Category Archives: General Microbiome

December 5, 2018

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Today’s digest features study on Lactobacillus reuteri HCM2 (against Enterotoxigenic Escherichia coli), microbiome and virome of deep terrestrial biosphere, immunostimulatory potential of the earliest gut microbiome, and more. Happy reading!

Gut microbiome

*Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential – Linda Wampach – Nature Communications

Review: Bone and the gut microbiome: a new dimension – Carolina Medina-Gomez – Journal of Laboratory and Precision Medicine

Review: Simple organizing principles in microbial communities – Jeff Gore – Current Opinion in Microbiology

Soil microbiome

*Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India – Avishek Dutta – Scientific Reports

Organic carbon amendments affect the chemodiversity of soil dissolved organic matter and its associations with soil microbial communities – Xiaoming Li – Environmental Science and Technology

Microbial organic matter degradation potential in Baltic Sea sediments influenced by depositional conditions and in situ geochemistry – Laura A. Zinke – Applied and Environmental Microbiology

Water microbiome

Performance and dynamic characteristics of microbial communities in multi-stage anaerobic reactors treating gibberellin wastewater – Erming Ouyang – Journal of Bioscience and Bioengineering

Phages and viruses

Bioaerosol Sampling for Respiratory Viruses in Singapore’s Mass Rapid Transit Network – Kristen Coleman – Scientific Reports

Review: Future management of viral diseases: role of new technologies and new approaches in microbial interactions – Fabrizio Maggi – Clinical Microbiology and Infection

*Viruses control dominant bacteria colonizing the terrestrial deep biosphere after hydraulic fracturing – Rebecca A. Daly – Nature Microbiology

Animal experiments

*Lactobacillus reuteri HCM2 protects mice against Enterotoxigenic Escherichia coli through modulation of gut microbiota – Tianwei Wang – Scientific Reports

Bioinformatics

Ultra-deep, long-read nanopore sequencing of mock microbial community standards – Samuel M. Nicholls – 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

December 2, 2018

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Highlights: Colonocyte metabolism shapes the gut microbiota, skin and gut microbiome of wild mammals, bacterial diversity in waterholes of Kruger National Park, Yeast diversity of glaciers, Laser MICROSAMPLING of soil community, origin & evolution of global RNA virome, Lymphoma virome dynamics, PUMA-for processing 16S rRNA taxonomy data  for analysis and visualization and many more.

General microbiome

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations – Raphael Eisenhofer – Trends in Microbiology

Review: Gut microbiota – our new important organ  – Rositsa Sandeva – Albanian Journal of Agricultural Sciences

Human gut microbiome

Altered gut microbiota after traumatic splenectomy is associated with endotoxemia – Hua Zhu – Emerging Microbes & Infections

Review: Colonocyte metabolism shapes the gut microbiota – Yael Litvak – Science

Gut Microbiota Modulates Interactions Between Polychlorinated Biphenyls and Bile Acid Homeostasis – Sunny Lihua Cheng – Toxilogical Sciences

Animal experiments 

An intensive milk replacer feeding program benefits immune response and intestinal microbiota of lambs during weaning – Qian Zhang – BMC Veterinary Research

Animal microbiome 

Bacterial diversity in the waterholes of the Kruger National Park: an eDNA metabarcoding approach – Maxwell J Farrell – Genome

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – BMC Microbiome

Meta-Omics Tools in the World of Insect-Microorganism Interactions – Antonino Malacrinò – MDPI

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Dong Zhu – Environmental Science and Technology

The equine gastrointestinal microbiome: Impacts of age and obesity – Philippa K. Morrison – Systems Microbiology

Changes in gut bacterial communities in canaries infected by Macrorhabdus ornithogaster – Patrizia Robino – Journal of Avian Pathology

Plant, root, and soil microbiome

Laser MICROSAMPLING of soil microbial community – M. V. Gorlenko – Journal of Biological Engineering

Poplar phyllosphere harbors disparate isoprene-degrading bacteria – Andrew T. Crombie – PNAS

Changes in litter quality induced by N deposition alter soil microbial communities – Yingbin Li – Soil Biology and Biochemistry

Analysis of Bacterial Communities in White Clover Seeds via High-Throughput Sequencing of 16S rRNA Gene – Wenna Gao – Current Microbiology

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah – PLoS One

Water and extremophile microbiome 

Preprint: Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure – Lauren Gillies Campbell – bioRxiv

Review: Microbiologically influenced corrosion and current mitigation strategies: A state of the art review – Bhavya Kachiprath – Data in Brief

Habitat-specificity and diversity of culturable cold-adapted yeasts of a cold-based glacier in the Tianshan Mountains, northwestern China – Baolong Luo – Applied Microbiology and Biotechnology

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal  – Aleksandra S. Zakharenko – Microbial Ecology

Phages and viruses

Origins and Evolution of the Global RNA Virome – Yuri I. Wolf – mBio

Lymphoma Virome Dynamics Revealed By Cell-Free DNA Sequencing – Joseph G Schroers-Martin – Blood

Techniques

Inner Workings: Mapping the microbiome location helps elucidate its role – Marcus Woo – PNAS

Preprint: FDA-ARGOS: A Public Quality-Controlled Genome Database Resource for Infectious Disease Sequencing Diagnostics and Regulatory Science Research – Heike Sichtig – bioRxiv

Preprint: PUMA: A tool for processing 16S rRNA taxonomy data for analysis and visualization – Keith Mitchell – bioRxiv

EMA-amplicon-based taxonomic characterisation of the viable bacterial community present in untreated and SODIS treated roof-harvested rainwater – André Strauss  -Environmental Science: Water Research & Technology

 

November 30, 2018

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Happy Friday! Today’s digest features the skin microbiome of lizards and frogs, bacterial changes during palm wine fermentation, and the impact of deforestation on soils in the Amazon.

General microbiome

Review: The microbiome in threatened species conservation – West – Biological Conservation

Human oral microbiome

Oxidative stress in the oral cavity is driven by individual-specific bacterial communities – Džunková – NPJ Biofilms and Microbiomes

Human gut microbiome

Alterations of the gut microbiome and plasma proteome in Chinese patients with adolescent idiopathic scoliosis – Shen – Bone

Animal experiments

Effect of gastric fluid aspiration on the lung microbiota of laboratory rats – Finn – Experimental Lung Research

Animal microbiome

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia – Weitzman – PeerJ

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Poulsen – PLoS One

Plant, root, and soil microbiome

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Zhu – Environmental Science and Technology

Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils – Khan – FEMS Microbiology Ecology

Review: VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes – Tyagi – Critical Reviews in Biotechnology

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Liang – Microbiological Research

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential – Martins – Microbiome

Extemophile microbiome

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities – Kalwasińska – Science of the Total Environment

Food microbiology

Preprint: Bacterial diversity and population dynamics during the fermentation of palm wine from Guerrero Mexico – Astudillo-Melgar – BioRxiv

Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues – Achmon – Bioresource Technology Reports

Science, publishing, and career

Preprint: Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community – Gallo – 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 19, 2018

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Today’s digest features shallow shotgun sequencing as a useful alternative to 16S sequencing, soil metaproteomics, virus genomes from deep sea sediments, and more. And there’s an important news: the MicroMundo has been launched in Portugal! Happy reading!

Events and jobs

Open Rank Faculty Position in Microbiome or Microbial Systems Research, Baylor College of Medicine in Houston, TX

Physalia courses: 16S/ITS Metabarcoding of microbial communities (Berlin, 1-5 April 2019) Instructors: Anna Sandionigi, Antti Karkman, Bruno Fosso

Physalia courses: Metagenomics (Berlin, 27-31 May 2019) Instructors: Dr. Curtis Huttenhower, Melanie Schirmer, Cesar Arze

Gut microbiome

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn’s Disease Patient – Xin Fang – Front. Microbio.

Preprint: Microbial Dysbiosis and polyamine metabolism as predictive markers for early detection during progression of pancreatic adenocarcinoma in spontaneous mouse model – Roberto Mendez – bioRxiv

Oral microbiome

Preprint: Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study – Francesco Beghini – bioRxiv

Preprint: Sociodemographic patterning in the oral microbiome of a diverse sample of New Yorkers – Audrey Renson – bioRxiv

Soil microbiome

*Review: Using proteins to study how microbes contribute to soil ecosystem services: The current state and future perspectives of soil metaproteomics – Robert Starke – Journal of Proteomics

Phages and viruses

Degenerate PCR Primers to Reveal the Diversity of Giant Viruses in Coastal Waters  – Yanze Li – Viruses

*Preprint: Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism – Disa Backstrom – bioRxiv

Bioinformatics

*Evaluating the Information Content of Shallow Shotgun Metagenomics – Benjamin Hillmann – MySystems

A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series – Fang Zhang – Stat Appl Genet Mol Biol.

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts – Breitwieser Florian – Genome Biol.

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data –Simon Lucas – Gigascience

Svetlana’s microbiology pick

* Last week was World Antibiotic Awareness Week and the MicroMundo project has been launched in Portugal:
Initially created in the USA (2012) as Small World Initiative, the MicroMundo is an innovative Citizen Science project where professors and researchers from the University of Porto encourage students to pursue career in science while addressing a worldwide health threat – antibiotic resistance.

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 14, 2018

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Today’s digest is about how dietary shifts and low gluten diet changes the intestinal microbiome, fecal microbiota transplant in intestinal disorders, characterization of the most abundant bacteriophage family in the human gut, and Raman spectroscopy based method for fast identification of antibiotic resistance bugs.

Human gut microbiome

Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis – Yinghong Wang – Nature Medicine

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults – Lea BS Hansen – Nature Communications

Resilience of human gut microbial communities for the long stay with multiple dietary shifts – Hong Liu – Gut

Microbiome and its relation to gestational diabetes – Ramon V. Cortez – Endocrine

Effect of bifidobacterium breve A-1 on anxiety and depressive symptoms in schizophrenia: A proof-of-concept study – Ryo Okubo – Journal of Affective Disorders

Fecal Akkermansia muciniphila Is Associated with Body Composition and Microbiota Diversity in Overweight and Obese Women with Breast Cancer Participating in a Presurgical Weight Loss Trial – Andrew D Fruge – Journal of the Academy of Nutrition and Dietetics

An Open-Labeled Study on Fecal Microbiota Transfer in Irritable Bowel Syndrome Patients Reveals Improvement in Abdominal Pain Associated with the Relative Abundance of Akkermansia Muciniphila – Cruz-Aguliar RM – Digestion

Animal experiments

Berberine alleviates insulin resistance by reducing peripheral branched-chain amino acids – Shi-Jun Yue – American Journal of Physiology Endocrinology and Metabolism

Air microbiome

A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations – Joan Cáliz – PNAS

Phages and viruses

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis – Andrey N Shkoporov – Nature Communications

Techniques

Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples – Yuan Gao – Nature Methods

Dynamic linear models guide design and analysis of microbiota studies within artificial human guts – Justin D Silverman – Microbiome

Microbes in the news

Chinese scientists develop novel instrument for rapid profiling of antimicrobial resistance – EurekaAlert

Microbes on the market

Chr. Hansen Receives Joint Innovation Fund Grant to Develop Next Generation Microbial Solutions for Agriculture – Microbiome times

Non-microbiology picks

Remission of Human Type 2 Diabetes Requires Decrease in Liver and Pancreas Fat Content but Is Dependent upon Capacity for β Cell Recovery – Roy Taylor – Cell Metabolism

 

November 10, 2018

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Human and General Microbiome

Review: Clinical Application and Potential of Fecal Microbiota Transplantation – R.E. Ooijevaar – Annual Review of Medicine

Editorial: A novel treatment for patients with constipation: Dawn of a new age for translational microbiome research? – Ayesha Shah – Indian Journal of Gastroenterology

Research Highlight: Of ethnicity, environment, and microbiota – Sundararajan Jayaraman – Cellular & Molecular Immunology

Minireview: Metabolic and Microbiota Measures as Peripheral Biomarkers in Major Depressive Disorder – Rachael Horne – Frontiers in Psychiatry

Case Report: Hirschsprung’s Associated Enterocolitis (HAEC) Personalized Treatment with Probiotics Based on Gene Sequencing Analysis of the Fecal Microbiome – Georg Singer – Case Reports in Pediatrics

News and Views: Rules of engagement in the gut microbiome – Elze Rackaityte – Nature Medicine

Preview: When Soluble Fibers Meet Hepatocellular Carcinoma: The Dark Side of Fermentation – Suchira Gallage – Cell Metabolism

Preview: A Microbiota Assimilation – Justin Sonnenburg – Cell Metabolism

Fecal microbiota transplantation: restoring the injured microbiome after allogeneic hematopoietic cell transplantation – Zachariah DeFilipp – Biology of Blood and Marrow Transplantation

Studies of nonhuman primates: key sources of data on zoonoses and microbiota – B.Davoust – New Microbes and New Infections

Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition –  Cristian Pasquaretta – Genes

Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans – Jennifer R. Bratburd – mBio

A randomized double-blind placebo-controlled trial showing rifaximin to improve constipation by reducing methane production and accelerating colon transit: A pilot study – Uday C. Ghoshal – Indian Journal of Gastroenterology

Zinc Deficiency and the Recurrence of Clostridium difficile Infection after Fecal Microbiota Transplant: A Retrospective Cohort Study – Blake A. Niccum – Journal of Nutrition and Metabolism

Recurrent Clostridium difficile Infection: Risk Factors, Treatment, and Prevention – Jung Hoon Song – Gut and Liver

Profiles and Perspectives: Mitochondrial dysfunction and gut microbiota imbalance: An intriguing relationship in chronic kidney disease – Denise Mafra – Mitochondrion

Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population – Filipa Godoy-Vitorino – Frontiers in Microbiology

Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels – Mary Rodríguez-Rabassa – International Journal of Environmental Research and Public Health

Minireview: Human bacterial repertoire of the urinary tract: a potential paradigm shift – Aurélie Morand – Journal of Clinical Microbiology

Review: Role of gut microbiota in intestinal wound healing and barrier function – Ashfaqul Alam – Tissue Barriers

Initial microbial community of the neonatal stomach immediately after birth – Sarah Bajorek – Gut Microbes

The Role of Diet, Micronutrients and the Gut Microbiota in Age-Related Macular Degeneration: New Perspectives from the Gut⁻Retina Axis – Emanuele Rinninella – Nutrients

Review: Candida Interactions with the Oral Bacterial Microbiota – Daniel Montelongo-Jauregui – Journal of Fungi

Microbial Community Dynamics in Mother’s Milk and Infant’s Mouth and Gut in Moderately Preterm Infants – Elena Biagi – Frontiers in Microbiology

First Insights into the Gut Microbiota of Mexican Patients with Celiac Disease and Non-Celiac Gluten Sensitivity – Jose F. Garcia-Mazcorro – Nutrients

Dietary Exposure to the Environmental Chemical, PFOS on the Diversity of Gut Microbiota, Associated With the Development of Metabolic Syndrome – Keng Po Lai – Frontiers in Microbiology

 

Death Microbiome

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue – Whitney A. Kodama – Journal of Forensic Sciences

 

Animal Microbiome / Animal Experiments

Review: Chicken Gut Microbiota: Importance and Detection Technology –  Yue Shang – Frontiers in Veterinary Sciences

Predator odor exposure in early adolescence influences the effects of the bacterial product, propionic acid, on anxiety, sensorimotor gating, and acoustic startle response in male rats in later adolescence and adulthood – Deanne Tak On Wah – Physiology & Behavior

Pharmacological Activation of PXR and CAR Down-regulates Distinct Bile Acid-metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis – Joseph L Dempsey – Toxicological Sciences

Protective effects of ghrelin on fasting-induced muscle atrophy in aging mice – Chia-Shan Wu – The Journals of Gerontology: Series A

The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice – Bei Gao – Chemical Research in Toxicology

Differential effects of coconut versus soy oil on gut microbiota composition and predicted metabolic function in adult mice – Vania Patrone – BMC Genomics

Pharmaceutical Impact of Houttuynia Cordata and Metformin Combination on High-Fat-Diet-Induced Metabolic Disorders: Link to Intestinal Microbiota and Metabolic Endotoxemia – Jing-Hua Wang – Frontiers in Endocrinology

Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice – Umesh D. Wankhade – Scientific Reports

Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice – Naoki Sasaki –  Frontiers in Microbiology

Effect of Grifola frondosa 95% ethanol extract on lipid metabolism and gut microbiota composition in high-fat diet-fed rats – Yu-Yang Pan – Food & Function

Reduction in butyrate-producing Lachnospiraceae contributes to stress-induced visceral hypersensitivity in rats – Jindong Zhang – Journal of Gastroenterology and Hepatology

 

Beneficial Compounds and Probiotics

Review: Potential Prebiotic Properties of Nuts and Edible Seeds and Their Relationship to Obesity – Clara S. A. Sugizaki – Nutrients

Review: Resveratrol, Metabolic Syndrome, and Gut Microbiota – Alice Chaplin – Nutrients

Isolation and Characterization of Potentially Probiotic Bacterial Strains from Mice: Proof of Concept for Personalized Probiotics – Larissa S. Celiberto – Nutrients

Two alkaline motifs in the Lactobacillus salivarius Lv72 OppA surface are important to its adhesin function – C. Martín – Beneficial Microbes

 

Protocols

Book Chapter: Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities – Christopher Whidbey – Current Topics in Microbiology and Immunology

 

Bioinformatics

Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome – Huiru Zheng – IEEE/ACM Transactions on Computational Biology and Bioinformatics

 

Food and Nutritional Microbiome

Microbiomes Associated With Foods From Plant and Animal Sources – Karen G. Jarvis – Frontiers in Microbiology

Fecal microbiota responses to bran particles are specific to cereal type and in vitro digestion methods that mimic upper gastrointestinal tract passage – Yunus Emre Tuncil – Journal of Agricultural and Food Chemistry

Gut carbohydrate inhibits GIP secretion via a microbiota/SCFA/FFAR3 pathway – : Eun-Young Lee – Journal of Endocrinology

Review: Human Breast Milk Bacteriome in Health and Disease – Anna Ojo-Okunola – Nutrients

Relative Validity and Reproducibility of a Food Frequency Questionnaire to Assess Nutrients and Food Groups of Relevance to the Gut Microbiota in Young Children – Claudia Leong – Nutrients

 

Other

Surface Exposure and Packing of Lipoproteins into Outer Membrane Vesicles Are Coupled Processes in Bacteroides – Ezequiel Valguarnera – mSphere

The Transferable Resistome of Produce – Khald Blau – mBio

November 7, 2018

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There’s lots of new work to catch up on! Some highlights include the skin virome in patients with immune deficiency, a mechanism for host-microbe mutualism in zebrafish, ecological pressures in soil that lead to smaller genomes, and a book chapter about the future of microbial forensics.

General Microbiome
Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness – Wen C. Aw – PLOS Genetics

Antifungal immune responses: emerging host–pathogen interactions and translational implications – Vinod Kumar – Genome Medicine

Pregnancy and early life
Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy. – Liisa Hantsoo – Brain, Behavior, and Immunity

Enabling precision medicine in neonatology, an integrated repository for preterm birth research – Marina Sirota – Scientific Data

Associations of birth mode with cord blood cytokines, white blood cells, and newborn intestinal bifidobacteria – Isabel Cristina Ribas Werlang – PLOS One

HPV infection and bacterial microbiota in breast milk and infant oral mucosa – Heidi Tuominen – PLOS One

Human skin microbiome
Expanded skin virome in DOCK8-deficient patients – Osnat Tirosh – Nature Medicine

Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris – George Zhanel – Antimicrobial Agents and Chemotherapy

Human vaginal microbiome
Preprint: Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota – Kavita Agarwal – bioRxiv

Human multi-site microbiome
The altered human serum metabolome induced by a marathon – Zinandré Stander – Metabolomics

The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media
Andrea Coleman
Microbiome

Human gut microbiome
An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men – Abigail J. S. Armstrong – Microbiome

Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial – Zhi-Dong Jiang – PLOS One

The long term effect of metabolic profile and microbiota status in early gastric cancer patients after subtotal gastrectomy – Xi-Hsuan Lin – PLOS One

Animal experiments
A bacterial immunomodulatory protein with lipocalin-like domains facilitates host–bacteria mutualism in larval zebrafish – Annah S Rolig – eLife

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin – Lulu Sun – Nature Medicine

Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model – Kazuyuki Kasahara – Nature Microbiology

Enteric infection coupled with chronic Notch pathway inhibition alters colonic mucus composition leading to dysbiosis, barrier disruption and colitis – Ishfaq Ahmed – PLOS One

Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A. Hatter – PLOS One

Plant, root, and soil microbiome
Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient – Jackson W. Sorensen – Nature Microbiology

Decomposition responses to climate depend on microbial community composition -Sydney I. Glassman – PNAS

The nanotechnology among US: are metal and metal oxides nanoparticles a nano or mega risk for soil microbial communities? – J. Parada – Critical Reviews in Biotechnology

Water and extremophile microbiome
Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia. – Nyok-Sean Lau – Microbial Ecology

Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient – Alexandra Meziti – The ISME Journal

Probiotics
Anti-diabetic effects of Lactobacillus casei fermented-yogurt through re-shaping gut microbiota structure in type 2 diabetic rats – Ling Qu – Journal of Agricultural and Food Chemistry

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis – Yanbo Wang – Applied Microbiology and Biotechnology

Techniques
Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling – Fei Teng – Scientific Reports

Science career/training and publishing
Preprint: The CURE for Culturing Fastidious Microbes – Arundhati Bakshi – bioRxiv

Meeting Report: Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. – Jacquelyn S. Meisel -Microbiome

In win for open access, two major funders won’t cover publishing in hybrid journals

Microbial Forensics
Book Chapter: Unique Individualistic Microflora: The Future of DNA Fingerprinting Technique – Pankaj Shrivastava – DNA Fingerprinting: Advancements and Future Endeavors

Alyson’s non-microbiology picks
Science candidates prevail in US midterm elections