitia Koppe et al. – Current Diabetes Reports

Sex differences in lipid metabolism are affected by presence of the gut microbiota – Annemarie Baars et al. – Scientific Reports

Age-dependent changes in GI physiology and microbiota: time to reconsider? – Ran An & Ellen Wilms et al. – Gut

Review: Bacteroides thetaiotaomicron – Nathan T. Porter et al. – Trends in Microbiology

** Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response – Yasuhiro Uchimura et al. – Immunity

Review: Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings – Suprabhat Mukherjee, Nikhilesh Joardar & Subhasree Sengupta et al. – The Journal of Nutritional Biochemistry

Review: A critical review on the impacts of β-glucans on gut microbiota and human health – Muthukumaran Jayachandran et al. – The Journal of Nutritional Biochemistry

Review: The microbiome in inflammatory bowel disease: from prevailing clinical evidence to future possibilities – Hari K. Somineni & Subra Kugathasan – Clinical Gastroenterology and Hepatology

Review: Influence of Early Life, Diet, and the Environment on the Microbiome – Tien S. Dong & Arpana Gupta – Clinical Gastroenterology and Hepatology

Review: Emerging Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease: From Composition to Function – S.R. Sharpton et al. – Clinical Gastroenterology and Hepatology

Preprint: Treatment-Specific Composition of Gut Microbiota Is Associated with Disease Remission in a Pediatric Crohn’s Disease Cohort – Daniel Sprockett et al. – bioRxiv

Human gut-microbiome-brain axis

Targeting the gut microbiota to influence brain development and function in early life – Shugui Wang et al. – Neuroscience & Biobehavioral Reviews

Human vaginal microbiome

Vaginal Bifidobacterium breve for preventing urogenital infections: development of delayed release mucoadhesive oral tablets – Barbara Giordani et al. – International Journal of Pharmaceutics

Animal experiments

Gut microbiota regulates mouse behaviors through glucocorticoid receptor pathway genes in the hippocampus – Yuanyuan Luo et al. – Translational Psychiatry

Review: Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington’s disease – Geraldine Kong et al. – Neurobiology of Disease

Animal microbiome

Influence of the symbiont Wolbachia on life history traits of the cabbage root fly (Delia radicum) – Valérie Lopez et al. – Journal of Invertebrate Pathology

Letter to editor: Towards the integrative analysis of tick microbiome – Agustín Estrada-Peña & Alejandro Cabezas-Cruz – Ticks and Tick-borne Diseases

Plant, root and soil microbiome

Impact of domestication on the evolution of rhizomicrobiome of rice in response to the presence of Magnaporthe oryzae – Shaohua Shi et al. – Plant Physiology and Biochemistry

Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions – Abid Ullah & Adnan Akbar et al. – Microbial Ecology

Characterization of microbial communities of soils from gold mine tailings and identification of mercury-resistant strain – Hongbing Ji et al. – Ecotoxicology and Environmental Safety

Plant-microbe competition: does injection of isotopes of C and N into the rhizosphere effectively characterise plant use of soil N? – Paul W. Hill & Davey L. Jones – New Phytologist

Water and extremophile microbiome

Temperature shapes the microbiota in anaerobic digestion and drives efficiency to a maximum at 45 °C – Sebastian Hupfauf et al. – Bioresource Technology

** Ruegeria sp. Strains Isolated from the Reef-Building Coral Galaxea fascicularis Inhibit Growth of the Temperature-Dependent Pathogen Vibrio coralliilyticus – Natsuko Miura et al. – Marine Biotechnology

Phages and viruses

Preprint: Potential application of phage therapy for prophylactic treatment against Pseudomonas aeruginosa biofilm Infections – Aditi Gurkar et al. – bioRxiv

Technology

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota – Gregory L. Medlock et al. – Cell Systems

Application of Bacillus velezensis NJAU-Z9 Enhanced Plant Growth Associated with Efficient Rhizospheric Colonization Monitored by qPCR with Primers Designed from the Whole Genome Sequence – Yang Zhang et al. – Current Microbiology

September 5, 2018

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Today’s Digest is not short of articles from all aspects of microbiome research. Highlights include a study on population dynamics during cycles of feast and famine, guidelines for FMT, and a 7-year experiment on the effect of warming and elevated carbon dioxide on soil carbon dynamics.

General microbiology

Microalgae-bacteria symbiosis in microalgal growth and biofuel production: a review – Shuo Yao et al. – Journal of Applied Microbiology

Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles – Zhanshan (Sam) Ma – Microbial Ecology

** Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine – Jason Merritt & Seppe Kuehn – Physical Review Letters

Review: Ecological effects of cellular computing in microbial populations – Maia Baskerville et al. – Natural Computing

Antibiotics/Antibiotic resistance

Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria – Lisa Mahler et al. – Scientific Reports

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer – Xue Zhou et al. – Science of The Total Environment

Comparative network analysis revealing the mechanisms of antibiotic resistance genes removal by leachate recirculation under different hydraulic loadings – Yinglong Sun et al. – Science of The Total Environment

Do plastics serve as a possible vector for the spread of antibiotic resistance? First insights from bacteria associated to a polystyrene piece from King George Island (Antarctica) – Pasqualina Laganà et al. – International Journal of Hygiene and Environmental Health

Forensic microbiome

Combining human STR and microbial population profiling: two case reports – Frederike C.A. Quaak et al. – FSI Genetics

Human lung microbiome

Review: The Genetics and Genomics of Asthma – Saffron A.G. Willis-Owen et al. – Annual Review of Genomics and Human Genetics

Human gut microbiome

In vitro: Impact of combining acerola by-product with a probiotic strain on a gut microbiome model – Fernanda Bianchi et al. – International Journal of Food Sciences and Nutrition

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village – Kelly V. Ruggles et al. – mSphere

Letter: Primum non nocere: is faecal microbiota transplantation doing harm to patients with IBS? – Paul Enck – Gut

Changes in gut microbiota and plasma inflammatory factors across the stages of colorectal tumorigenesis: a case-control study – Yongzhen Zhang et al. – BMC Microbiology

** The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H. Mullish et al. – Journal of Hospital Infection

Fecal microbiota transplantation: a promising strategy in preventing the progression of non-alcoholic steatohepatitis and improving the anti-cancer immune response – Vaihere Delaune et al. – Expert Opinion on Biological Therapy

Review: Modulation of the immune system by the gut microbiota in the development of Type 1 Diabetes – James A. Pearson et al. – Human Vaccines & Immunotherapeutics

Human gut-microbiome-brain axis

Altered Schaedler flora mice: An old defined microbiota animal model to study the new science of microbiota-gut-brain axis – J.M.Lyte et al. – Behavioural Brain Research

Animal experiments

Molecular networks affected by neonatal microbial colonization in porcine jejunum, luminally perfused with enterotoxigenic Escherichia coli, F4ac fimbria or Lactobacillus amylovorus – Paolo Trevisi et al. – PLoS One

Effects of Natural Flavonoid-Isoorientin on Growth Performance and Gut Microbiota of Mice – Li Xuan et al. – Journal of Agricultural and Food Chemistry

Host diet mediates a negative relationship between abundance and diversity of Drosophila gut microbiota – Berra Erkosar et al. – Ecology and Evolution

Animal microbiome

Effects of clove (Syzygium aromaticum) oil on quail growth, carcass traits, blood components, meat quality, and intestinal microbiota – Mohamed M A Hussein et al. – Poultry Science

The effect of lavender (Lavandula angustifolia) essential oil as a drinking water supplement on the production performance, blood biochemical parameters, and ileal microflora in broiler chickens – Michalina Adaszyńska-Skwirzyńska & Danuta Szczerbińska – Poultry Science

Review: Factors Influencing Individual Variation in Farm Animal Cognition and How to Account for These Statistically – Emily V. Bushby et al. – Frontiers in Veterinary Science

Broad Bean (Vicia faba L.) Induces Intestinal Inflammation in Grass Carp (Ctenopharyngodon idellus C. et V) by Increasing Relative Abundances of Intestinal Gram-Negative and Flagellated Bacteria – Zhifei Li et al. – Frontiers in Microbiology

Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors – Priscila Bascuñán et al. – Microbiome

Alterations in honey bee gut microorganisms caused by Nosema spp. and pest control methods – Tsiri Diaz et al. – Pest Management Science

Plant, root and soil microbiome

** Elevated CO2 and warming cause interactive effects on soil carbon and shifts in carbon use by bacteria – Yolima Carrillo et al. – Ecology Letters

The role of wetland microorganisms in plant-litter decomposition and soil organic matter formation: a critical review – Stephanie A Yarwood – FEMS Microbiology Ecology

Strong succession in arbuscular mycorrhizal fungal communities – Cheng Gao et al. – ISME J

Manipulation of the rhizosphere bacterial community by biofertilizers is associated with mitigation of cadmium phytotoxicity – Meng Wang et al. – Science of The Total Environment

Multi-substrate induced microbial respiration, nitrification potential and enzyme activities in metal-polluted, EDTA-washed soils – Guixiang Zhou et al. – Scientific Reports

Divergent accumulation of microbial necromass and plant lignin components in grassland soils – Tian Ma et al. – Nature Communications

Microbial Community Composition In Take-All Suppressive Soils – Paola Duran et al. – Frontiers in Microbiology

Differential biodiversity responses between kingdoms (plants, fungi, bacteria and metazoa) along an Alpine succession gradient – Matteo Montagna et al. – Molecular Ecology

Water and extremophile microbiome

Steep redox gradient and biogeochemical cycling driven by deeply sourced fluids and gases in a terrestrial mud volcano – Yueh-Ting Lin et al. – FEMS Microbiology Ecology

Pigmented microbial eukaryotes fuel the deep sea carbon pool in the tropical Western Pacific Ocean – Dapeng Xu – Environmental Microbiology

Biofilm Formation and Degradation of Commercially Available Biodegradable Plastic Films by Bacterial Consortiums in Freshwater Environments – Tomohiro Morohoshi et al. – Microbes and Environments

Dynamics and Functional Potential of Stormwater Microorganisms Colonizing Sand Filters – Andrea Naimah Fraser et al. – Water

Review: Lignin depolymerization and utilization by bacteria – Rong Xu et al. – Bioresource Technology

Microbes in the industry

From systems biology to metabolically engineered cells — an omics perspective on the development of industrial microbes – Judith Becker &Christoph Wittmann – Current Opinion in Microbiology

Phages and viruses

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems – Yulin Wang et al. – Environmental Science & Technology

Technology

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities – Ashley R. Coenen & Joshua S. Weitz – mSystems

A Sensitive Thresholding Method for Confocal Laser Scanning Microscope Image Stacks of Microbial Biofilms – Ting L. Luo et al. – Scientific Reports

A steam-based method to investigate biofilm – Jason Tasse et al. – Scientific Reports

August 28, 2018

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A brief Digest today featuring a review on how the microbiota affects drug disposition, a study adopting fungal growth measurement in the soil to that in the medium and in the plants, and a genetic approach to specifically depleting microbiome-derived metabolites in the host tissue.

General microbiology

* Minireview: How to determine the role of the microbiome in drug disposition – Jordan E Bisanz et al. – Drug Metabolism and Disposition

Loss of genomic diversity in a Neisseria meningitidis clone through a colonization bottleneck – Araceli Lamelas et al. – Genome Biology and Evolution

Human gut microbiome

Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol – Lara R. Dugas et al. – BMC Public Health

Multi-omics analyses to deliver the most effective treatment to every patient with inflammatory bowel disease – Rinse K. Weersma et al. – Gastroenterology

Plant, root and soil microbiome

Preprint: Antimicrobial, Antioxidant and Anti-Inflammatory Activities of Proteins of Phaseoulus lunatus (Fabaceae) Baby Lima Beans Produced in Ecuador – Javier Tamayo et al. – bioRxiv

* Preprint: Fungal growth is affected by and affects pH and redox potential (Eh) of the growth medium – Lydia Bousset et al. – bioRxiv

Water and extremophile microbiome

Preprint: The role of land use types and water chemical properties in structuring the microbiome of a connected lakes system – Sophi Marmen et al. – bioRxiv

Phages and viruses

Preprint: Repurposing of drugs as novel influenza inhibitors from clinical gene expression infection signatures – Mario Andres Pizzorno et al. – bioRxiv

Technology

Preprint: Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples – Fabien Cholet et al. – bioRxiv

** Preprint: Depletion of microbiome-derived molecules in the host using Clostridium genetics – Chun-Jun Guo et al. – bioRxiv

Bioinformatics

Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data – Benjamin Sobkowiak et al. – BMC Genomics